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1
ARTICLE

Lipidomics data analysis: Enrichment analysis

Olga (Olya) Vvedenskaya

Enrichment analysis helps to identify the most prominent features in lipidomics datasets.

Link: www.lipotype.com/

articles
data
2
ARTICLE

Lipid composition of cold-pressed seed oils

Olga (Olya) Vvedenskaya

Camelina, flax, and hemp oils lipidomics.

Link: www.lipotype.com/lipidomics-cold-pressed-oils

articles
diet, plant, oil-fat, other-application
3
The EMBO Journal

Non-vesicular phosphatidylinositol transfer plays critical roles in defining organelle lipid composition

Yeun Ju Kim, Joshua G Pemberton, Andrea Eisenreichova, Amrita Mandal, Alena Koukalova, Pooja Rohilla, Mira Sohn, Andrei W Konradi, Tracy T Tang, Evzen Boura, Tamas Balla

Phosphatidylinositol (PI) is the precursor lipid for the minor phosphoinositides (PPIns), which are critical for multiple functions in all eukaryotic cells. It is poorly understood how phosphatidylinositol, which is synthesized in the ER, reaches those membranes where PPIns are formed. Here, we used VT01454, a recently identified inhibitor of class I PI transfer proteins (PITPs), to unravel their roles in lipid metabolism, and solved the structure of inhibitor-bound PITPNA to gain insight into the mode of inhibition. We found that class I PITPs not only distribute PI for PPIns production in various organelles such as the plasma membrane (PM) and late endosomes/lysosomes, but that their inhibition also significantly reduced the levels of phosphatidylserine, di- and triacylglycerols, and other lipids, and caused prominent increases in phosphatidic acid. While VT01454 did not inhibit Golgi PI4P formation nor reduce resting PM PI(4,5)P2 levels, the recovery of the PM pool of PI(4,5)P2 after receptor-mediated hydrolysis required both class I and class II PITPs. Overall, these studies show that class I PITPs differentially regulate phosphoinositide pools and affect the overall cellular lipid landscape.

Link: doi.org/10.1038/s44318-024-00096-3

publications
human, cell, organelles, other-application
4
Advanced Science

Revealing the MRI-Contrast in Optically Cleared Brains

Shimrit Oz, Galit Saar, Shunit Olszakier, Ronit Heinrich, Mykhail O Kompanets, Shai Berlin

The current consensus holds that optically-cleared specimens are unsuitable for Magnetic Resonance Imaging (MRI); exhibiting absence of contrast. Prior studies combined MRI with tissue-clearing techniques relying on the latter’s ability to eliminate lipids, thereby fostering the assumption that lipids constitute the primary source of ex vivo MRI-contrast. Nevertheless, these findings contradict an extensive body of literature that underscores the contribution of other features to contrast. Furthermore, it remains unknown whether non-delipidating clearing methods can produce MRI-compatible specimens or whether MRI-contrast can be re-established. These limitations hinder the development of multimodal MRI-light-microscopy (LM) imaging approaches. This study assesses the relation between MRI-contrast, and delipidation in optically-cleared whole brains following different tissue-clearing approaches. It is demonstrated that uDISCO and ECi-brains are MRI-compatible upon tissue rehydration, despite both methods’ substantial delipidating-nature. It is also demonstrated that, whereas Scale-clearing preserves most lipids, Scale-cleared brain lack MRI-contrast. Furthermore, MRI-contrast is restored to lipid-free CLARITY-brains without introducing lipids. Our results thereby dissociate between the essentiality of lipids to MRI-contrast. A tight association is found between tissue expansion, hyperhydration and loss of MRI-contrast. These findings then enabled us to develop a multimodal MRI-LM-imaging approach, opening new avenues to bridge between the micro- and mesoscale for biomedical research and clinical applications.

Link: doi.org/10.1002/advs.202400316

publications
mouse-rat, tissue-organ, other-application
5
Proteomics

Imputation of missing values in lipidomic datasets

Nicolas Frölich, Christian Klose, Elisabeth Widén, Samuli Ripatti, Mathias J Gerl

Lipidomic data often exhibit missing data points, which can be categorized as missing completely at random (MCAR), missing at random, or missing not at random (MNAR). In order to utilize statistical methods that require complete datasets or to improve the identification of potential effects in statistical comparisons, imputation techniques can be employed. In this study, we investigate commonly used methods such as zero, half-minimum, mean, and median imputation, as well as more advanced techniques such as k-nearest neighbor and random forest imputation. We employ a combination of simulation-based approaches and application to real datasets to assess the performance and effectiveness of these methods. Shotgun lipidomics datasets exhibit high correlations and missing values, often due to low analyte abundance, characterized as MNAR. In this context, k-nearest neighbor approaches based on correlation and truncated normal distributions demonstrate best performance. Importantly, both methods can effectively impute missing values independent of the type of missingness, the determination of which is nearly impossible in practice. The imputation methods still control the type I error rate.

Link: doi.org/10.1002/pmic.202300606

publications
data, human, blood, other-application
6
nature communications

LDL receptor-related protein 5 selectively transports unesterified polyunsaturated fatty acids to intracellular compartments

Wenwen Tang, Yi Luan, Qianying Yuan, Ao Li, Song Chen, Stanley Menacherry, Lawrence Young, Dianqing Wu

Polyunsaturated fatty acids (PUFAs), which cannot be synthesized by animals and must be supplied from the diet, have been strongly associated with human health. However, the mechanisms for their accretion remain poorly understood. Here, we show that LDL receptor-related protein 5 (LRP5), but not its homolog LRP6, selectively transports unesterified PUFAs into a number of cell types. The LDLa ligand-binding repeats of LRP5 directly bind to PUFAs and are required and sufficient for PUFA transport. In contrast to the known PUFA transporters Mfsd2a, CD36 and FATP2, LRP5 transports unesterified PUFAs via internalization to intracellular compartments including lysosomes, and n-3 PUFAs depend on this transport mechanism to inhibit mTORC1. This LRP5-mediated PUFA transport mechanism suppresses extracellular trap formation in neutrophils and protects mice from myocardial injury during ischemia-reperfusion. Thus, this study reveals a biologically important mechanism for unesterified PUFA transport to intracellular compartments.

Link: doi.org/10.1038/s41467-024-47262-z

publications
mouse-rat, diet, cell, other-application
7
nature microbiology

Phosphatidylserine-exposing extracellular vesicles in body fluids are an innate defense against apoptotic mimicry viral pathogens

Rüdiger Groß, Hanna Reßin, Pascal von Maltitz, Dan Albers, Laura Schneider, Hanna Bley, Markus Hoffmann, Mirko Cortese, Dhanu Gupta, Miriam Deniz, Jae-Yeon Choi, Jenny Jansen, Christian Preußer, Kai Seehafer, Stefan Pöhlmann, Dennis R Voelker, Christine Goffinet, Elke Pogge-von Strandmann, Uwe Bunz, Ralf Bartenschlager, Samir El Andaloussi, Konstantin M J Sparrer, Eva Herker, Stephan Becker, Frank Kirchhoff, Jan Münch, Janis A Müller

Some viruses are rarely transmitted orally or sexually despite their presence in saliva, breast milk, or semen. We previously identified that extracellular vesicles (EVs) in semen and saliva inhibit Zika virus infection. However, the antiviral spectrum and underlying mechanism remained unclear. Here we applied lipidomics and flow cytometry to show that these EVs expose phosphatidylserine (PS). By blocking PS receptors, targeted by Zika virus in the process of apoptotic mimicry, they interfere with viral attachment and entry. Consequently, physiological concentrations of EVs applied in vitro efficiently inhibited infection by apoptotic mimicry dengue, West Nile, Chikungunya, Ebola and vesicular stomatitis viruses, but not severe acute respiratory syndrome coronavirus 2, human immunodeficiency virus 1, hepatitis C virus and herpesviruses that use other entry receptors. Our results identify the role of PS-rich EVs in body fluids in innate defence against infection via viral apoptotic mimicries, explaining why these viruses are primarily transmitted via PS-EV-deficient blood or blood-ingesting arthropods rather than direct human-to-human contact.

Link: doi.org/10.1038/s41564-024-01637-6

publications
human, subcellular, other-organism, organelles, microbiology
8
ARTICLE

Ganglioside lipidomics in CNS developmental myelination

Olga (Olya) Vvedenskaya

Researchers developed a method to quantify the full ganglioside lipidome during various central nervous system stages.

Link: lipotype.com/cns-myelination

articles
mouse-rat, neuroscience, tissue-organ, model-systems
9
The EMBO Journal

MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress

John Reinhard, Leonhard Starke, Christian Klose, Per Haberkant, Henrik Hammarén, Frank Stein, Ofir Klein, Charlotte Berhorst, Heike Stumpf, James P Sáenz, Jochen Hub, Maya Schuldiner, Robert Ernst

Bioological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.

Link: doi.org/10.1038/s44318-024-00063-y

publications
subcellular, yeast, model-systems, organelles, microbiology, other-application
10
Life

Stratum Corneum Lipids in Non-Lesional Atopic and Healthy Skin following Moisturizer Application: A Randomized Clinical Experiment

Malin Glindvad Ahlström, Rie Dybboe Bjerre, Magnus Glindvad Ahlström, Lone Skov, Jeanne Duus Johansen

It is an international standard to recommend patients with atopic dermatitis (AD) to use moisturizers; however, little is known about their effect on lipids in the stratum corneum (SC). In this randomized clinical experiment of 30 Caucasian participants (15 with AD and 15 healthy controls), the superficial SC lipid profile was assessed through tape stripping non-lesional skin following treatment thrice daily for seven days with a moisturizer, and subsequently compared with untreated skin. No discernible disparity in superficial SC lipid quantity was evident between the AD group and the control group. However, the SC lipid composition diverged significantly, with the AD group exhibiting diminished levels of long-chain EO CERs (p = 0.024) and elevated levels of short-chain C34 CERs (p = 0.025) compared to healthy skin. Moisturizer application significantly reduced the total SC lipids and all lipid subgroups in both groups. Within the AD group, a non-significant inclination towards an augmentation in EO CERs (p = 0.053) and reduction in C34 CERs (p = 0.073) was observed. The recent identification of distinctions in SC lipid composition between AD and healthy skin was substantiated by our findings. Topical moisturizer application, despite reducing overall total lipids, indicated a potential tendency towards a healthier lipid constitution in AD skin.

Link: doi.org/10.3390/life14030345

publications
human, dermatology, skin, clinical-research
11
ARTICLE

Lipidomics data analysis: Imputation

Olga (Olya) Vvedenskaya

Imputation helps to deal with missing values in lipidomics datasets.

Link: lipotype.com/imputation

articles
data
12
The Lipidomics Webinar

How to deal with lipidomics data?

Mathias J Gerl

In this webinar, we will explore key statistical and data analysis methods applied to lipidomics studies. Dr. Mathias Gerl, the Head of Data Science, will guide you through the crucial techniques, starting from the data imputation methods to address missing data points in obtained datasets. We further will cover statistical comparison options for lipidomics datasets and talk about the enrichment analysis. Finally, we will discuss Weighted Correlation Network Analysis (WGCNA), Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), and power analysis applications to lipidomics datasets.

Link: www.lipotype.com/data-analysis-2

webinars
data, biomarker
13
microbial cell

Quantifying yeast lipidomics by high-performance thin-layer chromatography (HPTLC) and comparison to mass spectrometry-based shotgun lipidomics

Thorsten Meyer, Oskar Knittelfelder, Martin Smolnig, Patrick Rockenfeller

Lipidomic analysis in diverse biological settings has become a frequent tool to increase our understanding of the processes of life. Cellular lipids play important roles not only as being the main components of cellular membranes, but also in the regulation of cell homeostasis as lipid signaling molecules. Yeast has been harnessed for biomedical research based on its good conservation of genetics and fundamental cell organisation principles and molecular pathways. Further application in so-called humanised yeast models have been developed which take advantage of yeast as providing the basics of a living cell with full control over heterologous expression. Here we present evidence that high-performance thin-layer chromatography (HPTLC) represents an effective alternative to replace cost intensive mass spectrometry-based lipidomic analyses. We provide statistical comparison of identical samples by both methods, which support the use of HPTLC for quantitative analysis of the main yeast lipid classes.

Link: doi.org/10.15698%2Fmic2024.02.815

publications
cell, yeast, model-systems, microbiology, other-application
14
nature communications

Multi-molecular hyperspectral PRM-SRS microscopy

Wenxu Zhang, Yajuan Li, Anthony A Fung, Zhi Li, Hongje Jang, Honghao Zha, Xiaoping Chen, Fangyuan Gao, Jane Y Wu, Huaxin Sheng, Junjie Yao, Dorota Skowronska-Krawczyk, Sanjay Jain, Lingyan Shi

Lipids play crucial roles in many biological processes. Mapping spatial distributions and examining the metabolic dynamics of different lipid subtypes in cells and tissues are critical to better understanding their roles in aging and diseases. Commonly used imaging methods (such as mass spectrometry-based, fluorescence labeling, conventional optical imaging) can disrupt the native environment of cells/tissues, have limited spatial or spectral resolution, or cannot distinguish different lipid subtypes. Here we present a hyperspectral imaging platform that integrates a Penalized Reference Matching algorithm with Stimulated Raman Scattering (PRM-SRS) microscopy. Using this platform, we visualize and identify high density lipoprotein particles in human kidney, a high cholesterol to phosphatidylethanolamine ratio inside granule cells of mouse hippocampus, and subcellular distributions of sphingosine and cardiolipin in human brain. Our PRM-SRS displays unique advantages of enhanced chemical specificity, subcellular resolution, and fast data processing in distinguishing lipid subtypes in different organs and species.

Link: doi.org/10.1038/s41467-024-45576-6

publications
mouse-rat, tissue-organ, other-application
15
International Journal of Molecular Sciences

Plasma Lipidomic Profiling Using Mass Spectrometry for Multiple Sclerosis Diagnosis and Disease Activity Stratification (LipidMS)

Seyed S J Lattau, Lisa-Marie Borsch, Kristina Auf Dem Brinke, Christian Klose, Liza Vinhoven, Manuel Nietert, Dirk Fitzner

This investigation explores the potential of plasma lipidomic signatures for aiding in the diagnosis of Multiple Sclerosis (MS) and evaluating the clinical course and disease activity of diseased patients. Plasma samples from 60 patients with MS (PwMS) were clinically stratified to either a relapsing-remitting (RRMS) or a chronic progressive MS course and 60 age-matched controls were analyzed using state-of-the-art direct infusion quantitative shotgun lipidomics. To account for potential confounders, data were filtered for age and BMI correlations. The statistical analysis employed supervised and unsupervised multivariate data analysis techniques, including a principal component analysis (PCA), a partial least squares discriminant analysis (oPLS-DA) and a random forest (RF). To determine whether the significant absolute differences in the lipid subspecies have a relevant effect on the overall composition of the respective lipid classes, we introduce a class composition visualization (CCV). We identified 670 lipids across 16 classes. PwMS showed a significant increase in diacylglycerols (DAG), with DAG 16:0;0_18:1;0 being proven to be the lipid with the highest predictive ability for MS as determined by RF. The alterations in the phosphatidylethanolamines (PE) were mainly linked to RRMS while the alterations in the ether-bound PEs (PE O-) were found in chronic progressive MS. The amount of CE species was reduced in the CPMS cohort whereas TAG species were reduced in the RRMS patients, both lipid classes being relevant in lipid storage. Combining the above mentioned data analyses, distinct lipidomic signatures were isolated and shown to be correlated with clinical phenotypes. Our study suggests that specific plasma lipid profiles are not merely associated with the diagnosis of MS but instead point toward distinct clinical features in the individual patient paving the way for personalized therapy and an enhanced understanding of MS pathology.

Link: doi.org/10.3390/ijms25052483

publications
human, blood, neuroscience, clinical-research, biomarker
16
Atherosclerosis

Neurotensin accelerates atherosclerosis and increases circulating levels of short-chain and saturated triglycerides

Jing Li, Liping Yang, Jun Song, Baoxiang Yan, Andrew J Morris, Hunter Moseley, Robert Flight, Chi Wang, Jinpeng Liu, Heidi L Weiss, Edward F Morris, Ilyes Abdelhamid, Mathias J Gerl, Olle Melander, Susan Smyth, B Mark Evers

Obesity and type 2 diabetes are significant risk factors for atherosclerotic cardiovascular disease (CVD) worldwide, but the underlying pathophysiological links are poorly understood. Neurotensin (NT), a 13-amino-acid hormone peptide, facilitates intestinal fat absorption and contributes to obesity in mice fed a high-fat diet. Elevated levels of pro-NT (a stable NT precursor produced in equimolar amounts relative to NT) are associated with obesity, type 2 diabetes, and CVD in humans. Whether NT is a causative factor in CVD is unknown.

Nt+/+ and Nt–/– mice were either injected with adeno-associated virus encoding PCSK9 mutants or crossed with Ldlr–/– mice and fed a Western diet. Atherosclerotic plaques were analyzed by en face analysis, Oil Red O and CD68 staining. In humans, we evaluated the association between baseline pro-NT and growth of carotid bulb thickness after 16.4 years. Lipidomic profiles were analyzed.

Atherosclerotic plaque formation is attenuated in Nt-deficient mice through mechanisms that are independent of reductions in circulating cholesterol and triglycerides but associated with remodeling of the plasma triglyceride pool. An increasing plasma concentration of pro-NT predicts atherosclerotic events in coronary and cerebral arteries independent of all major traditional risk factors, indicating a strong link between NT and atherosclerosis. This plasma lipid profile analysis confirms the association of pro-NT with remodeling of the plasma triglyceride pool in atherosclerotic events.

Our findings are the first to directly link NT to increased atherosclerosis and indicate the potential role for NT in preventive and therapeutic strategies for CVD.

Link: doi.org/10.1016/j.atherosclerosis.2024.117479

publications
data, human, blood, diet, cardiovascular-disease, clinical-research
17
ARTICLE

Starvation and lipid metabolism

Olga (Olya) Vvedenskaya

TANGO2 plays a role in lipid metabolism and affects cellular organization during starvation.

Link: lipotype.com/starvation-lipid-metabolism

articles
cell, model-systems, organelles, other-application
18
Theranostics

Gut ribotoxic stress responses facilitate dyslipidemia via metabolic reprogramming: an environmental health prediction

Juil Kim, Hoyoung Jeong, Navin Ray, Ki-Hyung Kim, Yuseok Moon

The gut and its accessory organ, the liver, are crucial determinants of metabolic homeostasis via the regulation of circulating lipids for cardiovascular health. In response to environmental insults, cells undergo diverse adaptation or pathophysiological processes via stress-responsive eukaryotic initiation factor 2 alpha (eIF2α) kinase signaling and subsequent cellular reprogramming. We noted that patients with inflammatory gut distress display enhanced levels of ribosomal stress-responsive eIF2α kinase, which is notably associated with lipid metabolic process genes. Based on an assumption that eukaryotic ribosomes are a promising stress-responsive module for molecular reprogramming, chemical ribosome-inactivating stressors (RIS) were assessed for their involvement in enterohepatic lipid regulation.

Experimental assessment was based on prediction using the clinical transcriptome and single-cell RNA-sequencing analysis of inflammatory bowel diseases and obesity. The prediction was verified using RIS exposure models of mice, gut organoids, and intestinal cells. The lipidomic profiling was performed to address RIS-induced intracellular fat alterations. Biochemical processes of the mechanisms were evaluated using RT-PCR, western blot analysis, luciferase reporter assays, and confocal microscopy of genetically ablated or chemically inhibited mice, organoids, and cells.

Chemical RIS including deoxynivalenol promoted enterohepatic lipid sequestration while lowering blood LDL cholesterol in normal and diet-induced obese mice. Although ribosomal stress caused extensive alterations in cellular lipids and metabolic genes, the cholesterol import-associated pathway was notably modulated. In particular, ribosomal stress enhanced gut levels of the low-density lipoprotein receptor (LDLR) via both transcriptional and post-transcriptional regulation. Subsequently, LDLR facilitated enterohepatic cholesterol accumulation, leading to dyslipidemia in response to ribosomal stress. Moreover, genetic features of stress-responsive LDLR modulators were consistently proven in the inflammation- and obesity-associated gut model.

The elucidated ribosome-linked gut lipid regulation provides predictive insights into stress-responsive metabolic rewiring in chronic human diseases as an environmental health prediction.

Link: doi.org/10.7150/thno.88586

publications
human, mouse-rat, metabolic-disorders, cell, biomarker, multiomics
19
ESC Heart Failure

An altered plasma lipidome–phenome network characterizes heart failure with preserved ejection fraction

Nina Jovanovic, Anna Foryst-Ludwig, Christian Klose, Cristina Rozados da Conceicao, Lina Alasfar, Till Birkner, Sofia K Forslund, Ulrich Kintscher, Frank Edelmann

Heart failure with preserved ejection fraction (HFpEF) is a multifactorial, multisystemic syndrome that involves alterations in lipid metabolism. This study aimed to test whether distinct plasma lipid profiles or lipid entities or both are associated with clinical and functional echocardiographic parameters in HFpEF.

We examined the human plasma lipidome in HFpEF patients (n = 18) with left ventricular ejection fraction ≥50% and N-terminal pro-brain natriuretic peptide (NT-proBNP) >125 pg/mL and control subjects (n = 12) using mass spectrometry-based shotgun lipidomics. The cohort included 8 women and 22 men with average age of 67.8 ± 8.6 SD. The control and disease groups were not significantly different with respect to age, body mass index, systolic and diastolic blood pressure, and waist-to-hip ratio. The disease group experienced more fatigue (P < 0.001), had more often coronary artery disease (P = 0.04), and received more medications (beta-blockers, P < 0.001). The disease group had significantly different levels of HFpEF-relevant parameters, including NT-proBNP (P < 0.001), left ventricular mass index (P = 0.005), left atrial volume index (P = 0.001), and left ventricular filling index (P < 0.001), and lower left ventricular end-diastolic diameter (P = 0.014), with no difference in left ventricular ejection fraction. Significant differences in lipid profiles between HFpEF patients and controls could not be detected, including no significant differences in abundance of circulating lipids binned by carbon chain length or by double bonds, nor at the level of individual lipid species. However, there was a striking correlation between selected lipids with smoking status that was independent of disease status, as well as between specific lipids and hyperlipidaemia [with corresponding significance of either false discovery rate (FDR) <0.1 or FDR < 0.01]. In an exploratory network analysis of correlations, we observed significantly stronger correlations within the HFpEF group between individual lipids from the cholesterol ester and phosphatidylcholine (PC) classes and clinical/echocardiographic parameters such as left atrial volume index, left ventricular end-diastolic diameters, and heart rate (FDR < 0.1). In contrast, the control group showed significantly stronger negative correlations (FDR < 0.1) between individual species from the PC and sphingomyelin classes and left ventricular mass index or systolic blood pressure.

We did not find significant direct associations between plasma lipidomic parameters and HFpEF and therefore could not conclude that any specific lipids are biomarkers of HFpEF. The validation in larger cohort is needed to confidently conclude the absence of first-order associations.

Link: doi.org/10.1002/ehf2.14654

publications
human, blood, cardiovascular-disease, clinical-research, biomarker
20
Bioactive Materials

Oral TNF-α siRNA delivery via milk-derived exosomes for effective treatment of inflammatory bowel disease

Geonhee Han, Hyosuk Kim, Hochung Jang, Eun S Kim, Sun H Kim, Yoosoo Yang

Oral administration facilitates the direct delivery of drugs to lesions within the small intestine and colon, making it an ideal approach for treating patients with inflammatory bowel disease. However, multiple physical barriers impede the delivery of oral RNA drugs through the gastrointestinal tract. Herein, we developed a novel oral siRNA delivery system that protects nucleic acids in extreme environments by employing exosomes derived from milk to encapsulate tumor necrosis factor-alpha (TNF-α) siRNA completely. The remarkable structural stability of milk-derived exosomes (M-Exos), as opposed to those from HEK293T cells, makes them exceptional siRNA carriers. Results demonstrate that milk exosomes loaded with TNF-α siRNA (M-Exo/siR) can effectively inhibit the expression of TNF-α-related inflammatory cytokines. Moreover, given that milk exosomes are composed of unique lipids with high bioavailability, orally administered M-Exo/siR effectively reach colonic tissues, leading to decreased TNF-α expression and successful alleviation of colitis symptoms in a dextran sulfate sodium-induced inflammatory bowel disease murine model. Hence, milk-derived exosomes carrying TNF-α siRNA can be effectively employed to treat inflammatory bowel disease. Indeed, using exosomes naturally derived from milk may shift the current paradigm of oral gene delivery, including siRNA.

Link: doi.org/10.1016/j.bioactmat.2023.12.010

publications
human, metabolic-disorders, exosome, other-organism, pharma
21
ARTICLE

Phospholipidomics of a murine eye

Olga (Olya) Vvedenskaya

Lipidomics analysis showed that over 82% of the total phosphatidylinositide pool in the mouse retina comprises arachidonic acid-containing species, PI 38:4, and PI 36:4. This acyl composition was consistent for mono- and bisphosphate phosphorylated forms (PIP 36:4/38:4 and PIP2 36:4/38:4), constituting ~7% of total retinal phosphatidylinositol. Using genetic phosphoinositide sensors, scientists studied the subcellular localization of PI(4,5)P2 and PI(4)P within rod photoreceptors. The main distinction in their distribution is that PI(4)P was present in the light-sensitive outer segment, while PI(4,5)P2 was mostly not present there yet present in photoreceptor synapses.

Link: lipotype.com/phospholipidomics-murine-eye

articles
mouse-rat, model-systems, organelles
22
Cancer Research

Adipose triglyceride lipase is a therapeutic target in advanced prostate cancer that promotes metabolic plasticity

Dominik Awad, Pham Hong Anh Cao, Thomas L Pulliam, Meredith Spradlin, Elavarasan Subramani, Tristen V Tellman, Caroline F Ribeiro, Riccardo Muzzioli, Brittany E Jewell, Hubert Pakula, Jeffrey J Ackroyd, Mollianne M Murray, Jenny J Han, Mei Leng, Antrix Jain, Badrajee Piyarathna, Jingjing Liu, Xingzhi Song, Jianhua Zhang, Albert R Klekers, Justin M Drake, Michael M Ittmann, Cristian Coarfa, David Piwnica-Worms, Mary C Farach-Carson, Massimo Loda, Livia S Eberlin, Daniel E Frigo

Lipid metabolism plays a central role in prostate cancer. To date, the major focus has centered on de novo lipogenesis and lipid uptake in prostate cancer, but inhibitors of these processes have not benefited patients. Better understanding of how cancer cells access lipids once they are created or taken up and stored could uncover more effective strategies to perturb lipid metabolism and treat patients. Here, we identified that expression of adipose triglyceride lipase (ATGL), an enzyme that controls lipid droplet homeostasis and a previously suspected tumor suppressor, correlates with worse overall survival in men with advanced, castration-resistant prostate cancer (CRPC). Molecular, genetic, or pharmacological inhibition of ATGL impaired human and murine prostate cancer growth in vivo and in cell culture or organoids under conditions mimicking the tumor microenvironment. Mass spectrometry imaging demonstrated ATGL profoundly regulates lipid metabolism in vivo, remodeling membrane composition. ATGL inhibition induced metabolic plasticity, causing a glycolytic shift that could be exploited therapeutically by co-targeting both metabolic pathways. Patient-derived phosphoproteomics identified ATGL serine 404 as a target of CAMKK2-AMPK signaling in CRPC cells. Mutation of serine 404 did not alter the lipolytic activity of ATGL but did decrease CRPC growth, migration, and invasion, indicating that non-canonical ATGL activity also contributes to disease progression. Unbiased immunoprecipitation/mass spectrometry suggested that mutation of serine 404 not only disrupts existing ATGL protein interactions but also leads to new protein-protein interactions. Together, these data nominate ATGL as a therapeutic target for CRPC and provide insights for future drug development and combination therapies.

Link: doi.org/10.1158/0008-5472.CAN-23-0555

publications
human, cell, oncology, pharma, organelles, clinical-research, multiomics
23
Journal of Biological Chemistry

Intracellular sphingolipid sorting drives membrane phase separation in the yeast vacuole

Hyesoo Kim, Itay Budin

The yeast vacuole membrane can phase separate into ordered and disordered domains, a phenomenon that is required for micro-lipophagy under nutrient limitation. Despite its importance as a biophysical model and physiological significance, it is not yet resolved if specific lipidome changes drive vacuole phase separation. Here we report that the metabolism of sphingolipids (SLs) and their sorting into the vacuole membrane can control this process. We first developed a vacuole isolation method to identify lipidome changes during the onset of phase separation in early stationary stage cells. We found that early stationary stage vacuoles are defined by an increased abundance of putative raft components, including 40% higher ergosterol content and a nearly 3-fold enrichment in complex SLs (CSLs). These changes were not found in the corresponding whole cell lipidomes, indicating that lipid sorting is associated with domain formation. Several facets of SL composition—headgroup stoichiometry, longer chain lengths, and increased hydroxylations—were also markers of phase-separated vacuole lipidomes. To test SL function in vacuole phase separation, we carried out a systematic genetic dissection of their biosynthetic pathway. The abundance of CSLs controlled the extent of domain formation and associated micro-lipophagy processes, while their headgroup composition altered domain morphology. These results suggest that lipid trafficking can drive membrane phase separation in vivo and identify SLs as key mediators of this process in yeast.

Link: doi.org/10.1016/j.jbc.2023.105496

publications
cell, subcellular, yeast, model-systems, organelles, microbiology
24
Cell Reports

Acid ceramidase regulates innate immune memory

Nils Rother, Cansu Yanginlar, Geoffrey Prévot, Inge Jonkman, Maaike Jacobs, Mandy M T van Leent, Julia van Heck, Vasiliki Matzaraki, Anthony Azzun, Judit Morla-Folch, Anna Ranzenigo, William Wang, Roy van der Meel, Zahi A Fayad, Niels P Riksen, Luuk B Hilbrands, Rik G H Lindeboom, Joost H A Martens, Michiel Vermeulen, Leo A B Joosten, Mihai G Netea, Willem J M Mulder, Johan van der Vlag, Abraham J P Teunissen, Raphaël Duivenvoorden

Innate immune memory, also called “trained immunity,” is a functional state of myeloid cells enabling enhanced immune responses. This phenomenon is important for host defense, but also plays a role in various immune-mediated conditions. We show that exogenously administered sphingolipids and inhibition of sphingolipid metabolizing enzymes modulate trained immunity. In particular, we reveal that acid ceramidase, an enzyme that converts ceramide to sphingosine, is a potent regulator of trained immunity. We show that acid ceramidase regulates the transcription of histone-modifying enzymes, resulting in profound changes in histone 3 lysine 27 acetylation and histone 3 lysine 4 trimethylation. We confirm our findings by identifying single-nucleotide polymorphisms in the region of ASAH1, the gene encoding acid ceramidase, that are associated with the trained immunity cytokine response. Our findings reveal an immunomodulatory effect of sphingolipids and identify acid ceramidase as a relevant therapeutic target to modulate trained immunity responses in innate immune-driven disorders.

Link: doi.org/10.1016/j.celrep.2023.113458

publications
human, cell, clinical-research, other-application
25
The EMBO Journal

Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome

Kailash Venkatraman, Christopher T Lee, Guadalupe C Garcia, Arijit Mahapatra, Daniel Milshteyn, Guy Perkins, Keun-Young Kim, H Amalia Pasolli, Sebastien Phan, Jennifer Lippincott-Schwartz, Mark H Ellisman, Padmini Rangamani, Itay Budin

Cristae are high-curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous lipid-based mechanisms have yet to be elucidated. Here, we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the inner mitochondrial membrane against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. This model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that cardiolipin is essential in low-oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of cardiolipin is dependent on the surrounding lipid and protein components of the IMM.

Link: doi.org/10.15252/embj.2023114054

publications
cell, subcellular, yeast, organelles
26
ARTICLE

Aging, gut microbiome, and lipid metabolism

Olga (Olya) Vvedenskaya

In this study, the researchers explored gut microbiome, muscle physiology, serum protein and lipid markers to establish a profile of age-related changes in both the gut microbiome and host physiology. This research paves the way to identifying the molecular mechanisms that drive microbiome-associated aging and offers potential directions for therapeutic interventions to promote healthy aging.

Link: lipotype.com/aging-gut-microbiome-lipids

articles
blood, mouse-rat, model-systems, other-application
27
Life Science Alliance

ESYT1 tethers the ER to mitochondria and is required for mitochondrial lipid and calcium homeostasis

Alexandre Janer, Jordan L Morris, Michiel Krols, Hana Antonicka, Mari J Aaltonen, Zhen-Yuan Lin, Hanish Anand, Anne-Claude Gingras, Julien Prudent, Eric A Shoubridge

Mitochondria interact with the ER at structurally and functionally specialized membrane contact sites known as mitochondria–ER contact sites (MERCs). Combining proximity labelling (BioID), co-immunoprecipitation, confocal microscopy and subcellular fractionation, we found that the ER resident SMP-domain protein ESYT1 was enriched at MERCs, where it forms a complex with the outer mitochondrial membrane protein SYNJ2BP. BioID analyses using ER-targeted, outer mitochondrial membrane-targeted, and MERC-targeted baits, confirmed the presence of this complex at MERCs and the specificity of the interaction. Deletion of ESYT1 or SYNJ2BP reduced the number and length of MERCs. Loss of the ESYT1–SYNJ2BP complex impaired ER to mitochondria calcium flux and provoked a significant alteration of the mitochondrial lipidome, most prominently a reduction of cardiolipins and phosphatidylethanolamines. Both phenotypes were rescued by reexpression of WT ESYT1 and an artificial mitochondria–ER tether. Together, these results reveal a novel function for ESYT1 in mitochondrial and cellular homeostasis through its role in the regulation of MERCs.

Link: doi.org/10.26508/lsa.202302335

publications
human, subcellular, organelles
28
ARTICLE

Lipidomics in stratum corneum research

Olga (Olya) Vvedenskaya

Lipidomics analysis of stratum corneum is essential in dermatology research and product development.

Link: lipotype.com/lipidomics-stratum-corneum

articles
human, application, sample-type, organism, dermatology, skin, clinical-research
29
nature communications

Genome-wide association analysis of plasma lipidome identifies 495 genetic associations

Linda Ottensmann, Rubina Tabassum, Sanni Ruotsalainen, Mathias J Gerl, Christian Klose, Elisabeth Widén, Kai Simons, Samuli Ripatti, Matti Pirinen

The human plasma lipidome captures risk for cardiometabolic diseases. To discover new lipid-associated variants and understand the link between lipid species and cardiometabolic disorders, we perform univariate and multivariate genome-wide analyses of 179 lipid species in 7174 Finnish individuals. We fine-map the associated loci, prioritize genes, and examine their disease links in 377,277 FinnGen participants. We identify 495 genome-trait associations in 56 genetic loci including 8 novel loci, with a considerable boost provided by the multivariate analysis. For 26 loci, fine-mapping identifies variants with a high causal probability, including 14 coding variants indicating likely causal genes. A phenome-wide analysis across 953 disease endpoints reveals disease associations for 40 lipid loci. For 11 coronary artery disease risk variants, we detect strong associations with lipid species. Our study demonstrates the power of multivariate genetic analysis in correlated lipidomics data and reveals genetic links between diseases and lipid species beyond the standard lipids.

Link: doi.org/10.1038/s41467-023-42532-8

publications
data, human, blood, metabolic-disorders, cardiovascular-disease, clinical-research, biomarker, multiomics
30
The Lipidomics Webinar

Navigating cardiovascular diseases

Olga (Olya) Vvedenskaya

During this webinar, we will talk about the role of the lipidome in risk prediction and differential diagnosis of cardiovascular diseases. The webinar will start with a general introduction to cardiovascular diseases. We will then talk about using lipidomics to differentiate between various cardiovascular and inflammatory diseases. Further, we will discuss the pivotal role lipids play in cardiovascular disease risk prediction in addition to the routinely measured clinical parameters and explore the role of multiomics in the prediction of cardiovascular risk development. Finally, we will review the application of lipidomics to translational heart failure research in mice and humans.

Link: www.lipotype.com/cvd-lipidomics-webinar

webinars
cardiovascular-disease, clinical-research, biomarker
31
ARTICLE

Lipidomics of extracellular vesicle subtypes

Olga (Olya) Vvedenskaya

Lipidomics analysis supports the preparation and analysis of nano plasma membrane vesicles (nPMVs).

Link: www.lipotype.com/extracellular-vesicles

articles
model-systems
32
nature metabolism

COX17 acetylation via MOF–KANSL complex promotes mitochondrial integrity and function

Sukanya Guhathakurta, Niyazi U Erdogdu, Juliane J Hoffmann, Iga Grzadzielewska, Alexander Schendzielorz, Janine Seyfferth, Christoph U Mårtensson, Mauro Corrado, Adam Karoutas, Bettina Warscheid, Nikolaus Pfanner, Thomas Becker, Asifa Akhtar

Reversible acetylation of mitochondrial proteins is a regulatory mechanism central to adaptive metabolic responses. Yet, how such functionally relevant protein acetylation is achieved remains unexplored. Here we reveal an unprecedented role of the MYST family lysine acetyltransferase MOF in energy metabolism via mitochondrial protein acetylation. Loss of MOF–KANSL complex members leads to mitochondrial defects including fragmentation, reduced cristae density and impaired mitochondrial electron transport chain complex IV integrity in primary mouse embryonic fibroblasts. We demonstrate COX17, a complex IV assembly factor, as a bona fide acetylation target of MOF. Loss of COX17 or expression of its non-acetylatable mutant phenocopies the mitochondrial defects observed upon MOF depletion. The acetylation-mimetic COX17 rescues these defects and maintains complex IV activity even in the absence of MOF, suggesting an activatory role of mitochondrial electron transport chain protein acetylation. Fibroblasts from patients with MOF syndrome who have intellectual disability also revealed respiratory defects that could be restored by alternative oxidase, acetylation-mimetic COX17 or mitochondrially targeted MOF. Overall, our findings highlight the critical role of MOF–KANSL complex in mitochondrial physiology and provide new insights into MOF syndrome.

Link: doi.org/10.1038/s42255-023-00904-w

publications
human, mouse-rat, metabolic-disorders, cell, subcellular, neuroscience, organelles
33
ARTICLE

Dietary fatty acids influence the cell membrane

Olga (Olya) Vvedenskaya

PUFAs coming from diet incorporate into the plasma membrane and affect its biophysical properties.

Link: www.lipotype.com/membranes-diet

articles
mouse-rat, diet, subcellular, other-organism, organelles
34
Heliyon

RIT1 regulation of CNS lipids RIT1 deficiency Alters cerebral lipid metabolism and reduces white matter tract oligodendrocytes and conduction velocities

Lei Wu, Fang Wang, Carole L Moncman, Mritunjay Pandey, Harrison A Clarke, Hilaree N Frazier, Lyndsay E A Young, Matthew S Gentry, Weikang Cai, Olivier Thibault, Ramon C Sun, Douglas A Andres

Oligodendrocytes (OLs) generate lipid-rich myelin membranes that wrap axons to enable efficient transmission of electrical impulses. Using a RIT1 knockout mouse model and in situ high-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) coupled with MS-based lipidomic analysis to determine the contribution of RIT1 to lipid homeostasis. Here, we report that RIT1 loss is associated with altered lipid levels in the central nervous system (CNS), including myelin-associated lipids within the corpus callosum (CC). Perturbed lipid metabolism was correlated with reduced numbers of OLs, but increased numbers of GFAP+ glia, in the CC, but not in grey matter. This was accompanied by reduced myelin protein expression and axonal conduction deficits. Behavioral analyses revealed significant changes in voluntary locomotor activity and anxiety-like behavior in RIT1KO mice. Together, these data reveal an unexpected role for RIT1 in the regulation of cerebral lipid metabolism, which coincide with altered white matter tract oligodendrocyte levels, reduced axonal conduction velocity, and behavioral abnormalities in the CNS.

Link: doi.org/10.1016/j.heliyon.2023.e20384

publications
mouse-rat, neuroscience, tissue-organ, multiomics
35
The Lipidomics Webinar

Lipidomics & ceramide analysis for skin research

Veronika Piskovatska

This webinar is dedicated to skin lipids and their role in skin health and disease and will discuss lipid composition and function in different skin structures. The webinar will begin with an overview of skin anatomy with a focus on the stratum corneum. The lipidome of normal skin will be discussed next, emphasizing the importance of ceramides. Our scientific talk will focus on the pivotal role ceramides play in skin physiology and their relevance in context of skin research and product claim support. During the webinar, factors contributing to variability in skin lipidome and ceramidome will be discussed, including age, sex, body part, pigmentation, depth of skin sampling, and seasonal differences. Finally, we will examine the alterations in the skin lipidome caused by various pathological conditions, such as xerosis, atopic dermatitis, and psoriasis, and explore the relationship between the skin lipidome and the skin microbiome.

Link: www.lipotype.com/skin-lipidomics-webinar

webinars
dermatology, microbiology, clinical-research
36
scientific reports

Differential intracellular management of fatty acids impacts on metabolic stress-stimulated glucose uptake in cardiomyocytes

Ettore Vanni, Karina Lindner, Anne-Claude Gavin, Christophe Montessuit

Stimulation of glucose uptake in response to ischemic metabolic stress is important for cardiomyocyte function and survival. Chronic exposure of cardiomyocytes to fatty acids (FA) impairs the stimulation of glucose uptake, whereas induction of lipid droplets (LD) is associated with preserved glucose uptake. However, the mechanisms by which LD induction prevents glucose uptake impairment remain elusive. We induced LD with either tetradecanoyl phorbol acetate (TPA) or 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR). Triacylglycerol biosynthesis enzymes were inhibited in cardiomyocytes exposed to FA ± LD inducers, either upstream (glycerol-3-phosphate acyltransferases; GPAT) or downstream (diacylglycerol acyltransferases; DGAT) of the diacylglycerol step. Although both inhibitions reduced LD formation in cardiomyocytes treated with FA and LD inducers, only DGAT inhibition impaired metabolic stress-stimulated glucose uptake. DGAT inhibition in FA plus TPA-treated cardiomyocytes reduced triacylglycerol but not diacylglycerol content, thus increasing the diacylglycerol/triacylglycerol ratio. In cardiomyocytes exposed to FA alone, GPAT inhibition reduced diacylglycerol but not triacylglycerol, thus decreasing the diacylglycerol/triacylglycerol ratio, prevented PKCδ activation and improved metabolic stress-stimulated glucose uptake. Changes in AMP-activated Protein Kinase activity failed to explain variations in metabolic stress-stimulated glucose uptake. Thus, LD formation regulates metabolic stress-stimulated glucose uptake in a manner best reflected by the diacylglycerol/triacylglycerol ratio.

Link: doi.org/10.1038/s41598-023-42072-7

publications
mouse-rat, cell, other-application
37
nature

Identification of an alternative triglyceride biosynthesis pathway

Gian-Luca McLelland, Marta Lopez-Osias, Cristy R C Verzijl, Brecht D Ellenbroek, Rafaela A Oliveira, Nicolaas J Boon, Marleen Dekker, Lisa G van den Hengel, Rahmen Ali, Hans Janssen, Ji-Ying Song, Paul Krimpenfort, Tim van Zutphen, Johan W Jonker, Thijn R Brummelkamp

Triacylglycerols (TAGs) are the main source of stored energy in the body, providing an important substrate pool for mitochondrial beta-oxidation. Imbalances in the amount of TAGs are associated with obesity, cardiac disease and various other pathologies. In humans, TAGs are synthesized from excess, coenzyme A-conjugated fatty acids by diacylglycerol O-acyltransferases (DGAT1 and DGAT2). In other organisms, this activity is complemented by additional enzymes, but whether such alternative pathways exist in humans remains unknown. Here we disrupt the DGAT pathway in haploid human cells and use iterative genetics to reveal an unrelated TAG-synthesizing system composed of a protein we called DIESL (also known as TMEM68, an acyltransferase of previously unknown function) and its regulator TMX1. Mechanistically, TMX1 binds to and controls DIESL at the endoplasmic reticulum, and loss of TMX1 leads to the unconstrained formation of DIESL-dependent lipid droplets. DIESL is an autonomous TAG synthase, and expression of human DIESL in Escherichia coli endows this organism with the ability to synthesize TAG. Although both DIESL and the DGATs function as diacylglycerol acyltransferases, they contribute to the cellular TAG pool under specific conditions. Functionally, DIESL synthesizes TAG at the expense of membrane phospholipids and maintains mitochondrial function during periods of extracellular lipid starvation. In mice, DIESL deficiency impedes rapid postnatal growth and affects energy homeostasis during changes in nutrient availability. We have therefore identified an alternative TAG biosynthetic pathway driven by DIESL under potent control by TMX1.

Link: doi.org/10.1038/s41586-023-06497-4

publications
human, cell, other-application
38
ARTICLE

Moisturizing cream impacts ceramides balance in skin

Olga (Olya) Vvedenskaya

The studied moisturizer cream demonstrated improved ceramide content and strengthened the skin barrier function. The cream’s efficacy can be attributed to its semi-occlusive effect, acting as an additional barrier. Importantly, the cream was shown to penetrate the stratum corneum without compromising its structure. The analyzed cream holds promise for treating individuals with impaired barrier function, such as those with atopic dermatitis and dry skin.

Link: lipotype.com/moisturizer-and-ceramides

articles
human, dermatology, skin, clinical-research
39
nature cell biology

Lipid saturation controls nuclear envelope function

Anete Romanauska, Alwin Köhler

The nuclear envelope (NE) is a spherical double membrane with elastic properties. How NE shape and elasticity are regulated by lipid chemistry is unknown. Here we discover lipid acyl chain unsaturation as essential for NE and nuclear pore complex (NPC) architecture and function. Increased lipid saturation rigidifies the NE and the endoplasmic reticulum into planar, polygonal membranes, which are fracture prone. These membranes exhibit a micron-scale segregation of lipids into ordered and disordered phases, excluding NPCs from the ordered phase. Balanced lipid saturation is required for NPC integrity, pore membrane curvature and nucleocytoplasmic transport. Oxygen deprivation amplifies the impact of saturated lipids, causing NE rigidification and rupture. Conversely, lipid droplets buffer saturated lipids to preserve NE architecture. Our study uncovers a fundamental link between lipid acyl chain structure and the integrity of the cell nucleus with implications for nuclear membrane malfunction in ischaemic tissues.

Link: doi.org/10.1038/s41556-023-01207-8

publications
cell, subcellular, yeast, organelles, microbiology
40
ARTICLE

Lipids promote ferroptosis in cancer cells

Olga (Olya) Vvedenskaya, Mariia Kuzina

Conjugated linoleates can act as ferroptosis inducers by promoting lipid peroxidation and cancer cell death.

Link: lipotype.com/ferroptosis-and-cancer

articles
human, mouse-rat, cell, oncology, tissue-organ, pharma
41
JCB

A membrane-sensing mechanism links lipid metabolism to protein degradation at the nuclear envelope

Shoken Lee, Jake W Carrasquillo Rodríguez, Holly Merta, Shirin Bahmanyar

Lipid composition determines organelle identity; however, whether the lipid composition of the inner nuclear membrane (INM) domain of the ER contributes to its identity is not known. Here, we show that the INM lipid environment of animal cells is under local control by CTDNEP1, the master regulator of the phosphatidic acid phosphatase lipin 1. Loss of CTDNEP1 reduces association of an INM-specific diacylglycerol (DAG) biosensor and results in a decreased percentage of polyunsaturated containing DAG species. Alterations in DAG metabolism impact the levels of the resident INM protein Sun2, which is under local proteasomal regulation. We identify a lipid-binding amphipathic helix (AH) in the nucleoplasmic domain of Sun2 that prefers membrane packing defects. INM dissociation of the Sun2 AH is linked to its proteasomal degradation. We suggest that direct lipid–protein interactions contribute to sculpting the INM proteome and that INM identity is adaptable to lipid metabolism, which has broad implications on disease mechanisms associated with the nuclear envelope.

Link: doi.org/10.1083/jcb.202304026

publications
human, cell, organelles, multiomics
42
ARTICLE

Lipidomics of cardiovascular diseases

Olga (Olya) Vvedenskaya

This study showed the heritability of plasma lipid levels and linked these metrics to risk for cardiovascular disease phenotypes. Omics-based studies that include lipidomics can be very informative. In this report, such data were used to establish new associations between genetic variants, plasma lipid species, and risk for cardiovascular diseases.

Link: lipotype.com/lipidomics-cardiovascular-diseases

articles
cardiovascular-disease, clinical-research
43
nature communications

Glycolytically impaired Drosophila glial cells fuel neural metabolism via β-oxidation

Ellen McMullen, Helen Hertenstein, Katrin Strassburger, Leon Deharde, Marko Brankatschk, Stefanie Schirmeier

Neuronal function is highly energy demanding and thus requires efficient and constant metabolite delivery by glia. Drosophila glia are highly glycolytic and provide lactate to fuel neuronal metabolism. Flies are able to survive for several weeks in the absence of glial glycolysis. Here, we study how Drosophila glial cells maintain sufficient nutrient supply to neurons under conditions of impaired glycolysis. We show that glycolytically impaired glia rely on mitochondrial fatty acid breakdown and ketone body production to nourish neurons, suggesting that ketone bodies serve as an alternate neuronal fuel to prevent neurodegeneration. We show that in times of long-term starvation, glial degradation of absorbed fatty acids is essential to ensure survival of the fly. Further, we show that Drosophila glial cells act as a metabolic sensor and can induce mobilization of peripheral lipid stores to preserve brain metabolic homeostasis. Our study gives evidence of the importance of glial fatty acid degradation for brain function, and survival, under adverse conditions in Drosophila.

Link: doi.org/10.1038/s41467-023-38813-x

publications
other-sample-type, diet, insect, neuroscience, tissue-organ
44
ARTICLE

Lipid metabolism genes

Olga (Olya) Vvedenskaya, Kateryna Ivanova

This proof-of-concept study demonstrates that quantitative lipidomics screens can produce reliable and reproducible data and that these screens should be further expanded to more genes and different cell lines. As a goal, it will be possible to create a comprehensive map of lipid pathways at the molecular level including proteins involved in each step of the lipid metabolism. This information is of crucial importance for developing new diagnostic and therapeutic approaches.

Link: www.lipotype.com/lipidomics-applications/lipid-metabolism-genes

articles
human, cell, model-systems, other-application, multiomics
45
nature communications

Identification of biomarkers for glycaemic deterioration in type 2 diabetes

Roderick C Slieker, Louise A Donnelly, Elina Akalestou, Livia Lopez-Noriega, Rana Melhem, Ayşim Güneş, Frederic Abou Azar, Alexander Efanov, Eleni Georgiadou, Hermine Muniangi-Muhitu, Mahsa Sheikh, Giuseppe N Giordano, Mikael Åkerlund, Emma Ahlqvist, Ashfaq Ali, Karina Banasik, Søren Brunak, Marko Barovic, Gerard A Bouland, Frederic Burdet, Mickaël Canouil, Iulian Dragan, Petra J M Elders, Céline Fernandez, Andreas Festa, Hugo Fitipaldi, Phillippe Froguel, Valborg Gudmundsdottir, Vilmundur Gudnason, Mathias J Gerl, Amber A van der Heijden, Lori L Jennings, Michael K Hansen, Min Kim, Isabelle Leclerc, Christian Klose, Dmitry Kuznetsov, Dina Mansour Aly, Florence Mehl, Diana Marek, Olle Melander, Anne Niknejad, Filip Ottosson, Imre Pavo, Kevin L Duffin, Samreen K Syed, Janice L Shaw, Over Cabrera, Timothy J Pullen, Kai Simons, Michele Solimena, Tommi Suvitaival, Asger Wretlind, Peter Rossing, Valeriya Lyssenko, Cristina Legido-Quigley, Leif Groop, Bernard Thorens, Paul W Franks, Gareth E Lim, Jennifer Estall, Mark Ibberson, Joline W J Beulens, Leen M ‘t Hart, Ewan R Pearson, Guy A Rutter

We identify biomarkers for disease progression in three type 2 diabetes cohorts encompassing 2,973 individuals across three molecular classes, metabolites, lipids and proteins. Homocitrulline, isoleucine and 2-aminoadipic acid, eight triacylglycerol species, and lowered sphingomyelin 42:2;2 levels are predictive of faster progression towards insulin requirement. Of ~1,300 proteins examined in two cohorts, levels of GDF15/MIC-1, IL-18Ra, CRELD1, NogoR, FAS, and ENPP7 are associated with faster progression, whilst SMAC/DIABLO, SPOCK1 and HEMK2 predict lower progression rates. In an external replication, proteins and lipids are associated with diabetes incidence and prevalence. NogoR/RTN4R injection improved glucose tolerance in high fat-fed male mice but impaired it in male db/db mice. High NogoR levels led to islet cell apoptosis, and IL-18R antagonised inflammatory IL-18 signalling towards nuclear factor kappa-B in vitro. This comprehensive, multi-disciplinary approach thus identifies biomarkers with potential prognostic utility, provides evidence for possible disease mechanisms, and identifies potential therapeutic avenues to slow diabetes progression.

Link: doi.org/10.1038/s41467-023-38148-7

publications
data, human, blood, metabolic-disorders, clinical-research, biomarker, multiomics
46
Communications Biology

High efficiency preparation of monodisperse plasma membrane derived extracellular vesicles for therapeutic applications

Claudio L Alter, Pascal Detampel, Roman B Schefer, Claudia Lotter, Patrick Hauswirth, Ramya D Puligilla, Vera J Weibel, Susanne H Schenk, Wolf Heusermann, Melanie Schürz, Nicole Meisner-Kober, Cornelia Palivan, Tomaž Einfalt, Jörg Huwyler

Extracellular vesicles (EVs) are highly interesting for the design of next-generation therapeutics. However, their preparation methods face challenges in standardization, yield, and reproducibility. Here, we describe a highly efficient and reproducible EV preparation method for monodisperse nano plasma membrane vesicles (nPMVs), which yields 10 to 100 times more particles per cell and hour than conventional EV preparation methods. nPMVs are produced by homogenizing giant plasma membrane vesicles following cell membrane blebbing and apoptotic body secretion induced by chemical stressors. nPMVs showed no significant differences compared to native EVs from the same cell line in cryo-TEM analysis, in vitro cellular interactions, and in vivo biodistribution studies in zebrafish larvae. Proteomics and lipidomics, on the other hand, suggested substantial differences consistent with the divergent origin of these two EV types and indicated that nPMVs primarily derive from apoptotic extracellular vesicles. nPMVs may provide an attractive source for developing EV-based pharmaceutical therapeutics.

Link: doi.org/10.1038/s42003-023-04859-2

publications
human, cell, exosome, pharma, organelles, other-application
47
ARTICLE

Lipid profiles of individuals with obesity

Olga (Olya) Vvedenskaya, Sarai Valerio Cabrera

This study presented a unique and extensive profiling of lipids, metabolites, and proteins in order to identify differences between healthy and unhealthy obesity. Such an approach can be utilized to differentiate other metabolism-related diseases and improve their prediction and treatment options.

Link: www.lipotype.com/healthy-obesity

articles
human, blood, clinical-research, biomarker, multiomics
48
Molecular Medicine

Impact of St. John’s wort extract Ze 117 on stress induced changes in the lipidome of PBMC

Hendrik Bussmann, Swen Bremer, Hanns Häberlein, Georg Boonen, Jürgen Drewe, Veronika Butterweck, Sebastian Franken

Membrane lipids have an important function in the brain as they not only provide a physical barrier segregating the inner and outer cellular environments, but are also involved in cell signaling. It has been shown that the lipid composition effects membrane fluidity which affects lateral mobility and activity of membrane-bound receptors.

Since changes in cellular membrane properties are considered to play an important role in the development of depression, the effect of St. John’s wort extract Ze 117 on plasma membrane fluidity in peripheral blood mononuclear cells (PBMC) was investigated using fluorescence anisotropy measurements. Changes in fatty acid residues in phospholipids after treatment of cortisol-stressed [1 μM] PBMCs with Ze 117 [10–50 µg/ml] were analyzed by mass spectrometry.

Cortisol increased membrane fluidity significantly by 3%, co-treatment with Ze 117 [50 µg/ml] counteracted this by 4.6%. The increased membrane rigidity by Ze 117 in cortisol-stressed [1 μM] PBMC can be explained by a reduced average number of double bonds and shortened chain length of fatty acid residues in phospholipids, as shown by lipidomics experiments.

The increase in membrane rigidity after Ze 117 treatment and therefore the ability to normalize membrane structure points to a new mechanism of antidepressant action of the extract.

Link: doi.org/10.1186/s10020-023-00644-3

publications
human, cell, neuroscience, organelles
49
Life Science Alliance

The role of the mitochondrial outer membrane protein SLC25A46 in mitochondrial fission and fusion

Jana Schuettpelz, Alexandre Janer, Hana Antonicka, Eric A Shoubridge

Mutations in SLC25A46 underlie a wide spectrum of neurodegenerative diseases associated with alterations in mitochondrial morphology. We established an SLC25A46 knock-out cell line in human fibroblasts and studied the pathogenicity of three variants (p.T142I, p.R257Q, and p.E335D). Mitochondria were fragmented in the knock-out cell line and hyperfused in all pathogenic variants. The loss of SLC25A46 led to abnormalities in the mitochondrial cristae ultrastructure that were not rescued by the expression of the variants. SLC25A46 was present in discrete puncta at mitochondrial branch points and tips of mitochondrial tubules, co-localizing with DRP1 and OPA1. Virtually, all fission/fusion events were demarcated by a SLC25A46 focus. SLC25A46 co-immunoprecipitated with the fusion machinery, and loss of function altered the oligomerization state of OPA1 and MFN2. Proximity interaction mapping identified components of the ER membrane, lipid transfer proteins, and mitochondrial outer membrane proteins, indicating that it is present at interorganellar contact sites. SLC25A46 loss of function led to altered mitochondrial lipid composition, suggesting that it may facilitate interorganellar lipid flux or play a role in membrane remodeling associated with mitochondrial fusion and fission.

Link: doi.org/10.26508/lsa.202301914

publications
human, subcellular, neuroscience, organelles
50
ARTICLE

Lipases & Parkinson’s disease

Olga (Olya) Vvedenskaya

Regulating fatty acid metabolism using lipases could be beneficial in Parkinson’s disease treatment.

Link: lipotype.com/lipases-parkinsons-disease

articles
human, cell, neuroscience, other-organism
51
eLife

Defects in lipid homeostasis reflect the function of TANGO2 in phospholipid and neutral lipid metabolism

Agustin L Lujan, Ombretta Foresti, Conor Sugden, Nathalie Brouwers, Alex M Farre, Alessio Vignoli, Mahshid Azamian, Alicia Turner, Jose Wojnacki, Vivek Malhotra

We show that TANGO2 in mammalian cells localizes predominantly to mitochondria and partially at mitochondria sites juxtaposed to lipid droplets (LDs) and the endoplasmic reticulum. HepG2 cells and fibroblasts of patients lacking TANGO2 exhibit enlarged LDs. Quantitative lipidomics revealed a marked increase in lysophosphatidic acid (LPA) and a concomitant decrease in its biosynthetic precursor phosphatidic acid (PA). These changes were exacerbated in nutrient-starved cells. Based on our data, we suggest that TANGO2 function is linked to acyl-CoA metabolism, which is necessary for the acylation of LPA to generate PA. The defect in acyl-CoA availability impacts the metabolism of many other fatty acids, generates high levels of reactive oxygen species, and promotes lipid peroxidation. We suggest that the increased size of LDs is a combination of enrichment in peroxidized lipids and a defect in their catabolism. Our findings help explain the physiological consequence of mutations in TANGO2 that induce acute metabolic crises, including rhabdomyolysis, cardiomyopathy, and cardiac arrhythmias, often leading to fatality upon starvation and stress.

Link: doi.org/10.7554/eLife.85345

publications
human, metabolic-disorders, cell, cardiovascular-disease, organelles, clinical-research
52
ARTICLE

Lipidomics risk scores in diabetes and cardiovascular disease

Olga (Olya) Vvedenskaya

Lipidome anaysis is important in predicting disease risk, and it opens the possibility of using lipidomic risk scores for early disease risk assessment for both T2D and CVD. Measuring the lipidome regularly over time could help to monitor a person’s health status and understand how lifestyle and diet can impact their health. This could be especially important in the early stages of a person’s life when risk assessment is critical for disease prevention and early intervention.

Link: www.lipotype.com/diabetes-cardiovascular-disease-risk-assessment

articles
human, metabolic-disorders, blood, cardiovascular-disease, clinical-research
53
Skin Pharmacology and Physiology

Evaluation of a novel skin emollient cream on skin lipidome and lipids organization

Carine Jacques, Caroline Dejean, Christian Klose, Emilie Leccia, Sandrine Bessou-Touya, Alain Delarue, Hélène Duplan

The stratum corneum (SC) matrix is composed of free fatty acids, cholesterol and ceramides (CERs), which play a key role in the skin barrier function. Changes in the composition and content of skin lipids will affect the function of the skin barrier. The effect of a glycerol/petrolatum-based emollient (G/P-emollient) cream on the lipid profiles of isolated ex vivo human SC and the SC of a reconstructed human epithelial (RHE) model were measured.
The spatial organization of the cream and the isolated SC intercellular matrix was studied using X-ray diffraction. The inter-bilayer distance in the multi-lamellar lipid structures and lattice type were analyzed using small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS), respectively. Lipidomic analysis using Shotgun Lipidomics was performed on reconstructed human epidermis (RHE) to quantify CER classes and chain lengths. This technology enables the analysis of thousands of lipids in a single biological sample.
The crystallized components of the cream are lipids, which were mainly packed in orthorhombic lattices, as well as hexagonal lattices and were similar to the SC structure. The cream penetrated the SC but did not alter the WAXS profile. It increased the amount of higher carbon number ceramides (> 42 carbons) and decreased lower carbon number ceramides (<42 carbons). All chain length acyl-CERs and acyl-CER classes (CER EOS, EOH, EOP, EOdS) were increased as the total CER classes. A decrease of the CER C34 for hydroxylated and non-hydroxylated CERs was also observed. The cream altered the [S] and [P] CER forms (increased the [NP]/[NS] and [AP]/[AS] ratios), indicating it could reduce the relative feedback mechanism observed in inflammatory pathologies e.g., atopic dermatitis. The cream increased CER[NP], which is decreased in dry skin.
G/P-emollient cream may be beneficial for skin pathologies by modifying SC lipids, balancing CER levels and ratios, and improving the barrier function. Importantly, the cream structure mimics that of the SC and penetrated the lower SC layers without compromising its lamellar structure.

Link: doi.org/10.1159/000529253

publications
human, dermatology, skin
54
nature communications

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

Leticia C Beltran, Virginija Cvirkaite-Krupovic, Jessalyn Miller, Fengbin Wang, Mark A B Kreutzberger, Jonasz B Patkowski, Tiago R D Costa, Stefan Schouten, Ilya Levental, Vincent P Conticello, Edward H Egelman, Mart Krupovic

Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been ‘domesticated’, that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.

Link: doi.org/10.1038/s41467-023-36349-8

publications
subcellular, bacterium, microbiology
55
npj Parkinson's Disease

Parkinsonism mutations in DNAJC6 cause lipid defects and neurodegeneration that are rescued by Synj1

Julie Jacquemyn, Sabine Kuenen, Jef Swerts, Benjamin Pavie, Vinoy Vijayan, Ayse Kilic, Dries Chabot, Yu-Chun Wang, Nils Schoovaerts, Nikky Corthout, Patrik Verstreken

Recent evidence links dysfunctional lipid metabolism to the pathogenesis of Parkinson’s disease, but the mechanisms are not resolved. Here, we generated a new Drosophila knock-in model of DNAJC6/Auxilin and find that the pathogenic mutation causes synaptic dysfunction, neurological defects and neurodegeneration, as well as specific lipid metabolism alterations. In these mutants, membrane lipids containing long-chain polyunsaturated fatty acids, including phosphatidylinositol lipid species that are key for synaptic vesicle recycling and organelle function, are reduced. Overexpression of another protein mutated in Parkinson’s disease, Synaptojanin-1, known to bind and metabolize specific phosphoinositides, rescues the DNAJC6/Auxilin lipid alterations, the neuronal function defects and neurodegeneration. Our work reveals a functional relation between two proteins mutated in Parkinsonism and implicates deregulated phosphoinositide metabolism in the maintenance of neuronal integrity and neuronal survival.

Link: doi.org/10.1038/s41531-023-00459-3

publications
insect, neuroscience, tissue-organ, organelles
56
nature communications

Glycolysis regulates KRAS plasma membrane localization and function through defined glycosphingolipids

Junchen Liu, Ransome van der Hoeven, Walaa E Kattan, Jeffrey T Chang, Dina Montufar-Solis, Wei Chen, Maurice Wong, Yong Zhou, Carlito B Lebrilla, John F Hancock

Oncogenic KRAS expression generates a metabolic dependency on aerobic glycolysis, known as the Warburg effect. We report an effect of increased glycolytic flux that feeds into glycosphingolipid biosynthesis and is directly linked to KRAS oncogenic function. High resolution imaging and genetic approaches show that a defined subset of outer leaflet glycosphingolipids, including GM3 and SM4, is required to maintain KRAS plasma membrane localization, with GM3 engaging in cross-bilayer coupling to maintain inner leaflet phosphatidylserine content. Thus, glycolysis is critical for KRAS plasma membrane localization and nanoscale spatial organization. Reciprocally oncogenic KRAS selectively upregulates cellular content of these same glycosphingolipids, whose depletion in turn abrogates KRAS oncogenesis in pancreatic cancer models. Our findings expand the role of the Warburg effect beyond ATP generation and biomass building to high-level regulation of KRAS function. The positive feedforward loop between oncogenic KRAS signaling and glycosphingolipid synthesis represents a vulnerability with therapeutic potential.

Link: doi.org/10.1038/s41467-023-36128-5

publications
human, cell, oncology, other-organism, organelles, other-application, multiomics
57
ARTICLE

Growth temperature influences membrane lipids

Olga (Olya) Vvedenskaya, Henri M Deda

The lipid composition of GPMVs in zebrafish cells is influenced by growth temperature. Cells grown at lower temperatures produce GPMVs with lower cholesterol levels and higher levels of polyunsaturated lipids. These changes in lipid composition suggest that cells adjust their membrane composition to maintain a specific level of stability and to exploit the unique physical properties of supercritical systems for biological functions.

Link: lipotype.com/thermoregulation-lipids

articles
subcellular, other-organism, model-systems, organelles, other-application
58
Science Advances

The ERAD system is restricted by elevated ceramides

Jiwon Hwang, Brian G Peterson, Jeffrey Knupp, Ryan D Baldridge

Misfolded proteins in the endoplasmic reticulum (ER) are removed through a process known as ER-associated degradation (ERAD). ERAD occurs through an integral membrane protein quality control system that recognizes substrates, retrotranslocates the substrates across the membrane, and ubiquitinates and extracts the substrates from the membrane for degradation at the cytosolic proteasome. While ERAD systems are known to regulate lipid biosynthetic enzymes, the regulation of ERAD systems by the lipid composition of cellular membranes remains unexplored. Here, we report that the ER membrane composition influences ERAD function by incapacitating substrate extraction. Unbiased lipidomic profiling revealed that elevation of specific very-long-chain ceramides leads to a marked increase in the level of ubiquitinated substrates in the ER membrane and concomitantly reduces extracted substrates in the cytoplasm. This work reveals a previously unrecognized mechanism in which ER membrane lipid remodeling changes the activity of ERAD.

Link: doi.org/10.1126/sciadv.add8579

publications
cell, subcellular, yeast, organelles
59
Chemical and Pharmaceutical Bulletin

Distribution of Domains Formed by Lateral Packing of Intercellular Lipid in the Stratum Corneum

Hiroki Ohnari, Eiji Naru, Osamu Sakata, Yasuko Obata

Intercellular lipids fill the interstices of corneocytes and serve a barrier function. The amount of transdermal water evaporation varies depending on the packing structure of intercellular lipids, as this structure is important for maintaining barrier efficacy. This packing structure consists of a mixture of crystals (orthorhombic and hexagonal) and liquid crystals (fluid phase), and the proportion of these phases is thought to affect barrier function. However, there have been no methods to visualize the actual distribution of the domains formed by packing structure in intercellular lipids. In this study, the planar distribution of intercellular lipid structures was determined using focal plane array (FPA)-based Fourier transform (FT) IR imaging analysis of stratum corneum cell units obtained by grid stripping. The lipid composition of ceramides was revealed by electrospray ionization tandem mass spectrometry (ESI-MS/MS)-based shotgun lipidomics. The distribution of domains formed by packing structures and the lipid composition of ceramides was compared in skin with high- or low-transepidermal water loss (TEWL). The orthorhombic proportion was lower in high-TEWL skin than in low-TEWL skin. ESI-MS/MS-based shotgun lipidomics analysis showed that the alpha-hydroxyceramide content in the low- and high-TEWL groups differed regarding the distribution of fatty acid chain lengths. The evaluation of stratum corneum cell units using FPA-based FTIR imaging is an innovative technology that can visualize the distribution of domains formed by intercellular lipid-packing structures. Increased proportions of alpha-hydroxyceramide subclasses such as alpha-hydroxy-sphingosine ceramide and alpha-hydroxy-phytosphingosine ceramide were associated with a reduced proportion of the orthorhombic packing structure domain.

Link: doi.org/10.1248/cpb.c22-00533

publications
human, dermatology, skin
60
Article

Endoplasmic reticulum stress & lipid metabolism

Olga (Olya) Vvedenskaya, Henri M Deda

Quantitative lipidomics analysis allows not only detect the changes in lipid metabolism triggering ER stress and UPR, but also to identify of the subsequent changes in lipid metabolism in a case when the ER stress resolves in autophagy, apoptosis, or cell reprogramming. Pinpointing these changes is essential to get deep insights into relevant diseases’ development and progression, thus allowing scientists to work on treatment and prevention as well.

Link: lipotype.com/er-stress

articles
metabolic-disorders, oncology, neuroscience, pharma
61
ARTICLE

Lipid profiles of cardiovascular & inflammatory diseases

Olga (Olya) Vvedenskaya, Henri M Deda

Lipidome profiles in the blood plasma of patients with cardiovascular diseases (CVD) and ischemic stroke (IS), as well as systemic lupus erythematosus (SLE) were analyzed. For this purpose, they analyzed the blood plasma of 427 individuals, including the control group, with shotgun lipidomics technology. This allowed for the detection, identification, and quantification of 596 lipids. This study showed that mass spectrometry analysis of plasma lipids is a promising tool for differential diagnosis of various atherosclerosis-related vascular diseases, such as cardiovascular diseases and ischemic stroke.

Link: lipotype.com/cardiovascuar-inflammatory-disease

articles
human, blood, cardiovascular-disease, clinical-research, biomarker
62
nature neuroscience

TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury

Alessandro Zambusi, Klara T Novoselc, Saskia Hutten, Sofia Kalpazidou, Christina Koupourtidou, Rico Schieweck, Sven Aschenbroich, Lara Silva, Ayse S Yazgili, Frauke van Bebber, Bettina Schmid, Gabriel Möller, Clara Tritscher, Christian Stigloher, Claire Delbridge, Swetlana Sirko, Zeynep I Günes, Sabine Liebscher, Jürgen Schlegel, Hananeh Aliee, Fabian Theis, Silke Meiners, Michael Kiebler, Dorothee Dormann, Jovica Ninkovic

Decreasing the activation of pathology-activated microglia is crucial to prevent chronic inflammation and tissue scarring. In this study, we used a stab wound injury model in zebrafish and identified an injury-induced microglial state characterized by the accumulation of lipid droplets and TAR DNA-binding protein of 43 kDa (TDP-43)+ condensates. Granulin-mediated clearance of both lipid droplets and TDP-43+ condensates was necessary and sufficient to promote the return of microglia back to the basal state and achieve scarless regeneration. Moreover, in postmortem cortical brain tissues from patients with traumatic brain injury, the extent of microglial activation correlated with the accumulation of lipid droplets and TDP-43+ condensates. Together, our results reveal a mechanism required for restoring microglia to a nonactivated state after injury, which has potential for new therapeutic applications in humans.

Link: doi.org/10.1038/s41593-022-01199-y

publications
neuroscience, tissue-organ, other-organism
63
PNAS

VpdC is a ubiquitin-activated phospholipase effector that regulates Legionella vacuole expansion during infection

Xiao Li, D Eric Anderson, Yuen-Yan Chang, Michal Jarnik, Matthias P Machner

Intravacuolar pathogens need to gradually expand their surrounding vacuole to accommodate the growing number of bacterial offspring during intracellular replication. Here we found that Legionella pneumophila controls vacuole expansion by fine-tuning the generation of lysophospholipids within the vacuolar membrane. Upon allosteric activation by binding to host ubiquitin, the type IVB (Dot/Icm) effector VpdC converts phospholipids into lysophospholipids which, at moderate concentrations, are known to promote membrane fusion but block it at elevated levels by generating excessive positive membrane curvature. Consequently, L. pneumophila overproducing VpdC were prevented from adequately expanding their surrounding membrane, trapping the replicating bacteria within spatially confined vacuoles and reducing their capability to proliferate intracellularly. Quantitative lipidomics confirmed a VpdC-dependent increase in several types of lysophospholipids during infection, and VpdC production in transiently transfected cells caused tubulation of organelle membranes as well as mitochondria fragmentation, processes that can be phenocopied by supplying cells with exogenous lysophospholipids. Together, these results demonstrate an important role for bacterial phospholipases in vacuolar expansion.

Link: doi.org/10.1073/pnas.2209149119

publications
human, cell, organelles, microbiology
64
ARTICLE

Lipids & kidney disease in diabetes

Olga (Olya) Vvedenskaya, Henri M Deda

A set of mice and cell culture experiments evaluated the disturbances in triglyceride synthesis as a key mechanism driving lipotoxicity in diabetic kidney disease. The diet in case of mice experiments, and enriched media in case of cell culture experiments, showed that oleic acid enhanced the production of triglycerides while palmitic acid increased the saturation levels of the diglyceride species and impaired triglyceride synthesis. Taken together, these results support the protective role of triglyceride-enriched lipid droplet formation and provide insights into the mechanisms leading to lipotoxicity in diabetes.

Link: lipotype.com/diabetic-kidney-disease

articles
mouse-rat, metabolic-disorders, diet, cell, tissue-organ, organelles
65
The Lipidomics Webinar

Role of lipids in CNS regeneration

Mikael Simons

Failure of regeneration capacity limits the restoration of nervous system functionality in demyelinating diseases such as multiple sclerosis. Yet, the responsible mechanisms are only partially understood. I will present data supporting a key role for lipid metabolisms (that is, lipid droplet biogenesis and cholesterol efflux) in phagocytes for regeneration of myelin. Stimulation of the lipid sensing Triggering receptor expressed on myeloid cells or nuclear liver X receptor are possible therapeutic strategies of how to enhance the capacity to regenerate lesioned tissue.

Link: lipotype.com/cns-regeneration

webinars
diet, neuroscience, organelles
66
nature communications

TLCD1 and TLCD2 regulate cellular phosphatidylethanolamine composition and promote the progression of non-alcoholic steatohepatitis

Kasparas Petkevicius, Henrik Palmgren, Matthew S Glover, Andrea Ahnmark, Anne-Christine Andréasson, Katja Madeyski-Bengtson, Hiroki Kawana, Erik L Allman, Delaney Kaper, Martin Uhrbom, Liselotte Andersson, Leif Aasehaug, Johan Forsström, Simonetta Wallin, Ingela Ahlstedt, Renata Leke, Daniel Karlsson, Hernán González-King, Lars Löfgren, Ralf Nilsson, Giovanni Pellegrini, Nozomu Kono, Junken Aoki, Sonja Hess, Grzegorz Sienski, Marc Pilon, Mohammad Bohlooly-Y, Marcello Maresca, Xiao-Rong Peng

The fatty acid composition of phosphatidylethanolamine (PE) determines cellular metabolism, oxidative stress, and inflammation. However, our understanding of how cells regulate PE composition is limited. Here, we identify a genetic locus on mouse chromosome 11, containing two poorly characterized genes Tlcd1 and Tlcd2, that strongly influences PE composition. We generated Tlcd1/2 double-knockout (DKO) mice and found that they have reduced levels of hepatic monounsaturated fatty acid (MUFA)-containing PE species. Mechanistically, TLCD1/2 proteins act cell intrinsically to promote the incorporation of MUFAs into PEs. Furthermore, TLCD1/2 interact with the mitochondria in an evolutionarily conserved manner and regulate mitochondrial PE composition. Lastly, we demonstrate the biological relevance of our findings in dietary models of metabolic disease, where Tlcd1/2 DKO mice display attenuated development of non-alcoholic steatohepatitis compared to controls. Overall, we identify TLCD1/2 proteins as key regulators of cellular PE composition, with our findings having broad implications in understanding and treating disease.

Link: doi.org/10.1038/s41467-022-33735-6

publications
human, mouse-rat, metabolic-disorders, cell, tissue-organ, other-application
67
iScience

Ganglioside lipidomics of central nervous system myelination using direct infusion shotgun mass spectrometry

Martina Arends, Melanie Weber, Cyrus Papan, Markus Damm, Michal A Surma, Christopher Spiegel, Minou Djannatian, Shengrong Li, Lisa Connell, Ludger Johannes, Martina Schifferer, Christian Klose, Mikael Simons

Gangliosides are present and concentrated in axons, and implicated in axon-myelin interactions, but how ganglioside composition changes during myelin formation is not known. Here, we present a direct infusion (shotgun) lipidomics method to analyse gangliosides in small amounts of tissue reproducibly and with high sensitivity. We resolve the mouse ganglioside lipidome during development and adulthood and determine the ganglioside content of mice lacking the St3gal5 and B4galnt1 genes that synthesize most ganglioside species. Our results reveal substantial changes of the ganglioside lipidome during formation of myelinated nerve fibers. In sum, we provide insights into the central nervous system ganglioside lipidome with a quantitative and sensitive mass spectrometry method. Since this method is compatible with global lipidomic profiling, it will provide insight into ganglioside function in physiology and pathology.

Link: doi.org/10.1016/j.isci.2022.105323

publications
mouse-rat, neuroscience, tissue-organ, model-systems, other-application
68
Nature communications

Deficiency of the frontotemporal dementia gene GRN results in gangliosidosis

Sebastian Boland, Sharan Swarup, Yohannes A Ambaw, Pedro C Malia, Ruth C Richards, Alexander W Fischer, Shubham Singh, Geetika Aggarwal, Salvatore Spina, Alissa L Nana, Lea T Grinberg, William W Seeley, Michal A Surma, Christian Klose, Joao A Paulo, Andrew D Nguyen, J Wade Harper, Tobias C Walther, Robert V Farese Jr

Haploinsufficiency of GRN causes frontotemporal dementia (FTD). The GRN locus produces progranulin (PGRN), which is cleaved to lysosomal granulin polypeptides. The function of lysosomal granulins and why their absence causes neurodegeneration are unclear. Here we discover that PGRN-deficient human cells and murine brains, as well as human frontal lobes from GRN-mutation FTD patients have increased levels of gangliosides, glycosphingolipids that contain sialic acid. In these cells and tissues, levels of lysosomal enzymes that catabolize gangliosides were normal, but levels of bis(monoacylglycero)phosphates (BMP), lipids required for ganglioside catabolism, were reduced with PGRN deficiency. Our findings indicate that granulins are required to maintain BMP levels to support ganglioside catabolism, and that PGRN deficiency in lysosomes leads to gangliosidosis. Lysosomal ganglioside accumulation may contribute to neuroinflammation and neurodegeneration susceptibility observed in FTD due to PGRN deficiency and other neurodegenerative diseases.

Link: doi.org/10.1038/s41467-022-33500-9

publications
human, neuroscience, tissue-organ
69
Journal of the American Heart Association

Lipidome‐ and Genome‐Wide Study to Understand Sex Differences in Circulatory Lipids

Rubina Tabassum, Sanni Ruotsalainen, Linda Ottensmann, Mathias J Gerl, Christian Klose, Taru Tukiainen, Matti Pirinen, Kai Simons, Elisabeth Widén, Samuli Ripatti

Despite well‐recognized differences in the atherosclerotic cardiovascular disease risk between men and women, sex differences in risk factors and sex‐specific mechanisms in the pathophysiology of atherosclerotic cardiovascular disease remain poorly understood. Lipid metabolism plays a central role in the development of atherosclerotic cardiovascular disease. Understanding sex differences in lipids and their genetic determinants could provide mechanistic insights into sex differences in atherosclerotic cardiovascular disease and aid in precise risk assessment. Herein, we examined sex differences in plasma lipidome and heterogeneity in genetic influences on lipidome in men and women through sex‐stratified genome‐wide association analyses.

We used data consisting of 179 lipid species measured by shotgun lipidomics in 7266 individuals from the Finnish GeneRISK cohort and sought for replication using independent data from 2045 participants. Significant sex differences in the levels of 141 lipid species were observed (P<7.0×10−4). Interestingly, 121 lipid species showed significant age‐sex interactions, with opposite age‐related changes in 39 lipid species. In general, most of the cholesteryl esters, ceramides, lysophospholipids, and glycerides were higher in 45‐ to 50‐year‐old men compared with women of same age, but the sex differences narrowed down or reversed with age. We did not observe any major differences in genetic effect in the sex‐stratified genome‐wide association analyses, which suggests that common genetic variants do not have a major role in sex differences in lipidome. Our study provides a comprehensive view of sex differences in circulatory lipids pointing to potential sex differences in lipid metabolism and highlights the need for sex‐ and age‐specific prevention strategies.

Link: doi.org/10.1161/JAHA.122.027103

publications
data, human, blood, cardiovascular-disease, clinical-research, biomarker, other-application, multiomics
70
ARTICLE

Lipid metabolism & microbiome of dry skin

Olga (Olya) Vvedenskaya, Henri M Deda

Xerosis, known as dry skin, affects one-third of the population worldwide, causing itching, irritation, and cracking or peeling. The external skin layer, the stratum corneum, is essential for skin barrier properties, allowing maintaining hydration and regulating trans-epidermal water loss. Here and further, when we talk about skin, we mean the stratum corneum layer. Particular lipids play an essential role in maintaining the skin lipid barrier functions, and lipidome alterations upon application of skin moisturizer can shed the light on the effectiveness of a body lotion. Finally, the skin microbiome has an impact on the condition of the skin. Both parameters, microbiome, and lipidome, are to be analyzed to evaluate the effect of a body lotion on (dry) skin

Link: lipotype.com/xerosis

articles
human, dermatology, skin, microbiology, multiomics
71
The Lipidomics Webinar

Composition, organization & function of living membranes

Ilya Levental

The plasma membrane is the interface between a cell and its environment and is therefore responsible for a myriad of parallel processing tasks that must be tightly regulated to avoid aberrant signaling. To achieve this functional complexity, mammalian cells produce hundreds of lipid species that are actively turned over and trafficked to produce spatial and temporal gradients between cellular compartments. In addition to the plethora of regulatory roles performed by individual lipid molecules, membrane physiology is strictly dependent on the biophysical phenotypes – including membrane fluidity, rigidity, lipid packing, and lateral organization – arising from the collective behaviors of lipids.
Here, we will present the results of several projects that address the lipidomic, biophysical, and functional aspects of mammalian plasma membranes. These projects explore the relationship between membrane organization and cellular function, ultimately demonstrating that membrane phenotypes are central regulators of cell physiology.

Link: lipotype.com/mammalian-cell-membranes

webinars
diet, organelles
72
ARTICLE

Lipid metabolism impacts remyelination

Olga (Olya) Vvedenskaya, Henri M Deda

Remyelination is a regenerative process that can occur during central nervous system (CNS) damage. In cases like multiple sclerosis or Alzheimer’s disease, remyelination often fails during the progressive phase of a disease. It is essential to understand the details of remyelination and lipid composition remodeling in order to work on the interventions of myelin sheath reconstruction. This study investigates the phagocytes function of clearing cholesterol excess that occurs as a result of a demyelinating injury.

Link: lipotype.com/remyelination

articles
mouse-rat, cell, neuroscience, organelles
73
ARTICLE

T cell function & lipid metabolism

Nuala Del Piccolo, Henri M Deda

The immune system works to protect an individual from external and internal threats and is composed of two complementary subsystems: innate and adaptive immunity. The innate immune system is present at birth; provides a rapid, non-specific response to foreign threats; and is composed of physical barriers like skin and mucus, and specialized cell types including monocytes and neutrophils. The adaptive immune system, on the other hand, learns about threats from the innate immune system and develops specific defenses against them, which can be long-lasting; it is composed of specialized cell types called lymphocytes. T cells are a subset of lymphocytes that – through unique, surface-bound proteins known as T cell receptors (TCRs) – directly recognize and target threat-associated antigens. T cells also communicate with other cells in the adaptive immune system by producing chemical signals known as cytokines. T cell signaling can, like other processes that occur at cellular membranes, be modified by the biophysical properties of membranes. For example, membrane lipid order – a measure of how efficiently lipids can pack together – influences the formation, persistence, and function of signaling platforms. Membrane lipid order depends on membrane composition, environmental temperature, lipid metabolism, and other factors. Overall, this study demonstrates that LXR activation alters lipid metabolism and, through mechanisms that involve membrane lipid order and subsequent modification of cell signaling, immune function in T helper cells. This finding indicates that LXR may be an effective therapeutic target for diseases that involve aberrant T cell signaling, such as cancers and autoimmune disorders.

Link: lipotype.com/t-cell-activation

articles
human, cell, organelles, other-application
74
The Lipidomics Webinar

What have lipids to do with the worst pandemic ever?

Kai Simons

Today we are under threat not only from Covid-19 but another even worse pandemic is spreading worldwide and that is obesity, unhealthy weight. This disease does not only cause serious health problems globally but it can also lead to other diseases such as diabetes type 2, cardiovascular disease, liver disease, dementia and cancer. Obesity is driven by the consumption of processed foods, snacks, and soft drinks that are designed so that they even can become addictive. Metabolic parameters can long be maintained in a physiological range. However, once the metabolic overload has overwhelmed the homeostatic control systems, the damage leads to disease.
It is here that the lipids come into play. Lipid homeostasis is central to health. When lipid metabolism becomes dysfunctional, it can turn into a driver for the gamut of obesity-related complications. Amazingly, what is lacking are diagnostic tests that can recognize dysmetabolism before it turns into disease and becomes irreversible. The situation for obesity is like trying to combat Covid without an assay for the virus.
Most excitingly, our studies demonstrate that lipids could provide a means to monitor dysmetabolism. Plasma cholesterol and triglycerides have already proven their worth as useful biomarkers. When you add the complement of lipids in our lipidomes to the analysis, then the differentiation power becomes formidable. The fact that pathological changes occurring in our body organs seem to be mirrored in the blood lipidome could provide the basis for the diagnosis of dysmetabolism. Strangely neglected, lipid metabolism is now emerging as a research area with great potential.

Link: lipotype.com/the-obesity-pandemic

webinars
metabolic-disorders, diet, biomarker
75
Nature communications

Chain flexibility of medicinal lipids determines their selective partitioning into lipid droplets

So-Hee Son, Gyuri Park, Junho Lim, Chang Yun Son, Seung Soo Oh, Ju Young Lee

In guiding lipid droplets (LDs) to serve as storage vessels that insulate high-value lipophilic compounds in cells, we demonstrate that chain flexibility of lipids determines their selective migration in intracellular LDs. Focusing on commercially important medicinal lipids with biogenetic similarity but structural dissimilarity, we computationally and experimentally validate that LD remodeling should be differentiated between overproduction of structurally flexible squalene and that of rigid zeaxanthin and β-carotene. In molecular dynamics simulations, worm-like flexible squalene is readily deformed to move through intertwined chains of triacylglycerols in the LD core, whereas rod-like rigid zeaxanthin is trapped on the LD surface due to a high free energy barrier in diffusion. By designing yeast cells with either much larger LDs or with a greater number of LDs, we observe that intracellular storage of squalene significantly increases with LD volume expansion, but that of zeaxanthin and β-carotene is enhanced through LD surface broadening; as visually evidenced, the outcomes represent internal penetration of squalene and surface localization of zeaxanthin and β-carotene. Our study shows the computational and experimental validation of selective lipid migration into a phase-separated organelle and reveals LD dynamics and functionalization.

Link: doi.org/10.1038/s41467-022-31400-6

publications
cell, yeast, pharma, organelles
76
scientific reports

A set of gene knockouts as a resource for global lipidomic changes

Aleksandra Spiegel, Chris Lauber, Mandy Bachmann, Anne-Kristin Heninger, Christian Klose, Kai Simons, Mihail Sarov, Mathias J Gerl

Enzyme specificity in lipid metabolic pathways often remains unresolved at the lipid species level, which is needed to link lipidomic molecular phenotypes with their protein counterparts to construct functional pathway maps. We created lipidomic profiles of 23 gene knockouts in a proof-of-concept study based on a CRISPR/Cas9 knockout screen in mammalian cells. This results in a lipidomic resource across 24 lipid classes. We highlight lipid species phenotypes of multiple knockout cell lines compared to a control, created by targeting the human safe-harbor locus AAVS1 using up to 1228 lipid species and subspecies, charting lipid metabolism at the molecular level. Lipid species changes are found in all knockout cell lines, however, some are most apparent on the lipid class level (e.g., SGMS1 and CEPT1), while others are most apparent on the fatty acid level (e.g., DECR2 and ACOT7). We find lipidomic phenotypes to be reproducible across different clones of the same knockout and we observed similar phenotypes when two enzymes that catalyze subsequent steps of the long-chain fatty acid elongation cycle were targeted.

Link: doi.org/10.1038/s41598-022-14690-0

publications
data, human, cell, model-systems, other-application, multiomics
77
EMBO reports

Metabolic routing maintains the unique fatty acid composition of phosphoinositides

Yeun Ju Kim, Nivedita Sengupta, Mira Sohn, Amrita Mandal, Joshua G Pemberton, Uimook Choi, Tamas Balla

Phosphoinositide lipids (PPIn) are enriched in stearic- and arachidonic acids (38:4) but how this enrichment is established and maintained during phospholipase C (PLC) activation is unknown. Here we show that the metabolic fate of newly synthesized phosphatidic acid (PA), the lipid precursor of phosphatidylinositol (PI), is influenced by the fatty acyl-CoA used with preferential routing of the arachidonoyl-enriched species toward PI synthesis. Furthermore, during agonist stimulation the unsaturated forms of PI(4,5P)2 are replenished significantly faster than the more saturated ones, suggesting a favored recycling of the unsaturated forms of the PLC-generated hydrolytic products. Cytidine diphosphate diacylglycerol synthase 2 (CDS2) but not CDS1 was found to contribute to increased PI resynthesis during PLC activation. Lastly, while the lipid transfer protein, Nir2 is found to contribute to rapid PPIn resynthesis during PLC activation, the faster re-synthesis of the 38:4 species does not depend on Nir2. Therefore, the fatty acid side-chain composition of the lipid precursors used for PI synthesis is an important determinant of their metabolic fates, which also contributes to the maintenance of the unique fatty acid profile of PPIn lipids.

Link: doi.org/10.15252/embr.202154532

publications
human, cell, other-application
78
npj Parkinson's disease

Lipase regulation of cellular fatty acid homeostasis as a Parkinson’s disease therapeutic strategy

Saranna Fanning, Haley Cirka, Jennifer L Thies, Jooyoung Jeong, Sarah M Niemi, Joon Yoon, Gary P H Ho, Julian A Pacheco, Ulf Dettmer, Lei Liu, Clary B Clish, Kevin J Hodgetts, John N Hutchinson, Christina R Muratore, Guy A Caldwell, Kim A Caldwell, Dennis Selkoe

Synucleinopathy (Parkinson’s disease (PD); Lewy body dementia) disease-modifying treatments represent a huge unmet medical need. Although the PD-causing protein α-synuclein (αS) interacts with lipids and fatty acids (FA) physiologically and pathologically, targeting FA homeostasis for therapeutics is in its infancy. We identified the PD-relevant target stearoyl-coA desaturase: inhibiting monounsaturated FA synthesis reversed PD phenotypes. However, lipid degradation also generates FA pools. Here, we identify the rate-limiting lipase enzyme, LIPE, as a candidate target. Decreasing LIPE in human neural cells reduced αS inclusions. Patient αS triplication vs. corrected neurons had increased pSer129 and insoluble αS and decreased αS tetramer:monomer ratios. LIPE inhibition rescued all these and the abnormal unfolded protein response. LIPE inhibitors decreased pSer129 and restored tetramer:monomer equilibrium in αS E46K-expressing human neurons. LIPE reduction in vivo alleviated αS-induced dopaminergic neurodegeneration in Caenorhabditis elegans. Co-regulating FA synthesis and degradation proved additive in rescuing PD phenotypes, signifying co-targeting as a therapeutic strategy.

Link: doi.org/10.1038/s41531-022-00335-6

publications
human, cell, neuroscience, other-organism
79
Genetics

Fine tuning Acetyl-CoA Carboxylase 1 activity through localization: Functional genomics reveal a role for the lysine acetyltransferase NuA4 and sphingolipid metabolism in regulating Acc1 activity and localization

Trang Pham, Elizabeth Walden, Sylvain Huard, John Pezacki, Morgan D Fullerton, Kristin Baetz

Acetyl-CoA Carboxylase 1 (Acc1) catalyzes the conversion of acetyl-CoA to malonyl-CoA, the committed step of de novo fatty acid synthesis. As a master-regulator of lipid synthesis, Acc1 has been proposed to be a therapeutic target for numerous metabolic diseases. We have shown that Acc1 activity is reduced in the absence of the lysine acetyltransferase NuA4 in Saccharomyces cerevisiae. This change in Acc1 activity is correlated with a change in localization. In wild-type cells Acc1 is localized throughout the cytoplasm in small punctate and rod-like structures. However, in NuA4 mutants, Acc1 localization becomes diffuse. To uncover mechanisms regulating Acc1 localization we performed a microscopy screen to identify other deletion mutants that impact Acc1 localization and then measured Acc1 activity in these mutants through chemical genetics and biochemical assays. Three phenotypes were identified. Mutants with hyper-active Acc1 form one or two rod-like structures centrally within the cytoplasm, mutants with mid-low Acc1 activity displayed diffuse Acc1, while the mutants with the lowest Acc1 activity (hypomorphs) formed thick rod-like Acc1 structures at the periphery of the cell. All the Acc1 hypomorphic mutants were implicated in sphingolipid metabolism or very-long chain fatty acid elongation and in common, their deletion causes an accumulation of palmitoyl-CoA. Through exogenous lipid treatments, enzyme inhibitors and genetics, we determined that increasing palmitoyl-CoA levels inhibits Acc1 activity and remodels Acc1 localization. Together this study suggests yeast cells have developed a dynamic feed-back mechanism in which downstream products of Acc1 can fine-tune the rate of fatty acid synthesis.

Link: doi.org/10.1093/genetics/iyac086

publications
cell, yeast, other-application, multiomics
80
ARTICLE

What is multiomics?

Nuala Del Piccolo, Henri M Deda

The production and analysis of so-called omics datasets – such as the genes, lipids, proteins, metabolites, or microbes – has rapidly gained popularity in biomedical research. Individual analysis of an omics dataset can identify links between the characterized feature and a specific biological phenomena. Multiomics is the integrated analysis of multiple omics datasets, and can identify mechanisms of action, biomarkers, networks, pathways, and other relationships present in physiological and pathological processes. Multiomics analyses have been used to characterize, monitor, and predict many disease states. The following case studies describe recent multiomics-based studies of four common diseases – namely, Alzheimer’s disease, cardiovascular disease, type I diabetes, and ovarian cancer – in which inclusion of lipidome data helped reveal something new about well-studied diseases.

Link: lipotype.com/what-is-multiomics

articles
multiomics
81
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Lifespan Extension of Podospora anserina Mic60-Subcomplex Mutants Depends on Cardiolipin Remodeling

Lisa-Marie Marschall, Verena Warnsmann, Anja C Meeßen, Timo Löser, Heinz D Osiewacz

Function of mitochondria largely depends on a characteristic ultrastructure with typical invaginations, namely the cristae of the inner mitochondrial membrane. The mitochondrial signature phospholipid cardiolipin (CL), the F1Fo-ATP-synthase, and the ‘mitochondrial contact site and cristae organizing system’ (MICOS) complex are involved in this process. Previous studies with Podospora anserina demonstrated that manipulation of MICOS leads to altered cristae structure and prolongs lifespan. While longevity of Mic10-subcomplex mutants is induced by mitohormesis, the underlying mechanism in the Mic60-subcomplex deletion mutants was unclear. Since several studies indicated a connection between MICOS and phospholipid composition, we now analyzed the impact of MICOS on mitochondrial phospholipid metabolism. Data from lipidomic analysis identified alterations in phospholipid profile and acyl composition of CL in Mic60-subcomplex mutants. These changes appear to have beneficial effects on membrane properties and promote longevity. Impairments of CL remodeling in a PaMIC60 ablated mutant lead to a complete abrogation of longevity. This effect is reversed by supplementation of the growth medium with linoleic acid, a fatty acid which allows the formation of tetra-octadecanoyl CL. In the PaMic60 deletion mutant, this CL species appears to lead to longevity. Overall, our data demonstrate a tight connection between MICOS, the regulation of mitochondrial phospholipid homeostasis, and aging of P. anserina.

Link: doi.org/10.3390/ijms23094741

publications
subcellular, other-organism, organelles, other-application
82
Journal of Cell Biology

Regulated targeting of the monotopic hairpin membrane protein Erg1 requires the GET pathway

Ákos Farkas, Henning Urlaub, Katherine E Bohnsack, Blanche Schwappach

The guided entry of tail-anchored proteins (GET) pathway targets C-terminally anchored transmembrane proteins and protects cells from lipotoxicity. Here, we reveal perturbed ergosterol production in ∆get3 cells and demonstrate the sensitivity of GET pathway mutants to the sterol synthesis inhibiting drug terbinafine. Our data uncover a key enzyme of sterol synthesis, the hairpin membrane protein squalene monooxygenase (Erg1), as a non-canonical GET pathway client, thus rationalizing the lipotoxicity phenotypes of GET pathway mutants. Get3 recognizes the hairpin targeting element of Erg1 via its classical client-binding pocket. Intriguingly, we find that the GET pathway is especially important for the acute upregulation of Erg1 induced by low sterol conditions. We further identify several other proteins anchored to the endoplasmic reticulum (ER) membrane exclusively via a hairpin as putative clients of the GET pathway. Our findings emphasize the necessity of dedicated targeting pathways for high-efficiency targeting of particular clients during dynamic cellular adaptation and highlight hairpin proteins as a potential novel class of GET clients.

Link: doi.org/10.1083/jcb.202201036

publications
cell, yeast, other-application
83
The Lipidomics Webinar

Shotgun lipidomics of tissue biopsies

Andrej Shevchenko

Liquid biopsies (e.g. plasma or serum) is an available clinical resource extensively exploited by lipidomics. However, plasma lipidome changes reflect the diseases progressing elsewhere in different organs only indirectly. The direct analysis of tissue biopsies could be in a better position to elucidate molecular details of pathophysiological mechanisms.
Biopsies lipidomics requires careful standardization, the collection of abundant meta- and histological data together with robust normalization of lipid abundances. By providing absolute (molar) abundances of lipid species in whole biopsies, it creates a generic and expandable lipidomics resource. Furthermore, shotgun lipidomics could address spatial distribution of lipids by analyzing histological features isolated by laser capture microdissection (LCM). Combining the material from many similar features increases the lipidome coverage and enables to complement lipidomics with proteomics to confirm the dissection specificity by quantifying histologically specific markers.
Systematic shotgun analysis of whole and LCM-dissected liver, colon and pancreas biopsies suggested that, in general, tissues tend to preserve their lipid composition even when histological analyses indicate profound changes in their morphology. Significant lipidome perturbation are specific to a few individual species within spatially defined zones and offer new and often unexpected look at the pathophysiological role of lipid metabolism.

Link: lipotype.com/shotgun-lipidomics-of-tissue-biopsies

webinars
metabolic-disorders, other-application
84
eLife

Reducing lipid bilayer stress by monounsaturated fatty acids protects renal proximal tubules in diabetes

Albert Pérez-Martí, Suresh Ramakrishnan, Jiayi Li, Aurelien Dugourd, Martijn R Molenaar, Luigi R De La Motte, Kelli Grand, Anis Mansouri, Mélanie Parisot, Soeren S Lienkamp, Julio Saez-Rodriguez, Matias Simons

In diabetic patients, dyslipidemia frequently contributes to organ damage such as diabetic kidney disease (DKD). Dyslipidemia is associated with both excessive deposition of triacylglycerol (TAG) in lipid droplets (LDs) and lipotoxicity. Yet, it is unclear how these two effects correlate with each other in the kidney and how they are influenced by dietary patterns. By using a diabetes mouse model, we find here that high-fat diet enriched in the monounsaturated oleic acid (OA) caused more lipid storage in LDs in renal proximal tubular cells (PTCs) but less tubular damage than a corresponding butter diet with the saturated palmitic acid (PA). This effect was particularly evident in S2/S3 but not S1 segments of the proximal tubule. Combining transcriptomics, lipidomics, and functional studies, we identify endoplasmic reticulum (ER) stress as the main cause of PA-induced PTC injury. Mechanistically, ER stress is caused by elevated levels of saturated TAG precursors, reduced LD formation, and, consequently, higher membrane order in the ER. Simultaneous addition of OA rescues the cytotoxic effects by normalizing membrane order and increasing both TAG and LD formation. Our study thus emphasizes the importance of monounsaturated fatty acids for the dietary management of DKD by preventing lipid bilayer stress in the ER and promoting TAG and LD formation in PTCs.

Link: doi.org/10.7554/eLife.74391

publications
mouse-rat, metabolic-disorders, cell, diet, tissue-organ, organelles, multiomics
85
Article

Multiomics analysis of cancer chemotherapy sensitivity

Nuala Del Piccolo, Henri M Deda

Ovarian cancers can be classified into four subtypes – serous, mucinous, endometrioid, and clear-cell – based on their histology. These subtypes exhibit varying sensitivity to platinum-based chemotherapy and seem to incorporate different amounts of lipids into their cells. The four ovarian cancer subtypes – serous, mucinous, endometrioid, and clear-cell – were modeled using cell lines, murine models, fixed patient tissue samples, and data from The Cancer Genome Atlas. These models were characterized via viability, chemosensitivity, lipidomic, and transcriptomic assays. In both ovarian cancer cell lines and patient samples, LDLR expression was high in endometrioid and clear-cell and low in serous and mucinous ovarian cancers. Additionally, in an in vitro assay, serous cells were more sensitive than clear-cell and endometrioid cells to cisplatin. Consistent with this observation, increasing LDLR expression in serous cells and knocking down expression in clear-cell and endometrioid cells respectively reduced and enhanced chemo-sensitivity. Overall, this study revealed that overexpression of LDLR reduces sensitivity to platinum-based therapy in ovarian cancer cell lines and murine models.

Link: lipotype.com/multiomics-of-cancer-chemotherapy-sensitivity

articles
human, mouse-rat, cell, oncology, tissue-organ, clinical-research, multiomics
86
Journal of Biological Chemistry

microRNA-27b regulates hepatic lipase enzyme LIPC and reduces triglyceride degradation during hepatitis C virus infection

Geneviève F Desrochers, Roxana Filip, Micheal Bastianelli, Tiffany Stern, John Paul Pezacki

MicroRNAs are short, non-coding RNAs that negatively and specifically regulate protein expression, the cumulative effects of which can result in broad changes to cell systems and architecture. The microRNA miR-27b is known to regulate lipid-regulatory pathways in the human liver and is also induced by the hepatitis C virus (HCV). However, miR-27b’s functional targets are not well established. Herein, an activity-based protein profiling method using a serine hydrolase probe, coupled with stable isotope labelling and mass spectrometry identified direct and indirect targets of miR-27b. The hepatic lipase LIPC stood out as both highly dependent on miR-27b and as a major modulator of lipid pathway misregulation. Modulation of miR-27b using both exogenous microRNA mimics and inhibitors demonstrated that transcription factors Jun, PPARα, and HNF4α all of which also influenced LIPC levels and activity, are regulated by miR-27b. LIPC was furthermore shown to affect the progress of the life cycle of HCV, and to decrease levels of intracellular triglycerides, upon which HCV is known to depend. In summary, this work has demonstrated that miR-27b mediates HCV infection by downregulating LIPC, thereby reducing triglyceride degradation, which in turn increases cellular lipid levels.

Link: doi.org/10.1016/j.jbc.2022.101983

publications
human, cell, other-application, multiomics
87
Life Science Alliance

Tricalbin proteins regulate plasma membrane phospholipid homeostasis

Ffion B Thomas, Deike J Omnus, Jakob M Bader, Gary HC Chung, Nozomu Kono, Christopher J Stefan

The evolutionarily conserved extended synaptotagmin (E-Syt) proteins are calcium-activated lipid transfer proteins that function at contacts between the ER and plasma membrane (ER-PM contacts). However, roles of the E-Syt family members in PM lipid organisation remain incomplete. Among the E-Syt family, the yeast tricalbin (Tcb) proteins are essential for PM integrity upon heat stress, but it is not known how they contribute to PM maintenance. Using quantitative lipidomics and microscopy, we find that the Tcb proteins regulate phosphatidylserine homeostasis at the PM. Moreover, upon heat-induced membrane stress, Tcb3 co-localises with the PM protein Sfk1 that is implicated in PM phospholipid asymmetry and integrity. The Tcb proteins also control the PM targeting of the known phosphatidylserine effector Pkc1 upon heat-induced stress. Phosphatidylserine has evolutionarily conserved roles in PM organisation, integrity, and repair. We propose that phospholipid regulation is an ancient essential function of E-Syt family members required for PM integrity.

Link: doi.org/10.26508/lsa.202201430

publications
cell, yeast, organelles, other-application
88
The Lipidomics Webinar

How to yeast lipidomics research

Christian Klose

The yeast Saccharomyces cerevisiae is a powerful model system for cell and molecular biology research. This is mostly due to the availability of simple and straightforward genetic and molecular tools and methods to manipulate almost any cell biological process.
Lipidomics has become an indispensable method for the quantitative assessment of lipid metabolism and membrane biology in studies employing yeast as an experimental system. Here we show how lipidomics is applied to investigate the influence of a variety of commonly used growth conditions on the yeast lipidome, including glycerophospholipids, triglycerides, ergosterol as well as complex sphingolipids, establishing a baseline for future lipidomic experiments in yeast.
Based on this work, we review acyl chain remodeling as a fundamental aspect of membrane biology, the roles of lipids in the unfolded protein response (UPR) in both endoplasmic reticulum (ER) and mitochondria, as well as the lipid-based regulation of key biological process like control of cell size and growth rate. These studies provide mechanistic insights into the amazing diversity of lipid functions in essential cellular processes conserved throughout the eukaryotic domain of life.

Link: lipotype.com/how-to-yeast-lipidomics-research

webinars
model-systems, organelles, microbiology
89
EMBO Molecular Medicine

AAV-delivered diacylglycerol kinase DGKk achieves long-term rescue of fragile X syndrome mouse model

Karima Habbas, Oktay Cakil, Boglárka Zámbó, Ricardos Tabet, Fabrice Riet, Doulaye Dembele, Jean-Louis Mandel, Michaël Hocquemiller, Ralph Laufer, Françoise Piguet, Hervé Moine

Fragile X syndrome (FXS) is the most frequent form of familial intellectual disability. FXS results from the lack of the RNA-binding protein FMRP and is associated with the deregulation of signaling pathways downstream of mGluRI receptors and upstream of mRNA translation. We previously found that diacylglycerol kinase kappa (DGKk), a main mRNA target of FMRP in cortical neurons and a master regulator of lipid signaling, is downregulated in the absence of FMRP in the brain of Fmr1-KO mouse model. Here we show that adeno-associated viral vector delivery of a modified and FMRP-independent form of DGKk corrects abnormal cerebral diacylglycerol/phosphatidic acid homeostasis and FXS-relevant behavioral phenotypes in the Fmr1-KO mouse. Our data suggest that DGKk is an important factor in FXS pathogenesis and provide preclinical proof of concept that its replacement could be a viable therapeutic strategy in FXS.

Link: doi.org/10.15252/emmm.202114649

publications
mouse-rat, neuroscience, tissue-organ
90
MDPI Molecules

Shotgun Lipidomic Analysis for Differentiation of Niche Cold Pressed Oils

Hanna Nikolaichuk, Kacper Przykaza, Anna Kozub, Magdalena Montowska, Grażyna Wójcicka, Jolanta Tomaszewska-Gras, Emilia Fornal

The fast-growing food industry is bringing significant number of new products to the market. To protect consumers’ health and rights, it is crucial that food control laboratories are able to ensure reliable quality testing, including product authentication and detection of adulterations. In our study, we applied a fast and eco-friendly method based on shotgun-lipidomic mass spectrometry for the authentication of niche edible oils. Comprehensive lipid profiles of camelina (CA), flax (FL) and hemp (HP) seed oils were obtained. With the aid of principal component analysis (PCA), it was possible to detect and distinguish each of them based on their lipid profiles. Lipidomic markers characteristic ofthe oils were also identified, which can be used as targets and expedite development of new multiplexed testing methods.

Link: doi.org/10.3390/molecules27061848

publications
diet, plant, oil-fat, other-application
91
Scientific reports

Alteration of barrier properties, stratum corneum ceramides and microbiome composition in response to lotion application on cosmetic dry skin

Barry Murphy, Sally Grimshaw, Michael Hoptroff, Sarah Paterson, David Arnold, Andrew Cawley, Suzanne E Adams, Francesco Falciani, Tony Dadd, Richard Eccles, Alex Mitchell, William F Lathrop, Diana Marrero, Galina Yarova, Ana Villa, John S Bajor, Lin Feng, Dawn Mihalov, Andrew E Mayes

Xerosis, commonly referred to as dry skin, is a common dermatological condition affecting almost a third of the population. Successful treatment of the condition traditionally involves the application of cosmetic products facilitating the moisturisation of the skin with a range of ingredients including glycerol and fatty acids. While the effectiveness of these treatments is not in question, limited information exists on the impact on the skin microbiome following use of these products and the improvement in skin hydration. Here, we describe improvements in skin barrier properties together with increased levels of cholesterol, ceramides and long-chain fatty acids following application of Body Lotion. Concomitant alterations in the skin microbiome are also seen via 16S rRNA metataxonomics, in combination with both traditional and novel informatics analysis. Following 5 weeks of lotion use, beneficial skin bacteria are increased, with improvements in microbiome functional potential, and increases in pathways associated with biosynthesis of multiple long chain fatty acids.

Link: doi.org/10.1038/s41598-022-09231-8

publications
human, dermatology, skin, microbiology, clinical-research, multiomics
92
Article

Cardiolipin synthesis & protein import during mtUPR

Nuala Del Piccolo, Henri M Deda

Like the cell’s unfolded protein response, the mitochondrial unfolded protein response (mtUPR) is a protective mechanism triggered by organelle dysfunction – often due to mutations, aging, exposure to toxins, or other stress. During mtUPR, metabolism, gene expression, and/or other processes are modified to protect the organelle – and especially oxidative phosphorylation – and the cell. Kinetic analyses in isolated mitochondria showed that protein import increased in the early phase of mtUPR (2-10 hours after induction) compared to wild-type yeast. In the late phase of mtUPR (20 hours after induction), protein import decreased. In search of a mechanism underlying these observations, mitochondrial lipid composition was characterized. Membrane lipid composition is known to modulate the function of membrane proteins – like those involved in protein import. These lipidomic data identified increases in the abundance of cardiolipin and its metabolic precursor and a decrease in cardiolipin acyl chain length during the early phase of mtUPR. Overall, this study identified and characterized two phases of mtUPR. In the early phase of mtUPR, protein import increased, and this was accompanied by cardiolipin synthesis and remodeling. In the late phase of mtUPR, protein import decreased.

Link: lipotype.com/mitochondrial-unfolded-protein-response

articles
subcellular, yeast, organelles, microbiology, other-application
93
Article

Chain length impacts membrane fluidity

Nuala Del Piccolo, Henri M Deda

Cellular membranes are heterogeneous, flexible, 2D structures composed of lipids, proteins, and carbohydrates. They are the site of many essential biological functions, including signal transduction, nutrient/waste transport, and energy generation. To optimize membranes for each of these varied functions, cells tune membrane biophysical properties, such as structure, composition, and fluidity. In eukaryotes, the glycerophospholipid phosphatidylcholine (PC) is abundant in the membrane – it can account for over 50% of membrane lipids – and has functional roles in signal transduction and metabolism. To probe how yeast adapt to the lack of PC, whole-cell lipids were isolated and characterized via mass spectrometry-based shotgun lipidomics and thin layer chromatography. Overall, this study demonstrates that yeast can adapt to the absence of PC by reducing the activity of the enzyme Acc1, thus decreasing acyl chain length and restoring membrane fluidity.

Link: lipotype.com/fatty-acid-chain-length-membrane-fluidity

articles
cell, yeast, model-systems, organelles, microbiology
94
PLOS Biology

Lipidomic risk scores are independent of polygenic risk scores and can predict incidence of diabetes and cardiovascular disease in a large population cohort

Chris Lauber, Mathias J Gerl, Christian Klose, Filip Ottosson, Olle Melander, Kai Simons

Type 2 diabetes (T2D) and cardiovascular disease (CVD) represent significant disease burdens for most societies and susceptibility to these diseases is strongly influenced by diet and lifestyle. Physiological changes associated with T2D or CVD, such has high blood pressure and cholesterol and glucose levels in the blood, are often apparent prior to disease incidence. Here we integrated genetics, lipidomics, and standard clinical diagnostics to assess future T2D and CVD risk for 4,067 participants from a large prospective population-based cohort, the Malmö Diet and Cancer-Cardiovascular Cohort. By training Ridge regression-based machine learning models on the measurements obtained at baseline when the individuals were healthy, we computed several risk scores for T2D and CVD incidence during up to 23 years of follow-up. We used these scores to stratify the participants into risk groups and found that a lipidomics risk score based on the quantification of 184 plasma lipid concentrations resulted in a 168% and 84% increase of the incidence rate in the highest risk group and a 77% and 53% decrease of the incidence rate in lowest risk group for T2D and CVD, respectively, compared to the average case rates of 13.8% and 22.0%. Notably, lipidomic risk correlated only marginally with polygenic risk, indicating that the lipidome and genetic variants may constitute largely independent risk factors for T2D and CVD. Risk stratification was further improved by adding standard clinical variables to the model, resulting in a case rate of 51.0% and 53.3% in the highest risk group for T2D and CVD, respectively. The participants in the highest risk group showed significantly altered lipidome compositions affecting 167 and 157 lipid species for T2D and CVD, respectively. Our results demonstrated that a subset of individuals at high risk for developing T2D or CVD can be identified years before disease incidence. The lipidomic risk, which is derived from only one single mass spectrometric measurement that is cheap and fast, is informative and could extend traditional risk assessment based on clinical assays.

Link: doi.org/10.1371/journal.pbio.3001561

publications
data, human, blood, metabolic-disorders, cardiovascular-disease, clinical-research, biomarker, multiomics
95
Brain

Sphingolipid changes in Parkinson L444P GBA mutation fibroblasts promote α-synuclein aggregation

Céline Galvagnion, Frederik Ravnkilde Marlet, Silvia Cerri, Anthony H V Schapira, Fabio Blandini, Donato A Di Monte

Intraneuronal accumulation of aggregated α-synuclein is a pathological hallmark of Parkinson’s disease. Therefore, mechanisms capable of promoting α-synuclein deposition bear important pathogenetic implications. Mutations of the glucocerebrosidase 1 (GBA) gene represent a prevalent Parkinson’s disease risk factor. They are associated with loss of activity of a key enzyme involved in lipid metabolism, glucocerebrosidase, supporting a mechanistic relationship between abnormal α-synuclein–lipid interactions and the development of Parkinson pathology.

In this study, the lipid membrane composition of fibroblasts isolated from control subjects, patients with idiopathic Parkinson’s disease and Parkinson’s disease patients carrying the L444P GBA mutation (PD-GBA) was assayed using shotgun lipidomics.

The lipid profile of PD-GBA fibroblasts differed significantly from that of control and idiopathic Parkinson’s disease cells. It was characterized by an overall increase in sphingolipid levels. It also featured a significant increase in the proportion of ceramide, sphingomyelin and hexosylceramide molecules with shorter chain length and a decrease in the percentage of longer-chain sphingolipids. The extent of this shift was correlated to the degree of reduction of fibroblast glucocerebrosidase activity. Lipid extracts from control and PD-GBA fibroblasts were added to recombinant α-synuclein solutions. The kinetics of α-synuclein aggregation were significantly accelerated after addition of PD-GBA extracts as compared to control samples. Amyloid fibrils collected at the end of these incubations contained lipids, indicating α-synuclein–lipid co-assembly. Lipids extracted from α-synuclein fibrils were also analysed by shotgun lipidomics. Data revealed that the lipid content of these fibrils was significantly enriched by shorter-chain sphingolipids. In a final set of experiments, control and PD-GBA fibroblasts were incubated in the presence of the small molecule chaperone ambroxol. This treatment restored glucocerebrosidase activity and sphingolipid levels and composition of PD-GBA cells. It also reversed the pro-aggregation effect that lipid extracts from PD-GBA fibroblasts had on α-synuclein.

Taken together, the findings of this study indicate that the L444P GBA mutation and consequent enzymatic loss are associated with a distinctly altered membrane lipid profile that provides a biological fingerprint of this mutation in Parkinson fibroblasts. This altered lipid profile could also be an indicator of increased risk for α-synuclein aggregate pathology.

Link: doi.org/10.1093/brain/awab371

publications
human, cell, subcellular, neuroscience, clinical-research
96
The Lipidomics Webinar

How to make sense of lipidomics data?

Mathias J Gerl

Lipidomics provide unprecedented phenotypic details by accumulating large amounts of data. While these are potentially of great value, the amount and complexity of the data can be intimidating initially. This webinar is designed to show the basics of lipidomics analysis. It will cover the characteristics of the datasets, e.g. their lipid substructure and multicollinearity, and how to deal with them. We will go through data preparation, how to calculate new features and how to use principal component analysis as a first impression. Then we will focus on univariate and correlation analysis combined with enrichment analysis.

Link: lipotype.com/how-to-make-sense-of-lipidomics-data

webinars
data
97
Frontiers in Cell and Developmental Biology

Sterol Metabolism Differentially Contributes to Maintenance and Exit of Quiescence

Carlotta Peselj, Mahsa Ebrahimi, Filomena Broeskamp, Simon Prokisch, Lukas Habernig, Irene Alvarez-Guerra, Verena Kohler, F-Nora Vögtle, Sabrina Büttner

Nutrient starvation initiates cell cycle exit and entry into quiescence, a reversible, non-proliferative state characterized by stress tolerance, longevity and large-scale remodeling of subcellular structures. Depending on the nature of the depleted nutrient, yeast cells are assumed to enter heterogeneous quiescent states with unique but mostly unexplored characteristics. Here, we show that storage and consumption of neutral lipids in lipid droplets (LDs) differentially impacts the regulation of quiescence driven by glucose or phosphate starvation. Upon prolonged glucose exhaustion, LDs were degraded in the vacuole via Atg1-dependent lipophagy. In contrast, yeast cells entering quiescence due to phosphate exhaustion massively over-accumulated LDs that clustered at the vacuolar surface but were not engulfed via lipophagy. Excessive LD biogenesis required contact formation between the endoplasmic reticulum and the vacuole at nucleus-vacuole junctions and was accompanied by a shift of the cellular lipid profile from membrane towards storage lipids, driven by a transcriptional upregulation of enzymes generating neutral lipids, in particular sterol esters. Importantly, sterol ester biogenesis was critical for long-term survival of phosphate-exhausted cells and supported rapid quiescence exit upon nutrient replenishment, but was dispensable for survival and regrowth of glucose-exhausted cells. Instead, these cells relied on de novo synthesis of sterols and fatty acids for quiescence exit and regrowth. Phosphate-exhausted cells efficiently mobilized storage lipids to support several rounds of cell division even in presence of inhibitors of fatty acid and sterol biosynthesis. In sum, our results show that neutral lipid biosynthesis and mobilization to support quiescence maintenance and exit is tailored to the respective nutrient scarcity.

Link: doi.org/10.3389/fcell.2022.788472

publications
cell, diet, yeast, model-systems, microbiology, multiomics
98
International Journal of Cosmetic Science

Changes in levels of omega-O-acylceramides and related processing enzymes of sun-exposed and sun-protected facial stratum corneum in differently pigmented ethnic groups

Anthony V Rawlings, Rotraut Schoop, Christian Klose, Jean-Marc Monneuse, Beverley Summers, Rainer Voegeli

We report on the differences in ceramide composition and levels of omega-O-acylceramide processing enzymes of sun-exposed and sun-protected facial stratum corneum (SC) among Albino African, Black African and Caucasian women living in South Africa. Tape strippings were taken from the sun-exposed cheek and the sun-protected postauricular site (PA). In two subsets proteomic (n=18) and lipidomic (n=24) analysis were performed using mass-spectrometry-based shotgun platforms. No significant differences in total ceramide levels or ceramide subtypes were found between the Black African and Caucasian women in either the cheek or PA samples. Compared to the other two groups the levels of total ceramide as well as selected omega-O-acylceramide species were increased in Albino Africans. On the cheek, ceramide (CER) EOS, EOH along with CER AS were increased relative to the Caucasian women, while CER EOP and EOdS were elevated relative to the Black African women. Moreover, on the PA site CER EOP and EOdS were elevated compared with the Black African women and CER EOdS in Caucasians. Decreases in mass levels of 12R-LOX and eLOX3 were observed on cheeks compared with the PA sites in all ethnic groups. On the PA sites 12R-LOX was particularly lower in the Albino Africans compared with the Black African and Caucasian women. On the cheeks mass levels of SDR9C7 was also lower in the Albino Africans. The mass levels of the ceramides were similar between Black African and Caucasian women. However, elevated total ceramides and excessively elevated selected omega-O-acylceramides were apparent in the Albino African women. The findings in the Albino women were unexpected as these participants suffer from impaired skin barrier function. However, the elevated levels omega-O-acylceramides can contribute to barrier insufficiency by directly impacting SC lipid phase behaviour and/or secondly elevated omega-O-acylceramide levels may indicate a reduced attachment of ceramides to the corneocyte lipid envelope and reduced corneocyte maturation that can also impair the barrier. Indeed, differences in the mass levels of omega-O-acylceramide processing enzymes were observed for 12R-LOX and SDR9C7 for the Albino Africans. This indicates a corneocyte lipid scaffold disorder in the Albino African women.

Link: doi.org/10.1111/ics.12765

publications
human, dermatology, skin, clinical-research, multiomics
99
Article

Anorexia, refeeding & lipid metabolism

Nuala Del Piccolo, Henri M Deda

Anorexia nervosa, an eating disorder, manifests itself as self-starvation, excessive weight loss and a distorted body image. Due to chronic undernutrition, anorexia patients may also experience changes in the body’s metabolism and endocrine system. Refeeding therapy – in which anorexia patients are hospitalized and fed a prescribed diet to induce weight gain – is the most successful current therapy. However, the optimal number of calories, nutritional content, and pacing of this therapy remain largely unexplored. The plasma lipid profile has recently emerged as a marker of metabolic health. Preliminary evidence suggests that the plasma lipidome may also provide insight on the metabolic health of patients with anorexia before, during, and/or after refeeding therapy.

Link: lipotype.com/lipid-metabolism-in-anorexia-refeeding-therapy

articles
mouse-rat, metabolic-disorders, blood, diet, clinical-research
100
Cell

Fundamental behaviors emerge from simulations of a living minimal cell

Zane R Thornburg, David M Bianchi, Troy A Brier, Benjamin R Gilbert, Tyler M Earnest, Marcelo C R Melo, Nataliya Safronova, James P Sáenz, András T Cook, Kim S Wise, Clyde A Hutchison III, Hamilton O Smith, John I Glass, Zaida Luthey-Schulten

We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.

Link: doi.org/10.1016/j.cell.2021.12.025

publications
cell, bacterium, model-systems, microbiology, other-application, multiomics
101
Article

Insulin sensitivity & circadian lipid metabolism

Nuala Del Piccolo, Henri M Deda

Lipid metabolism is regulated by circadian rhythms and therefore altered in people with atypical sleeping cycles, including those who work night shifts. Unfortunately, changes in lipid metabolism are also linked to metabolic diseases, including diabetes. Insulin sensitivity, a measure of the body’s responsiveness to insulin, is linked to lipid metabolism and reduced in type II diabetes. Here we show how the molecular mechanisms that contribute to insulin sensitivity are impacted by meal timing and composition – two external factors that influence circadian rhythms.

Link: lipotype.com/circadian-lipid-metabolism-and-insulin-sensitivity

articles
human, metabolic-disorders, blood, diet, tissue-organ, clinical-research
102
The Lipidomics Webinar

Why population health studies must apply lipidomics

Christian Klose

In the past century, population health studies have proven a powerful approach to reveal connections between diseases and their risk factors in epidemiology. We have now moved into an era, in which population health studies frequently rely on omics technologies (such as genomics, transcriptomics, metabolomics, and lipidomics) to identify disease risk factors at the molecular level.
Omics technologies provide unprecedented phenotypic details by accumulating vast amounts of data. While these are potentially of enormous value, biomarker identification studies benefit only if the data are of high quality and reliably reproducible. Fortunately, shotgun lipidomics fulfills these requirements and can therefore successfully be applied in biomarker identification studies covering indications such as obesity, diabetes, cardiovascular, and neurodegenerative diseases. Most importantly, human plasma lipidomics seems to reflect the body metabolism and has the potential to fill a hole in clinical diagnostics that lacks methods to measure metabolism.
Besides revealing promising potential multiparametric diagnostic and prognostic markers, large population health studies have proven that lipidomics is a powerful approach to shed light on disease mechanisms or relationships between genotype and phenotype in studies run over several years and involving tens of thousands of participants.

Link: lipotype.com/population-health-studies

webinars
clinical-research, biomarker, multiomics
103
Molecular Metabolism

Plasma triacylglycerols are biomarkers of β-cell function in mice and humans

Ana Rodríguez Sánchez-Archidona, Céline Cruciani-Guglielmacci, Clara Roujeau, Leonore Wigger, Justine Lallement, Jessica Denom, Marko Barovic, Nadim Kassis, Florence Mehl, Jürgen Weitz, Marius Distler, Christian Klose, Kai Simons, Mark Ibberson, Michele Solimena, Christophe Magnan, Bernard Thorens

We conducted a systems biology approach to characterize the plasma lipidomes of C57Bl/6J, DBA/2J, and BALB/cJ mice under different nutritional conditions, as well as their pancreatic islet and liver transcriptomes. We searched for correlations between plasma lipids and tissue gene expression modules to find plasma biomarkers prognostic of type 2 diabetes, which could also inform on pancreatic β-cell deregulations or defects in the function of insulin target tissues. We identified strong correlation between plasma triacylglycerols (TAGs) and islet gene modules that comprise key regulators of glucose- and lipid-regulated insulin secretion and of the insulin signaling pathway, the two top hits were Gck and Abhd6 for negative and positive correlations, respectively. Correlations were also found between sphingomyelins and islet gene modules that overlapped in part with the gene modules correlated with TAGs. In the liver, the gene module most strongly correlated with plasma TAGs was enriched in mRNAs encoding fatty acid and carnitine transporters as well as multiple enzymes of the β-oxidation pathway. In humans, plasma TAGs also correlated with the expression of several of the same key regulators of insulin secretion and the insulin signaling pathway identified in mice. This cross-species comparative analysis further led to the identification of PITPNC1 as a candidate regulator of glucose-stimulated insulin secretion. TAGs emerge as biomarkers of a liver-to-β-cell axis that links hepatic β-oxidation to β-cell functional mass and insulin secretion.

Link: doi.org/10.1016/j.molmet.2021.101355

publications
metabolic-disorders, blood, mouse-rat, biomarker
104
Developmental Cell

Cell cycle regulation of ER membrane biogenesis protects against chromosome missegregation

Holly Merta, Jake W Carrasquillo Rodríguez, Maya I Anjur-Dietrich, Tevis Vitale, Mitchell E Granade, Thurl E Harris, Daniel J Needleman, Shirin Bahmanyar

Failure to reorganize the endoplasmic reticulum (ER) in mitosis results in chromosome missegregation. Here, we show that accurate chromosome segregation in human cells requires cell cycle-regulated ER membrane production. Excess ER membranes increase the viscosity of the mitotic cytoplasm to physically restrict chromosome movements, which impedes the correction of mitotic errors leading to the formation of micronuclei. Mechanistically, we demonstrate that the protein phosphatase CTDNEP1 counteracts mTOR kinase to establish a dephosphorylated pool of the phosphatidic acid phosphatase lipin 1 in interphase. CTDNEP1 control of lipin 1 limits the synthesis of fatty acids for ER membrane biogenesis in interphase that then protects against chromosome missegregation in mitosis. Thus, regulation of ER size can dictate the biophysical properties of mitotic cells, providing an explanation for why ER reorganization is necessary for mitotic fidelity. Our data further suggest that dysregulated lipid metabolism is a potential source of aneuploidy in cancer cells.

Link: doi.org/10.1016/j.devcel.2021.11.009

publications
human, cell, oncology, organelles, other-application
105
Article

Cancer, hypoxia & mitochondria lipids

Nuala Del Piccolo, Henri M Deda

Though cancer is a heterogeneous disease, tumor microenvironments across organs share characteristic features. One of these features is hypoxia, or low oxygen tension. Hypoxia is considered a therapeutic target, but the molecular mechanisms underlying the role of hypoxia in cancer development and progression have not been fully described. A CRISPR-Cas9 knockout library in hepatocellular carcinoma cells was used to follow a hypoxia-driven negative selection process revealing that the protein “protein-tyrosine phosphatase mitochondrial 1” (PTPMT1) enables cells to adapt to hypoxic conditions.

Link: lipotype.com/mitochondrial-lipid-metabolism-in-hypoxic-cancer

articles
human, mouse-rat, cell, oncology, tissue-organ, organelles, multiomics
106
BBA MOLECULAR AND CELL BIOLOGY OF LIPIDS

Lipid droplets in skeletal muscle during grass snake (Natrix natrix L.) development

Magda Dubińska-Magiera, Damian Lewandowski, Dominik Cysewski, Seweryn Pawlak, Bartłomiej Najbar, Małgorzata Daczewska

Lipid droplets (LDs) are common organelles observed in Eucaryota. They are multifunctional organelles (involved in lipid storage, metabolism, and trafficking) that originate from endoplasmic reticulum (ER). LDs consist of a neutral lipid core, made up of diacyl- and triacylglycerols (DAGs and TAGs) and cholesterol esters (CEs), surrounded by a phospholipid monolayer and proteins, which are necessary for their structure and dynamics.

Here, we report the protein and lipid composition as well as characterization and dynamics of grass snake (Natrix natrix) skeletal muscle LDs at different developmental stages. In the present study, we used detailed morphometric, LC-MS, quantitative lipidomic analyses of LDs isolated from the skeletal muscles of the snake embryos, immunofluorescence, and TEM.

Our study also provides a valuable insight concerning the LDs’ multifunctionality and ability to interact with a variety of organelles. These LD features are reflected in their proteome composition, which contains scaffold proteins, metabolic enzymes signalling polypeptides, proteins necessary for the formation of docking sites, and many others. We also provide insights into the biogenesis and growth of muscle LDs goes beyond the conventional mechanism based on the synthesis and incorporation of TAGs and LD fusion. We assume that the formation and functioning of grass snake muscle LDs are based on additional mechanisms that have not yet been identified, which could be related to the unique features of reptiles that are manifested in the after-hatching period of life, such as a reptile-specific strategy for energy saving during hibernation.

Link: doi.org/10.1016/j.bbalip.2021.159086

publications
subcellular, other-organism, model-systems, organelles, other-application, multiomics
107
iScience

Depletion of cardiac cardiolipin synthase alters systolic and diastolic function

Elia Smeir, Sarah Leberer, Annelie Blumrich, Georg Vogler, Anastasia Vasiliades, Sandra Dresen, Carsten Jaeger, Yoann Gloaguen, Christian Klose, Dieter Beule, P Christian Schulze, Rolf Bodmer, Anna Foryst-Ludwig, Ulrich Kintscher

Cardiolipin (CL) is a major cardiac mitochondrial phospholipid maintaining regular mitochondrial morphology and function in cardiomyocytes. Cardiac CL production includes its biosynthesis and a CL remodeling process. Here we studied the impact of CL biosynthesis and the enzyme cardiolipin synthase (CLS) on cardiac function. CLS and cardiac CL species were significantly downregulated in cardiomyocytes following catecholamine-induced cardiac damage in mice, accompanied by increased oxygen consumption rates, signs of oxidative stress, and mitochondrial uncoupling. RNAi-mediated cardiomyocyte-specific knockdown of CLS in Drosophila melanogaster resulted in marked cardiac dilatation, severe impairment of systolic performance, and slower diastolic filling velocity assessed by fluorescence-based heart imaging. Finally, we showed that CL72:8 is significantly decreased in cardiac samples from patients with heart failure with reduced ejection fraction (HFrEF). In summary, we identified CLS as a regulator of cardiac function. Considering the cardiac depletion of CL species in HFrEF, pharmacological targeting of CLS may be a promising therapeutic approach.

Link: doi.org/10.1016/j.isci.2021.103314

publications
human, mouse-rat, cell, tissue-organ, cardiovascular-disease, organelles
108
Cell Reports

Regulatory T cell differentiation is controlled by αKG-induced alterations in mitochondrial metabolism and lipid homeostasis

Maria I Matias, Carmen S Yong, Amir Foroushani, Chloe Goldsmith, Cédric Mongellaz, Erdinc Sezgin, Kandice R Levental, Ali Talebi, Julie Perrault, Anais Rivière, Jonas Dehairs, Océane Delos, Justine Bertand-Michel, Jean-Charles Portais, Madeline Wong, Julien C Marie, Ameeta Kelekar, Sandrina Kinet, Valérie S Zimmermann, Ilya Levental, Laurent Yvan-Charvet, Johannes V Swinnen, Stefan A Muljo, Hector Hernandez-Vargas, Saverio Tardito, Naomi Taylor, Valérie Dardalhon

Suppressive regulatory T cell (Treg) differentiation is controlled by diverse immunometabolic signaling pathways and intracellular metabolites. Here we show that cell-permeable α-ketoglutarate (αKG) alters the DNA methylation profile of naive CD4 T cells activated under Treg polarizing conditions, markedly attenuating FoxP3+ Treg differentiation and increasing inflammatory cytokines. Adoptive transfer of these T cells into tumor-bearing mice results in enhanced tumor infiltration, decreased FoxP3 expression, and delayed tumor growth. Mechanistically, αKG leads to an energetic state that is reprogrammed toward a mitochondrial metabolism, with increased oxidative phosphorylation and expression of mitochondrial complex enzymes. Furthermore, carbons from ectopic αKG are directly utilized in the generation of fatty acids, associated with lipidome remodeling and increased triacylglyceride stores. Notably, inhibition of either mitochondrial complex II or DGAT2-mediated triacylglyceride synthesis restores Treg differentiation and decreases the αKG-induced inflammatory phenotype. Thus, we identify a crosstalk between αKG, mitochondrial metabolism and triacylglyceride synthesis that controls Treg fate.

Link: doi.org/10.1016/j.celrep.2021.109911

publications
human, mouse-rat, cell, organelles, other-application
109
Cell Reports

Proteomic and lipidomic profiling of demyelinating lesions identifies fatty acids as modulators in lesion recovery

Horst Penkert, Alix Bertrand, Vini Tiwari, Stephan Breimann, Stephan A Müller, Paul M Jordan, Mathias J Gerl, Christian Klose, Ludovico Cantuti-Castelvetri, Mar Bosch-Queralt, Ilya Levental, Stefan F Lichtenthaler, Oliver Werz, Mikael Simons

After demyelinating injury of the central nervous system, resolution of the mounting acute inflammation is crucial for the initiation of a regenerative response. Here, we aim to identify fatty acids and lipid mediators that govern the balance of inflammatory reactions within demyelinating lesions. Using lipidomics, we identify bioactive lipids in the resolution phase of inflammation with markedly elevated levels of n-3 polyunsaturated fatty acids. Using fat-1 transgenic mice, which convert n-6 fatty acids to n-3 fatty acids, we find that reduction of the n-6/n-3 ratio decreases the phagocytic infiltrate. In addition, we observe accelerated decline of microglia/macrophages and enhanced generation of oligodendrocytes in aged mice when n-3 fatty acids are shuttled to the brain. Thus, n-3 fatty acids enhance lesion recovery and may, therefore, provide the basis for pro-regenerative medicines of demyelinating diseases in the central nervous system.

Link: doi.org/10.1016/j.celrep.2021.109898

publications
data, mouse-rat, neuroscience, tissue-organ, multiomics
110
PNAS

Ceramide accumulation induces mitophagy and impairs β-oxidation in PINK1 deficiency

Marija Dulovic-Mahlow, Frida Mandik, Lisa Frese, Yuliia Kanana, Sokhna H Diaw, Julia Depperschmidt, Claudia Böhm, Jonas Rohr, Thora Lohnau, Inke R König, Christine Klein

Energy production via the mitochondrial electron transport chain (ETC) and mitophagy are two important processes affected in Parkinson’s disease (PD). Interestingly, PINK1, mutations of which cause early-onset PD, plays a key role in both processes, suggesting that these two mechanisms are connected. However, the converging link of both pathways currently remains enigmatic. Recent findings demonstrated that lipid aggregation, along with defective mitochondria, is present in postmortem brains of PD patients. In addition, an increasing body of evidence shows that sphingolipids, including ceramide, are altered in PD, supporting the importance of lipids in the pathophysiology of PD. Here, we identified ceramide to play a crucial role in PINK1-related PD that was previously linked almost exclusively to mitochondrial dysfunction. We found ceramide to accumulate in mitochondria and to negatively affect mitochondrial function, most notably the ETC. Lowering ceramide levels improved mitochondrial phenotypes in pink1-mutant flies and PINK1-deficient patient-derived fibroblasts, showing that the effects of ceramide are evolutionarily conserved. In addition, ceramide accumulation provoked ceramide-induced mitophagy upon PINK1 deficiency. As a result of the ceramide accumulation, β-oxidation in PINK1 mutants was decreased, which was rescued by lowering ceramide levels. Furthermore, stimulation of β-oxidation was sufficient to rescue PINK1-deficient phenotypes. In conclusion, we discovered a cellular mechanism resulting from PD-causing loss of PINK1 and found a protective role of β-oxidation in ETC dysfunction, thus linking lipids and mitochondria in the pathophysiology of PINK1-related PD. Furthermore, our data nominate β-oxidation and ceramide as therapeutic targets for PD.

Link: doi.org/10.1073/pnas.2025347118

publications
insect, subcellular, neuroscience, tissue-organ, organelles
111
The Lipidomics Webinar

Are mouse & lipidomics the perfect match?

Christian Klose

Lipidomics is an indispensable method for the quantitative assessment of lipid metabolism in basic, clinical, and pharmaceutical research. It allows for the generation of information-dense datasets in a large variety of experimental setups and model organisms and is successfully applied in translation research.
Previous research, mostly conducted in mice (Mus musculus), has shown a remarkable specificity of the lipid compositions of different cell types, tissues, and organs. However, a systematic analysis of the overall complexity and variation of the mouse lipidome is lacking. Thus, we have investigated lipid compositions of different mouse organs and tissues and the effects of diet, sex, and genotype on the mouse lipidomes.
We provide insights into the organ-specific lipidomic variation. This analyses serve as a valuable resource for experimental design (for example for sample number estimation) and facilitate interpretation of lipidomic phenotypes in mouse studies, including time-dose or mode-of-action studies in pharmaceutical research.

Link: lipotype.com/mouse-lipidomics-for-clinical-research

webinars
model-systems
112
International Journal of Molecular Sciences

Histone Deacetylase Inhibition Regulates Lipid Homeostasis in a Mouse Model of Amyotrophic Lateral Sclerosis

Thibaut Burg, Elisabeth Rossaert, Matthieu Moisse, Philip Van Damme, Ludo Van Den Bosch

Amyotrophic lateral sclerosis (ALS) is an incurable and fatal neurodegenerative disorder of the motor system. While the etiology is still incompletely understood, defects in metabolism act as a major contributor to the disease progression. Recently, histone deacetylase (HDAC) inhibition using ACY-738 has been shown to restore metabolic alterations in the spinal cord of a FUS mouse model of ALS, which was accompanied by a beneficial effect on the motor phenotype and survival. In this study, we investigated the specific effects of HDAC inhibition on lipid metabolism using untargeted lipidomic analysis combined with transcriptomic analysis in the spinal cord of FUS mice. We discovered that symptomatic FUS mice recapitulate lipid alterations found in ALS patients and in the SOD1 mouse model. Glycerophospholipids, sphingolipids, and cholesterol esters were most affected. Strikingly, HDAC inhibition mitigated lipid homeostasis defects by selectively targeting glycerophospholipid metabolism and reducing cholesteryl esters accumulation. Therefore, our data suggest that HDAC inhibition is a potential new therapeutic strategy to modulate lipid metabolism defects in ALS and potentially other neurodegenerative diseases.

Link: doi.org/10.3390/ijms222011224

publications
mouse-rat, neuroscience, tissue-organ, pharma
113
ARTICLE

Multiomics profiling of Alzheimer’s disease

Nuala Del Piccolo, Henri M Deda

The human nervous system generates motion, regulates bodily functions, and transmits information about environmental conditions. These functions are essential to life; hence the nervous system has several layers of protection. Despite its natural defenses, the nervous system is susceptible to multiple degenerative diseases. Alzheimer’s disease involves progressive neurodegeneration – or, damage to neurons and loss of communication between neurons. Multiomics technologies identify and quantity molecules in tissue samples. Through comparison of multiomics analyses across samples, molecular signaling pathways involved in physiological and pathological processes that explain variance and predict disease progression were identified.

Link: lipotype.com/multiomics-analysis-and-alzheimers-disease

articles
other-sample-type, human, neuroscience, biomarker, multiomics
114
MDPI Cells

Mitochondrial Phospholipid Homeostasis Is Regulated by the i-AAA Protease PaIAP and Affects Organismic Aging

Timo Löser, Aljoscha Joppe, Andrea Hamann, Heinz D Osiewacz

Mitochondria are ubiquitous organelles of eukaryotic organisms with a number of essential functions, including synthesis of iron-sulfur clusters, amino acids, lipids, and adenosine triphosphate (ATP). During aging of the fungal aging model Podospora anserina, the inner mitochondrial membrane (IMM) undergoes prominent morphological alterations, ultimately resulting in functional impairments. Since phospholipids (PLs) are key components of biological membranes, maintenance of membrane plasticity and integrity via regulation of PL biosynthesis is indispensable. Here, we report results from a lipidomic analysis of isolated mitochondria from P. anserina that revealed an age-related reorganization of the mitochondrial PL profile and the involvement of the i-AAA protease PaIAP in proteolytic regulation of PL metabolism. The absence of PaIAP enhances biosynthesis of characteristic mitochondrial PLs, leads to significant alterations in the acyl composition of the mitochondrial signature PL cardiolipin (CL), and induces mitophagy. These alterations presumably cause the lifespan increase of the PaIap deletion mutant under standard growth conditions. However, PaIAP is required at elevated temperatures and for degradation of superfluous CL synthase PaCRD1 during glycolytic growth. Overall, our study uncovers a prominent role of PaIAP in the regulation of PL homeostasis in order to adapt membrane plasticity to fluctuating environmental conditions as they occur in nature.

Link: doi.org/10.3390/cells10102775

publications
subcellular, other-organism, organelles, microbiology, other-application
115
Journal of Obesity

Proteomic and Metabolomic Characterization of Metabolically Healthy Obesity: A Descriptive Study from a Swedish Cohort

Johan Korduner, Peter M Nilsson, Olle Melander, Mathias J Gerl, Gunnar Engström, Erasmus Bachus, Martin Magnusson, Filip Ottosson

Obesity is a well-established risk factor for the development of numerous chronic diseases. However, there is a small proportion of obese individuals that seem to escape these aforementioned conditions—Metabolically Healthy Obesity (MHO). Our aim was to do a metabolic and biomarker profiling of MHO individuals. Associations between different biomarkers (proteomics, lipidomics, and metabolomics) coupled to either MHO or metabolically unhealthy obese (MUO) individuals were analyzed through principal component analysis (PCA). Subjects were identified from a subsample of 416 obese individuals, selected from the Malmö Diet and Cancer study—Cardiovascular arm (MDCS-CV, n = 3,443). They were further divided into MHO (n = 143) and MUO (n = 273) defined by a history of hospitalization, or not, at baseline inclusion, and nonobese subjects (NOC, n = 3,027). Two distinctive principle components (PL2, PP5) were discovered with a significant difference and thus further investigated through their main loadings. MHO individuals had a more metabolically favorable lipid and glucose profile than MUO subjects, that is, lower levels of traditional blood glucose and triglycerides, as well as a trend of lower metabolically unfavorable lipid biomarkers. PL2 (lipidomics, p = 0.02) showed stronger associations of triacylglycerides with MUO, whereas phospholipids correlated with MHO. PP5 (proteomics, p = 0.01) included interleukin-1 receptor antagonist (IL-1ra) and leptin with positive relations to MUO and galanin that correlated positively to MHO. The group differences in metabolite profiles were to a large extent explained by factors included in the metabolic syndrome. Compared to MUO individuals, corresponding MHO individuals present with a more favorable lipid metabolic profile, accompanied by a downregulation of potentially harmful proteomic biomarkers. This unique and extensive biomarker profiling presents novel data on potentially differentiating traits between these two obese phenotypes.

Link: doi.org/10.1155/2021/6616983

publications
data, human, blood, metabolic-disorders, clinical-research, biomarker, multiomics
116
Journal of Experimental Medicine

TREM2-dependent lipid droplet biogenesis in phagocytes is required for remyelination

Garyfallia Gouna, Christian Klose, Mar Bosch-Queralt, Lu Liu, Ozgun Gokce, Martina Schifferer, Ludovico Cantuti-Castelvetri, Mikael Simons

Upon demyelinating injury, microglia orchestrate a regenerative response that promotes myelin repair, thereby restoring rapid signal propagation and protecting axons from further damage. Whereas the essential phagocytic function of microglia for remyelination is well known, the underlying metabolic pathways required for myelin debris clearance are poorly understood. Here, we show that cholesterol esterification in male mouse microglia/macrophages is a necessary adaptive response to myelin debris uptake and required for the generation of lipid droplets upon demyelinating injury. When lipid droplet biogenesis is defective, innate immune cells do not resolve, and the regenerative response fails. We found that triggering receptor expressed on myeloid cells 2 (TREM2)–deficient mice are unable to adapt to excess cholesterol exposure, form fewer lipid droplets, and build up endoplasmic reticulum (ER) stress. Alleviating ER stress in TREM2-deficient mice restores lipid droplet biogenesis and resolves the innate immune response. Thus, we conclude that TREM2-dependent formation of lipid droplets constitute a protective response required for remyelination to occur.

Link: doi.org/10.1084/jem.20210227

publications
mouse-rat, cell, neuroscience, organelles
117
MDPI Molecular Sciences

Lipidomic and Proteomic Alterations Induced by Even and Odd Medium-Chain Fatty Acids on Fibroblasts of Long-Chain Fatty Acid Oxidation Disorders

Khaled I Alatibi, Stefan Tholen, Zeinab Wehbe, Judith Hagenbuchner, Daniela Karall, Michael J Ausserlechner, Oliver Schilling, Sarah C Grünert, Jerry Vockley, Sara Tucci

Medium-chain fatty acids (mc-FAs) are currently applied in the treatment of long-chain fatty acid oxidation disorders (lc-FAOD) characterized by impaired β-oxidation. Here, we performed lipidomic and proteomic analysis in fibroblasts from patients with very long-chain acyl-CoA dehydrogenase (VLCADD) and long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHADD) deficiencies after incubation with heptanoate (C7) and octanoate (C8). Defects of β-oxidation induced striking proteomic alterations, whereas the effect of treatment with mc-FAs was minor. However, mc-FAs induced a remodeling of complex lipids. Especially C7 appeared to act protectively by restoring sphingolipid biosynthesis flux and improving the observed dysregulation of protein homeostasis in LCHADD under control conditions.

Link: doi.org/10.3390/ijms221910556

publications
human, cell, diet, other-application, multiomics
118
Scientific Reports

Mouse lipidomics reveals inherent flexibility of a mammalian lipidome

Michal A Surma, Mathias J Gerl, Ronny Herzog, Jussi Helppi, Kai Simons, Christian Klose

Lipidomics has become an indispensable method for the quantitative assessment of lipid metabolism in basic, clinical, and pharmaceutical research. It allows for the generation of information-dense datasets in a large variety of experimental setups and model organisms. Previous studies, mostly conducted in mice (Mus musculus), have shown a remarkable specificity of the lipid compositions of different cell types, tissues, and organs. However, a systematic analysis of the overall variation of the mouse lipidome is lacking. To fill this gap, in the present study, the effect of diet, sex, and genotype on the lipidomes of mouse tissues, organs, and bodily fluids has been investigated. Baseline quantitative lipidomes consisting of 796 individual lipid molecules belonging to 24 lipid classes are provided for 10 different sample types. Furthermore, the susceptibility of lipidomes to the tested parameters is assessed, providing insights into the organ-specific lipidomic plasticity and flexibility. This dataset provides a valuable resource for basic and pharmaceutical researchers working with murine models and complements existing proteomic and transcriptomic datasets. It will inform experimental design and facilitate interpretation of lipidomic datasets.

Link: doi.org/10.1038/s41598-021-98702-5

publications
data, blood, mouse-rat, diet, tissue-organ, pharma, model-systems, clinical-research, biomarker, other-application
119
Article

Clinical indicators of metabolic obesity

Nuala Del Piccolo, Henri M Deda

Obesity is linked to a number of health problems – including cardiovascular disease and type II diabetes – and afflicts over 650 million adults worldwide (~13% of the population). The incidence of obesity is rising so rapidly that many scientists and healthcare workers consider obesity to be a pandemic. To diagnose obesity, clinicians and researchers estimate body fat using a series of indicators. Unfortunately, these standard indicators struggle to accurately classify individuals by obesity status. They do not account for known heterogeneity in body fat with age, sex, and ethnicity. Recent research suggests that molecular measures of metabolism – for example, of cholesterol or metabolomics in the plasma – may classify obesity status more accurately than standard indicators. Additionally, lipid profiles in the body may detect, predict, and/or stratify patients with other diseases. In this study, shotgun mass spectrometry was used to characterize the plasma lipidome of 1,061 samples from the 2012 National FINRISK Study. Next, these data were used to train a series of machine learning models to estimate indicators of obesity. Then, the best-fit machine learning model was validated on a second plasma lipidome dataset, which was composed of 250 samples from the 2014 Malmö Diet and Cancer Cardiovascular Cohort. The study results show that the plasma lipidome can reveal features of obesity inaccessible by existing indicators and the model may improve the identification of patients in need for weight reducing therapy who do not qualify by BMI.

Link: lipotype.com/clinical-indicators-of-metabolic-obesity

articles
human, metabolic-disorders, blood, clinical-research, biomarker
120
The Lipidomics Webinar

Lipids are cool again!

Kai Simons

Before the DNA revolution the lipids were center stage in cell membrane research and also important players in metabolic research. But then they slowly disappeared into the background, being relegated to a boring matrix for proteins in membranes. This is now changing.
Lipids are coming back on all fronts. They regulate the functions of cell membranes essential for life. The lipid composition in cells is tightly regulated to allow cell metabolism to function as a coordinated whole. This homeostasis is today under threat because our lifestyle is out of sync, causing an obesity pandemic with deadly consequences.
We developed a mass spectrometry-based platform with unprecedented precision and have used this technology to analyze and establish multi-parametric lipid signatures that measure health and disease. Our data suggest that the blood lipidome reflects the metabolic status of the body. These lipidomic profiles could provide a navigation tool to stem the obesity affliction.

Link: lipotype.com/introduction-to-lipids-and-lipidomics

webinars
metabolic-disorders, organelles, other-application
121
The EMBO Journal

Shortening of membrane lipid acyl chains compensates for phosphatidylcholine deficiency in choline-auxotroph yeast

Xue Bao, Martijn C Koorengevel, Marian J A Groot Koerkamp, Amir Homavar, Amrah Weijn, Stefan Crielaard, Mike F Renne, Joseph H Lorent, Willie J C Geerts, Michal A Surma, Muriel Mari, Frank C P Holstege, Christian Klose, Anton I P M de Kroon

Phosphatidylcholine (PC) is an abundant membrane lipid component in most eukaryotes, including yeast, and has been assigned multiple functions in addition to acting as building block of the lipid bilayer. Here, by isolating S. cerevisiae suppressor mutants that exhibit robust growth in the absence of PC, we show that PC essentiality is subject to cellular evolvability in yeast. The requirement for PC is suppressed by monosomy of chromosome XV or by a point mutation in the ACC1 gene encoding acetyl-CoA carboxylase. Although these two genetic adaptations rewire lipid biosynthesis in different ways, both decrease Acc1 activity, thereby reducing average acyl chain length. Consistently, soraphen A, a specific inhibitor of Acc1, rescues a yeast mutant with deficient PC synthesis. In the aneuploid suppressor, feedback inhibition of Acc1 through acyl-CoA produced by fatty acid synthase (FAS) results from upregulation of lipid synthesis. The results show that budding yeast regulates acyl chain length by fine-tuning the activities of Acc1 and FAS and indicate that PC evolved by benefitting the maintenance of membrane fluidity.

Link: doi.org/10.15252/embj.2021107966

publications
cell, yeast, model-systems, organelles, microbiology
122
Metabolites

Cross-Platform Evaluation of Commercially Targeted and Untargeted Metabolomics Approaches to Optimize the Investigation of Psychiatric Disease

Lauren E Chaby, Heather C Lasseter, Kévin Contrepois, Reza M Salek, Christoph W Turck, Andrew Thompson, Timothy Vaughan, Magali Haas, Andreas Jeromin

Metabolomics methods often encounter trade-offs between quantification accuracy and coverage, with truly comprehensive coverage only attainable through a multitude of complementary assays. Due to the lack of standardization and the variety of metabolomics assays, it is difficult to integrate datasets across studies or assays. To inform metabolomics platform selection, with a focus on posttraumatic stress disorder (PTSD), we review platform use and sample sizes in psychiatric metabolomics studies and then evaluate five prominent metabolomics platforms for coverage and performance, including intra-/inter-assay precision, accuracy, and linearity. We found performance was variable between metabolite classes, but comparable across targeted and untargeted approaches. Within all platforms, precision and accuracy were highly variable across classes, ranging from 0.9–63.2% (coefficient of variation) and 0.6–99.1% for accuracy to reference plasma. Several classes had high inter-assay variance, potentially impeding dissociation of a biological signal, including glycerophospholipids, organooxygen compounds, and fatty acids. Coverage was platform-specific and ranged from 16–70% of PTSD-associated metabolites. Non-overlapping coverage is challenging; however, benefits of applying multiple metabolomics technologies must be weighed against cost, biospecimen availability, platform-specific normative levels, and challenges in merging datasets. Our findings and open-access cross-platform dataset can inform platform selection and dataset integration based on platform-specific coverage breadth/overlap and metabolite-specific performance.

Link: doi.org/10.3390/metabo11090609

publications
human, blood, neuroscience, clinical-research, biomarker, other-application, multiomics
123
Article

Variability of skin lipidomics profiles

Nuala Del Piccolo, Henri M Deda

Human skin is a dynamic organ that functions as a protective barrier between an individual and their environment. The uppermost layer of the skin, the stratum corneum, is composed of sheets of keratinocytes embedded in a lipid-rich extracellular matrix. The skin lipid profile is known to vary with factors like age, sex, season of the year, and certain skin conditions. These relationships have not been comprehensively characterized, but may affect skin barrier function. To address this gap, the lipid profile in skin samples from 104 individuals was characterized using mass spectrometry-based lipidomics. The results reveal how the skin lipidome varies with skin depth, within individuals, and between individuals.

Link: lipotype.com/skin-lipid-profile-analysis-and-variability

articles
human, dermatology, skin, clinical-research, other-application
124
MDPI Microorganisms

The Role of Sch9 and the V-ATPase in the Adaptation Response to Acetic Acid and the Consequences for Growth and Chronological Lifespan

Marie-Anne Deprez, Jeroen M Maertens, Lisbeth Olsson, Maurizio Bettiga, Joris Winderickx

Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9Δ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan.

Link: doi.org/10.3390/microorganisms9091871

publications
cell, yeast, model-systems, other-application
125
Scientific Reports

Molecular-dynamics-simulation-guided membrane engineering allows the increase of membrane fatty acid chain length in Saccharomyces cerevisiae

Jeroen M Maertens, Simone Scrima, Matteo Lambrughi, Samuel Genheden, Cecilia Trivellin, Leif A Eriksson, Elena Papaleo, Lisbeth Olsson, Maurizio Bettiga

The use of lignocellulosic-based fermentation media will be a necessary part of the transition to a circular bio-economy. These media contain many inhibitors to microbial growth, including acetic acid. Under industrially relevant conditions, acetic acid enters the cell predominantly through passive diffusion across the plasma membrane. The lipid composition of the membrane determines the rate of uptake of acetic acid, and thicker, more rigid membranes impede passive diffusion. We hypothesized that the elongation of glycerophospholipid fatty acids would lead to thicker and more rigid membranes, reducing the influx of acetic acid. Molecular dynamics simulations were used to predict the changes in membrane properties. Heterologous expression of Arabidopsis thaliana genes fatty acid elongase 1 (FAE1) and glycerol-3-phosphate acyltransferase 5 (GPAT5) increased the average fatty acid chain length. However, this did not lead to a reduction in the net uptake rate of acetic acid. Despite successful strain engineering, the net uptake rate of acetic acid did not decrease. We suggest that changes in the relative abundance of certain membrane lipid headgroups could mitigate the effect of longer fatty acid chains, resulting in a higher net uptake rate of acetic acid.

Link: doi.org/10.1038/s41598-021-96757-y

publications
cell, yeast, organelles, microbiology, other-application
126
Environmental Epimediology

Assessing the impact of exposome on the course of chronic obstructive pulmonary disease and cystic fibrosis

Manon Benjdir, Étienne Audureau, Ariel Beresniak, Patrice Coll, Ralph Epaud, Kristina Fiedler, Bénédicte Jacquemin, Laurent Niddam, Spyros N Pandis, Gerhard Pohlmann, Torkjel M Sandanger, Kai Simons, Mette Sørensen, Patrick Wagner, Sophie Lanone

Because of the direct interaction of lungs with the environment, respiratory diseases are among the leading causes of environment-related deaths in the world. Chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF) are two highly debilitating diseases that are of particular interest in the context of environmental studies; they both are characterized by a similar progressive loss of lung function with small bronchi alterations, and a high phenotypic variability of unknown origin, which prevents a good therapeutic efficacy. In the last years, there has been an evolution in the apprehension of the study of diseases going from a restricted “one exposure, one disease” approach to a broader concept with other associating factors, the exposome. The overall objective of the REMEDIA project is to extend the understanding of the contribution of the exposome to COPD and CF diseases. To achieve our aim, we will (1) exploit data from existing cohorts and population registries to create a unified global database gathering phenotype and exposome information; (2) develop a flexible individual sensor device combining environmental and biomarker toolkits; (3) use a versatile atmospheric simulation chamber to simulate the health effects of complex exposomes; (4) use machine learning supervised analyses and causal inference models to identify relevant risk factors; and (5) develop econometric and cost-effectiveness models to assess the costs, performance, and cost-effectiveness of a selection of prevention strategies. The results will be used to develop guidelines to better predict disease risks and constitute the elements of the REMEDIA toolbox. The multidisciplinary approach carried out by the REMEDIA European project should represent a major breakthrough in reducing the morbidity and mortality associated with COPD and CF diseases.

Link: doi.org/10.1097/EE9.0000000000000165

publications
human, clinical-research, biomarker, other-application, multiomics
127
The EMBO Journal

Torsin and NEP1R1-CTDNEP1 phosphatase affect interphase nuclear pore complex insertion by lipid-dependent and lipid-independent mechanisms

Julie Jacquemyn, Joyce Foroozandeh, Katlijn Vints, Jef Swerts, Patrik Verstreken, Natalia V Gounko, Sandra F Gallego, Rose E Goodchild

The interphase nuclear envelope (NE) is extensively remodeled during nuclear pore complex (NPC) insertion. How this remodeling occurs and why it requires Torsin ATPases, which also regulate lipid metabolism, remains poorly understood. Here, we show that Drosophila Torsin (dTorsin) affects lipid metabolism via the NEP1R1-CTDNEP1 phosphatase and the Lipin phosphatidic acid (PA) phosphatase. This includes that Torsins remove NEP1R1-CTDNEP1 from the NE in fly and mouse cells, leading to subsequent Lipin exclusion from the nucleus. NEP1R1-CTDNEP1 downregulation also restores nuclear pore membrane fusion in post-mitotic dTorsinKO fat body cells. However, dTorsin-associated nuclear pore defects do not correlate with lipidomic abnormalities and are not resolved by silencing of Lipin. Further testing confirmed that membrane fusion continues in cells with hyperactivated Lipin. It also led to the surprising finding that excessive PA metabolism inhibits recruitment of the inner ring complex Nup35 subunit, resulting in elongated channel-like structures in place of mature nuclear pores. We conclude that the NEP1R1-CTDNEP1 phosphatase affects interphase NPC biogenesis by lipid-dependent and lipid-independent mechanisms, explaining some of the pleiotropic effects of Torsins.

Link: doi.org/10.15252/embj.2020106914

publications
insect, tissue-organ, organelles, other-application
128
Article

Cardiac lipid metabolism in heart failure

Nuala Del Piccolo, Henri M Deda

Heart failure occurs when the organ progressively loses its capacity to pump blood to the rest of the body. The condition is typically caused by damage to cardiac tissue through myocardial infarction, coronary artery disease, or genetics. Heart failure is accompanied by an increase in lipid metabolism in adipose tissue, cardiac tissue, and other organs. As a result, the lipidome – which is hypothesized to modulate heart function – is altered. Moreover, a growing body of evidence suggests a key role for cross-tissue/organ communication in physiology and pathology. Hence, lipidomic analyses during heart failure may elucidate the mechanisms of disease, identify novel therapeutic targets, and represent a non-invasive diagnostic tool. Here, lipid metabolism during left-sided systolic heart failure was investigated in mice and humans. The results suggest that lipid metabolism in adipose tissue may regulate cardiac tissue function.

Link: lipotype.com/cardiac-lipid-metabolism-after-heart-failure

articles
human, blood, mouse-rat, tissue-organ, cardiovascular-disease, model-systems, biomarker
129
EBioMedicine

Shotgun mass spectrometry-based lipid profiling identifies and distinguishes between chronic inflammatory diseases

Rune Matthiesen, Chris Lauber, Júlio L Sampaio, Neuza Domingues, Liliana Alves, Mathias J Gerl, Manuel S Almeida, Gustavo Rodrigues, Pedro Araújo-Gonçalves, Jorge Ferreira, Claudia Borbinha, João Pedro Marto, Marisa Neves, Frederico Batista, Miguel Viana-Baptista, Jose Alves, Kai Simons, Winchil L C Vaz, Otilia V Vieira

Localized stress and cell death in chronic inflammatory diseases may release tissue-specific lipids into the circulation causing the blood plasma lipidome to reflect the type of inflammation. However, deep lipid profiles of major chronic inflammatory diseases have not been compared.
Plasma lipidomes of patients suffering from two etiologically distinct chronic inflammatory diseases, atherosclerosis-related vascular disease, including cardiovascular (CVD) and ischemic stroke (IS), and systemic lupus erythematosus (SLE), were screened by a top-down shotgun mass spectrometry-based analysis without liquid chromatographic separation and compared to each other and to age-matched controls. Lipid profiling of 596 lipids was performed on a cohort of 427 individuals. Machine learning classifiers based on the plasma lipidomes were used to distinguish the two chronic inflammatory diseases from each other and from the controls.
Analysis of the lipidomes enabled separation of the studied chronic inflammatory diseases from controls based on independent validation test set classification performance (CVD vs control – Sensitivity: 0.94, Specificity: 0.88; IS vs control – Sensitivity: 1.0, Specificity: 1.0; SLE vs control – Sensitivity: 1, Specificity: 0.93) and from each other (SLE vs CVD ‒ Sensitivity: 0.91, Specificity: 1; IS vs SLE – Sensitivity: 1, Specificity: 0.82). Preliminary linear discriminant analysis plots using all data clearly separated the clinical groups from each other and from the controls, and partially separated CVD severities, as classified into five clinical groups. Dysregulated lipids are partially but not fully counterbalanced by statin treatment.
Dysregulation of the plasma lipidome is characteristic of chronic inflammatory diseases. Lipid profiling accurately identifies the diseases and in the case of CVD also identifies sub-classes.

Link: doi.org/10.1016/j.ebiom.2021.103504

publications
data, human, blood, cardiovascular-disease, clinical-research, biomarker, other-application
130
PLOS Genetics

Increased mitochondrial protein import and cardiolipin remodelling upon early mtUPR

Daniel Poveda-Huertes, Asli A Taskin, Ines Dhaouadi, Lisa Myketin, Adinarayana Marada, Lukas Habernig, Sabrina Büttner, F-Nora Vögtle

Mitochondrial defects can cause a variety of human diseases and protective mechanisms exist to maintain mitochondrial functionality. Imbalances in mitochondrial proteostasis trigger a transcriptional program, termed mitochondrial unfolded protein response (mtUPR). However, the temporal sequence of events in mtUPR is unclear and the consequences on mitochondrial protein import are controversial. Here, we have quantitatively analyzed all main import pathways into mitochondria after different time spans of mtUPR induction. Kinetic analyses reveal that protein import into all mitochondrial subcompartments strongly increases early upon mtUPR and that this is accompanied by rapid remodelling of the mitochondrial signature lipid cardiolipin. Genetic inactivation of cardiolipin synthesis precluded stimulation of protein import and compromised cellular fitness. At late stages of mtUPR upon sustained stress, mitochondrial protein import efficiency declined. Our work clarifies the enigma of protein import upon mtUPR and identifies sequential mtUPR stages, in which an early increase in protein biogenesis to restore mitochondrial proteostasis is followed by late stages characterized by a decrease in import capacity upon prolonged stress induction.

Link: doi.org/10.1371/journal.pgen.1009664

publications
subcellular, yeast, organelles, microbiology, other-application
131
Nature Metabolism

Multi-omics profiling of living human pancreatic islet donors reveals heterogeneous beta cell trajectories towards type 2 diabetes

Leonore Wigger, Marko Barovic, Andreas-David Brunner, Flavia Marzetta, Eyke Schöniger, Florence Mehl, Nicole Kipke, Daniela Friedland, Frederic Burdet, Camille Kessler, Mathias Lesche, Bernard Thorens, Ezio Bonifacio, Cristina Legido-Quigley, Pierre Barbier Saint Hilaire, Philippe Delerive, Andreas Dahl, Christian Klose, Mathias J Gerl, Kai Simons, Daniela Aust, Jürgen Weitz, Marius Distler, Anke M Schulte, Matthias Mann, Mark Ibberson, Michele Solimena

Most research on human pancreatic islets is conducted on samples obtained from normoglycaemic or diseased brain-dead donors and thus cannot accurately describe the molecular changes of pancreatic islet beta cells as they progress towards a state of deficient insulin secretion in type 2 diabetes (T2D). Here, we conduct a comprehensive multi-omics analysis of pancreatic islets obtained from metabolically profiled pancreatectomized living human donors stratified along the glycemic continuum, from normoglycemia to T2D. We find that islet pools isolated from surgical samples by laser-capture microdissection display remarkably more heterogeneous transcriptomic and proteomic profiles in patients with diabetes than in non-diabetic controls. The differential regulation of islet gene expression is already observed in prediabetic individuals with impaired glucose tolerance. Our findings demonstrate a progressive, but disharmonic, remodelling of mature beta cells, challenging current hypotheses of linear trajectories toward precursor or transdifferentiation stages in T2D. Furthermore, through integration of islet transcriptomics with preoperative blood plasma lipidomics, we define the relative importance of gene coexpression modules and lipids that are positively or negatively associated with HbA1c levels, pointing to potential prognostic markers.

Link: doi.org/10.1038/s42255-021-00420-9

publications
data, human, blood, metabolic-disorders, clinical-research, biomarker, multiomics
132
Article

Multiomics analysis in type 1 diabetes research

Nuala Del Piccolo, Henri M Deda

Insulin, a hormone produced by beta cells in the pancreas, regulates sugar levels in the bloodstream and metabolic processes in the liver. Insulin deficiency occurs when beta cells stop producing insulin; this is the primary cause of type I diabetes. Insulin deficiency inhibits glucose and lipid storage and metabolism throughout the body, which can lead to fatigue, blindness, and even death. And insulin plays a key role in regulating metabolism of glucose, glycogen, and fatty acids in the liver. However, the impact of chronic insulin deficiency on liver function is incompletely characterized. To address this gap, the research team analyzed diabetic and wild-type liver tissue from their biobank using multiomics: namely, transcriptomics, proteomics, metabolomics, and lipidomics.

Link: lipotype.com/multiomics-in-type-1-diabetes-research

articles
metabolic-disorders, tissue-organ, other-organism, clinical-research, multiomics
133
Diabetologia

Replication and cross-validation of type 2 diabetes subtypes based on clinical variables: an IMI-RHAPSODY study

Roderick C Slieker, Louise A Donnelly, Hugo Fitipaldi, Gerard A Bouland, Giuseppe N Giordano, Mikael Åkerlund, Mathias J Gerl, Emma Ahlqvist, Ashfaq Ali, Iulian Dragan, Andreas Festa, Michael K Hansen, Dina Mansour Aly, Min Kim, Dmitry Kuznetsov, Florence Mehl, Christian Klose, Kai Simons, Imre Pavo, Timothy J Pullen, Tommi Suvitaival, Asger Wretlind, Peter Rossing, Valeriya Lyssenko, Cristina Legido-Quigley, Leif Groop, Bernard Thorens, Paul W Franks, Mark Ibberson, Guy A Rutter, Joline W J Beulens, Leen M ‘t Hart, Ewan R Pearson

Five clusters based on clinical characteristics have been suggested as diabetes subtypes: one autoimmune and four subtypes of type 2 diabetes. In the current study we replicate and cross-validate these type 2 diabetes clusters in three large cohorts using variables readily measured in the clinic.
In three independent cohorts, in total 15,940 individuals were clustered based on age, BMI, HbA1c, random or fasting C-peptide, and HDL-cholesterol. Clusters were cross-validated against the original clusters based on HOMA measures. In addition, between cohorts, clusters were cross-validated by re-assigning people based on each cohort’s cluster centres. Finally, we compared the time to insulin requirement for each cluster.
Five distinct type 2 diabetes clusters were identified and mapped back to the original four All New Diabetics in Scania (ANDIS) clusters. Using C-peptide and HDL-cholesterol instead of HOMA2-B and HOMA2-IR, three of the clusters mapped with high sensitivity (80.6–90.7%) to the previously identified severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD) and mild obesity-related diabetes (MOD) clusters. The previously described ANDIS mild age-related diabetes (MARD) cluster could be mapped to the two milder groups in our study: one characterised by high HDL-cholesterol (mild diabetes with high HDL-cholesterol [MDH] cluster), and the other not having any extreme characteristic (mild diabetes [MD]). When these two milder groups were combined, they mapped well to the previously labelled MARD cluster (sensitivity 79.1%). In the cross-validation between cohorts, particularly the SIDD and MDH clusters cross-validated well, with sensitivities ranging from 73.3% to 97.1%. SIRD and MD showed a lower sensitivity, ranging from 36.1% to 92.3%, where individuals shifted from SIRD to MD and vice versa. People belonging to the SIDD cluster showed the fastest progression towards insulin requirement, while the MDH cluster showed the slowest progression.
Clusters based on C-peptide instead of HOMA2 measures resemble those based on HOMA2 measures, especially for SIDD, SIRD and MOD. By adding HDL-cholesterol, the MARD cluster based upon HOMA2 measures resulted in the current clustering into two clusters, with one cluster having high HDL levels. Cross-validation between cohorts showed generally a good resemblance between cohorts. Together, our results show that the clustering based on clinical variables readily measured in the clinic (age, HbA1c, HDL-cholesterol, BMI and C-peptide) results in informative clusters that are representative of the original ANDIS clusters and stable across cohorts. Adding HDL-cholesterol to the clustering resulted in the identification of a cluster with very slow glycaemic deterioration.

Link: doi.org/10.1007/s00125-021-05490-8

publications
data, human, metabolic-disorders, blood, clinical-research, biomarker
134
Article

Exosome characterization for targeted drug delivery

Nuala Del Piccolo, Henri M Deda

Exosomes – or, nanometer-sized particles derived from the lipid membranes of cells – play an integral role in communication between cells and organs in the human body. These particles consist of a lipid shell surrounding cargo, which is delivered to specific sites in the body and alters the function of the recipient cell. Exosome-mediated communication has been implicated in the immune response, cancer, and neurodegeneration. Recently, exosomes have attracted the attention of scientists studying targeted drug delivery. These scientists hope to adapt exosomes to deliver therapies, instead of their natural cargo, to specific cells. For example, these reengineered exosomes might deliver a vaccine to stimulate the immune system or a chemotherapy drug to a breast cancer cell but not the surrounding healthy tissue. However, attempts to reengineer exosomes for targeted drug delivery have met with limited success to date.

Link: lipotype.com/exosomes-lipidomics-for-drug-delivery

articles
exosome, other-organism, pharma, organelles, other-application
135
PNAS

LXR directly regulates glycosphingolipid synthesis and affects human CD4+ T cell function

Kirsty E Waddington, George A Robinson, Beatriz Rubio-Cuesta, Eden Chrifi-Alaoui, Sara Andreone, Kok-Siong Poon, Iveta Ivanova, Lucia Martin-Gutierrez, Dylan M Owen, Elizabeth C Jury, Inés Pineda-Torra

The liver X receptor (LXR) is a key transcriptional regulator of cholesterol, fatty acid, and phospholipid metabolism. Dynamic remodeling of immunometabolic pathways, including lipid metabolism, is a crucial step in T cell activation. Here, we explored the role of LXR-regulated metabolic processes in primary human CD4+ T cells and their role in controlling plasma membrane lipids (glycosphingolipids and cholesterol), which strongly influence T cell immune signaling and function. Crucially, we identified the glycosphingolipid biosynthesis enzyme glucosylceramide synthase as a direct transcriptional LXR target. LXR activation by agonist GW3965 or endogenous oxysterol ligands significantly altered the glycosphingolipid:cholesterol balance in the plasma membrane by increasing glycosphingolipid levels and reducing cholesterol. Consequently, LXR activation lowered plasma membrane lipid order (stability), and an LXR antagonist could block this effect. LXR stimulation also reduced lipid order at the immune synapse and accelerated activation of proximal T cell signaling molecules. Ultimately, LXR activation dampened proinflammatory T cell function. Finally, compared with responder T cells, regulatory T cells had a distinct pattern of LXR target gene expression corresponding to reduced lipid order. This suggests LXR-driven lipid metabolism could contribute to functional specialization of these T cell subsets. Overall, we report a mode of action for LXR in T cells involving the regulation of glycosphingolipid and cholesterol metabolism and demonstrate its relevance in modulating T cell function.

Link: doi.org/10.1073/pnas.2017394118

publications
human, cell, organelles, other-application
136
MDPI Cells

Different Lipid Signature in Fibroblasts of Long-Chain Fatty Acid Oxidation Disorders

Khaled I Alatibi, Judith Hagenbuchner, Zeinab Wehbe, Daniela Karall, Michael J Ausserlechner, Jerry Vockley, Ute Spiekerkoetter, Sarah C Grünert, Sara Tucci

Long-chain fatty acid oxidation disorders (lc-FAOD) are a group of diseases affecting the degradation of long-chain fatty acids. In order to investigate the disease specific alterations of the cellular lipidome, we performed undirected lipidomics in fibroblasts from patients with carnitine palmitoyltransferase II, very long-chain acyl-CoA dehydrogenase, and long-chain 3-hydroxyacyl-CoA dehydrogenase. We demonstrate a deep remodeling of mitochondrial cardiolipins. The aberrant phosphatidylcholine/phosphatidylethanolamine ratio and the increased content of plasmalogens and of lysophospholipids support the theory of an inflammatory phenotype in lc-FAOD. Moreover, we describe increased ratios of sphingomyelin/ceramide and sphingomyelin/hexosylceramide in LCHAD deficiency which may contribute to the neuropathic phenotype of LCHADD/mitochondrial trifunctional protein deficiency.

Link: doi.org/10.3390/cells10051239

publications
human, cell, clinical-research, other-application
137
THE EMBO JOURNAL

Cellular stress promotes NOD1/2-dependent inflammation via the endogenous metabolite sphingosine-1-phosphate

Gang Pei, Joanna Zyla, Lichun He, Pedro Moura‐Alves, Heidrun Steinle, Philippe Saikali, Laura Lozza, Natalie Nieuwenhuizen, January Weiner, Hans‐Joachim Mollenkopf, Kornelia Ellwanger, Christine Arnold, Mojie Duan, Yulia Dagil, Mikhail Pashenkov, Ivo Gomperts Boneca, Thomas A Kufer, Anca Dorhoi, Stefan H E Kaufmann

Cellular stress has been associated with inflammation, yet precise underlying mechanisms remain elusive. In this study, various unrelated stress inducers were employed to screen for sensors linking altered cellular homeostasis and inflammation. We identified the intracellular pattern recognition receptors NOD1/2, which sense bacterial peptidoglycans, as general stress sensors detecting perturbations of cellular homeostasis. NOD1/2 activation upon such perturbations required generation of the endogenous metabolite sphingosine‐1‐phosphate (S1P). Unlike peptidoglycan sensing via the leucine‐rich repeats domain, cytosolic S1P directly bound to the nucleotide binding domains of NOD1/2, triggering NF‐κB activation and inflammatory responses. In sum, we unveiled a hitherto unknown role of NOD1/2 in surveillance of cellular homeostasis through sensing of the cytosolic metabolite S1P. We propose S1P, an endogenous metabolite, as a novel NOD1/2 activator and NOD1/2 as molecular hubs integrating bacterial and metabolic cues.

Link: doi.org/10.15252/embj.2020106272

publications
human, cell, organelles, microbiology, other-application
138
Article

Breast cancer & phospholipid metabolism

Henri M Deda

Of all breast cancer patients, 10 to 20 % are diagnosed with triple-negative breast cancer (TNBC). TNBC is a type of breast cancer that is more likely to be found in people younger than age 50, it is more aggressive, and has poorer prognosis than other types of breast cancer. The growth of triple-negative breast cancer is not fueled by estrogen, progesterone, or the HER2 protein. Thus, it does not respond to hormonal therapies based on estrogen or progesterone receptors or medications targeting the HER2 protein receptors – it is triple negative. Though other medicines exist, new therapeutic approaches for TNBC are required to improve treatment quality. Targeting lipid metabolism, specifically phospholipid metabolism, has been shown a promising breast cancer research subject. Lipidomics analysis revealed a mechanism for how interfering with phospholipid metabolism inhibits tumor growth of TNBC – in vitro and in vivo. The results serve as a starting point for new medications and treatment methods against triple-negative breast cancer.

Link: lipotype.com/breast-cancer-lipid-metabolism

articles
human, cell, oncology, organelles, other-application
139
Nature Communications

Ferroptotic cell death triggered by conjugated linolenic acids is mediated by ACSL1

Alexander Beatty, Tanu Singh, Yulia Y Tyurina, Vladimir A Tyurin, Svetlana Samovich, Emmanuelle Nicolas, Kristen Maslar, Yan Zhou, Kathy Q Cai, Yinfei Tan, Sebastian Doll, Marcus Conrad, Aravind Subramanian, Hülya Bayır, Valerian E Kagan, Ulrike Rennefahrt, Jeffrey R Peterson

Ferroptosis is associated with lipid hydroperoxides generated by the oxidation of polyunsaturated acyl chains. Lipid hydroperoxides are reduced by glutathione peroxidase 4 (GPX4) and GPX4 inhibitors induce ferroptosis. However, the therapeutic potential of triggering ferroptosis in cancer cells with polyunsaturated fatty acids is unknown. Here, we identify conjugated linoleates including α-eleostearic acid (αESA) as ferroptosis inducers. αESA does not alter GPX4 activity but is incorporated into cellular lipids and promotes lipid peroxidation and cell death in diverse cancer cell types. αESA-triggered death is mediated by acyl-CoA synthetase long-chain isoform 1, which promotes αESA incorporation into neutral lipids including triacylglycerols. Interfering with triacylglycerol biosynthesis suppresses ferroptosis triggered by αESA but not by GPX4 inhibition. Oral administration of tung oil, naturally rich in αESA, to mice limits tumor growth and metastasis with transcriptional changes consistent with ferroptosis. Overall, these findings illuminate a potential approach to ferroptosis, complementary to GPX4 inhibition.

Link: doi.org/10.1038/s41467-021-22471-y

publications
human, mouse-rat, cell, oncology, tissue-organ, pharma
140
Alzheimer's Research & Therapy

An integrative multi-omics approach reveals new central nervous system pathway alterations in Alzheimer’s disease

Christopher Clark, Loïc Dayon, Mojgan Masoodi, Gene L Bowman, Julius Popp

Multiple pathophysiological processes have been described in Alzheimer’s disease (AD). Their inter-individual variations, complex interrelations, and relevance for clinical manifestation and disease progression remain poorly understood. We hypothesize that specific molecular patterns indicating both known and yet unidentified pathway alterations are associated with distinct aspects of AD pathology. We performed multi-level cerebrospinal fluid (CSF) omics in a well-characterized cohort of older adults with normal cognition, mild cognitive impairment, and mild dementia. Proteomics, metabolomics, lipidomics, one-carbon metabolism, and neuroinflammation related molecules were analyzed at single-omic level with correlation and regression approaches. Multi-omics factor analysis was used to integrate all biological levels. Identified analytes were used to construct best predictive models of the presence of AD pathology and of cognitive decline with multifactorial regression analysis. Pathway enrichment analysis identified pathway alterations in AD. Multi-omics integration identified five major dimensions of heterogeneity explaining the variance within the cohort and differentially associated with AD. Further analysis exposed multiple interactions between single ‘omics modalities and distinct multi-omics molecular signatures differentially related to amyloid pathology, neuronal injury, and tau hyperphosphorylation. Enrichment pathway analysis revealed overrepresentation of the hemostasis, immune response, and extracellular matrix signaling pathways in association with AD. Finally, combinations of four molecules improved prediction of both AD (protein 14-3-3 zeta/delta, clusterin, interleukin-15, and transgelin-2) and cognitive decline (protein 14-3-3 zeta/delta, clusterin, cholesteryl ester 27:1 16:0 and monocyte chemoattractant protein-1). Applying an integrative multi-omics approach we report novel molecular and pathways alterations associated with AD pathology. These findings are relevant for the development of personalized diagnosis and treatment approaches in AD.

Link: doi.org/10.1186/s13195-021-00814-7

publications
human, other-sample-type, neuroscience, clinical-research, biomarker, multiomics
141
Article

Lipid profiles of neurons & glia cells

Henri M Deda

The mammalian brain is the second-most lipid-rich organ. About 75% of all mammalian lipid species are exclusively found in neural tissues. In their variety, lipids contribute to the morphological and functional diversity of the central nervous system consisting of neurons and glia cells. Neurons transport information to other cells. Glia cells include oligodendrocytes, astrocytes, and microglia. The primary function of oligodendrocytes is to generate myelin. Astrocytes recycle neurotransmitters, shape synaptic circuits, and maintain the blood-brain barrier. Microglia are related to immune responses and brain homeostasis. A cell-type-resolved lipid profile of the mouse brain found clear differences in lipid composition and lipid metabolism of neurons, oligodendrocytes, astrocytes, and microglia. These profiles serve as an atlas for further research of the human brain, its diseases and mental disorders.

Link: lipotype.com/lipids-of-neurons-glia-cells

articles
mouse-rat, diet, cell, neuroscience, model-systems
142
Patent

Skin Care Composition Comprising Mevalonolactone

Heli Anglenius, Carole Gherardi, Laura T M Huuskonen, Juho Järvinen, Henrik M Jensen, Hannu Koivikko, Jyrki Kuusisto, Tero T Mentunen, Juha Nurmi, Piera M Pericu, Pertti M Särelä, Jani Siitonen, Kirsti Tiihonen, Gregory M Whited

The skin functions as a barrier protecting the organism from drying out as well as protecting the organism against the penetration of external, often harmful, substances. The human skin consists of two main layers of cells, epidermis and dermis. The epidermis constitutes the outermost layer of the skin and is mainly formed of terminally differentiated keratinocytes and lipids, living dividing keratinocytes located beneath the terminally differentiated ones. The outer layer of the epidermis is the part which is in contact with the environment and the particular structure of the horny layer protects the skin as well as stabilizes its own flexibility by binding a defined amount of water. The main function of the epidermis is to form permeability barrier against environmental challenges, such as UV radiation, heat, chemicals, pollution, and pathogens, such as bacteria, fungi, parasites, and viruses. It also protects the body from uncontrolled water evaporation from inside out, maintaining the hydration balance and skin metabolism. In the dermis, the most abundant cell type, dermal fibroblasts, are responsible of generating the connective tissue by producing extracellular matrix (ECM). This ECM is composed of two main classes of macromolecules: proteoglycans (PGs) and fibrous proteins; the most abundant fibrous proteins are type I collagen fibrils, elastins, laminins and fibronectins. During aging the collagen fibrils become fragmented, fibroblasts produce less ECM proteins and more ECM degrading matrix metalloproteinases (MMPs), that leads to imbalance in the ECM. There remains a need to find methods and compositions for providing skin benefits, such as but not limiting to methods and compositions for providing a skin care benefit selected from the group consisting of skin moisturizing, skin exfoliation (also referred to as skin peeling, desquamation, skin shedding, skin resurfacing, skin regeneration, skin renewal, improving epidermal cell turnover, preventing or retarding the appearance of the signs of aging of the skin (anti-aging), reducing the appearance of skin wrinkles, skin rejuvenation, strengthening the skin barrier function, or any one combination thereof) to a skin. In this patent, compositions and methods are provided for topical applications for skin care, skin supplement, hair care, oral care, comprising mevalonolactone, mevalonic acid, mevalonate, salts of mevalonic acid, mevalonolactone monohydrate, or any combination thereof.

Link: freepatentsonline.com/WO2021041363A1.html

patents
dermatology
143
Journal of the American Academy of Child & Adolescent Psychiatry

Adverse Effects of Refeeding on the Plasma Lipidome in Young Individuals With Anorexia Nervosa?

Friederike I Tam, Mathias J Gerl, Christian Klose, Michal A Surma, Joseph A King, Maria Seidel, Kerstin Weidner, Veit Roessner, Kai Simons, Stefan Ehrlich

Refeeding is the cornerstone of anorexia nervosa (AN) treatment, but little is known regarding the optimal pace and dietary composition or possible adverse effects of current clinical practices. Plasma lipids may be a moderating factor underlying unfavorable refeeding effects in AN, such as an abnormal central body fat distribution. The objective of this study was to analyze the plasma lipidome in the acutely underweight state of AN before and after refeeding. Using high-throughput quantitative mass spectrometry-based shotgun lipidomics, we measured 13 lipid classes and 204 lipid species or subspecies in the plasma of young female patients with acute AN, before (n=39) and after short-term weight restoration during an intensive inpatient refeeding program (n=23, median BMI increase 26.4%), in comparison to healthy control participants (n=37). Before inpatient treatment, patients with AN exhibited increased concentrations of cholesterol and several other lipid classes. After refeeding, multiple lipid classes including cholesterol and ceramides as well as certain ceramide species previously associated with obesity or overfeeding showed increased concentrations, and a pattern of shorter and more saturated triacylgycerides emerged. A machine learning model trained to predict BMI based on the lipidomic profiles revealed a sizable overprediction in patients with AN after weight restoration. The results point towards a profound lipid dysregulation with similarities to obesity and other features of the metabolic syndrome after short-term weight restoration. Thus, this study provides evidence for possible short-term adverse effects of current refeeding practices on the metabolic state and should inspire more research on nutritional interventions in AN.

Link: doi.org/10.1016/j.jaac.2021.02.014

publications
data, human, blood, metabolic-disorders, diet, neuroscience, clinical-research
144
nature metabolism

Diet-dependent regulation of TGFβ impairs reparative innate immune responses after demyelination

Mar Bosch-Queralt, Ludovico Cantuti-Castelvetri, Alkmini Damkou, Martina Schifferer, Kai Schlepckow, Ioannis Alexopoulos, Dieter Lütjohann, Christian Klose, Lenka Vaculčiaková, Takahiro Masuda, Marco Prinz, Kathryn M Monroe, Gilbert Di Paolo, Joseph W Lewcock, Christian Haass, Mikael Simons

Proregenerative responses are required for the restoration of nervous-system functionality in demyelinating diseases such as multiple sclerosis (MS). Yet, the limiting factors responsible for poor CNS repair are only partially understood. Here, we test the impact of a Western diet (WD) on phagocyte function in a mouse model of demyelinating injury that requires microglial innate immune function for a regenerative response to occur. We find that WD feeding triggers an ageing-related, dysfunctional metabolic response that is associated with impaired myelin-debris clearance in microglia, thereby impairing lesion recovery after demyelination. Mechanistically, we detect enhanced transforming growth factor beta (TGFβ) signalling, which suppresses the activation of the liver X receptor (LXR)-regulated genes involved in cholesterol efflux, thereby inhibiting phagocytic clearance of myelin and cholesterol. Blocking TGFβ or promoting triggering receptor expressed on myeloid cells 2 (TREM2) activity restores microglia responsiveness and myelin-debris clearance after demyelinating injury. Thus, we have identified a druggable microglial immune checkpoint mechanism regulating the microglial response to injury that promotes remyelination.

Link: doi.org/10.1038/s42255-021-00341-7

publications
mouse-rat, diet, cell, neuroscience
145
Communications Biology

Lipidomic and in-gel analysis of maleic acid co-polymer nanodiscs reveals differences in composition of solubilized membranes

Marta Barniol-Xicota, Steven H L Verhelst

Membrane proteins are key in a large number of physiological and pathological processes. Their study often involves a prior detergent solubilization step, which strips away the membrane and can jeopardize membrane protein integrity. A recent alternative to detergents encompasses maleic acid based copolymers (xMAs), which disrupt the lipid bilayer and form lipid protein nanodiscs (xMALPs) soluble in aqueous buffer. Although xMALPs are often referred to as native nanodiscs, little is known about the resemblance of their lipid and protein content to the native bilayer. Here we have analyzed prokaryotic and eukaryotic xMALPs using lipidomics and in-gel analysis. Our results show that the xMALPs content varies with the chemical properties of the used xMA.

Link: doi.org/10.1038/s42003-021-01711-3

publications
subcellular, bacterium, other-application
146
Article

Lipid biomarkers for multiple sclerosis

Olga (Olya) Vvedenskaya

In multiple sclerosis (MS), a chronic inflammatory and neurodegenerative disease of the central nervous system, the body attacks the protective myelin sheath of neurons in the brain and the spinal cord. The damaged myelin causes communication problems between the central nervous system and the rest of the body. To this day, there is no cure for MS. Neurobiological researchers believe that MS does not only cause the clinical symptoms we look for as of today but also alters a patient’s lipid metabolism. Detailed, molecular lipid analysis can discover specific biomarkers for MS to support fast and accurate diagnosis, better treatment, and monitoring.

Link: lipotype.com/lipid-biomarkers-for-multiple-sclerosis

articles
human, blood, neuroscience, clinical-research, biomarker
147
International Journal of Cardiology

A plasma lipid signature predicts incident coronary artery disease

Filip Ottosson, Payam Emami Khoonsari, Mathias J Gerl, Kai Simons, Olle Melander, Céline Fernandez

Dyslipidemia is a hallmark of cardiovascular disease but is characterized by crude measurements of triglycerides, HDL- and LDL cholesterol. Lipidomics enables more detailed measurements of plasma lipids, which may help improve risk stratification and understand the pathophysiology of cardiovascular disease. Lipidomics was used to measure 184 lipids in plasma samples from the Malmö Diet and Cancer – Cardiovascular Cohort (N = 3865), taken at baseline examination. During an average follow-up time of 20.3 years, 536 participants developed coronary artery disease (CAD). Least absolute shrinkage and selection operator (LASSO) were applied to Cox proportional hazards models in order to identify plasma lipids that predict CAD. Eight plasma lipids improved prediction of future CAD on top of traditional cardiovascular risk factors. Principal component analysis of CAD-associated lipids revealed one principal component (PC2) that was associated with risk of future CAD (HR per SD increment =1.46, C·I = 1.35–1.48, P < 0.001). The risk increase for being in the highest quartile of PC2 (HR = 2.33, P < 0.001) was higher than being in the top quartile of systolic blood pressure. Addition of PC2 to traditional risk factors achieved an improvement (2%) in the area under the ROC-curve for CAD events occurring within 10 (P = 0.03), 15 (P = 0.003) and 20 (P = 0.001) years of follow-up respectively. A lipid pattern improved CAD prediction above traditional risk factors, highlighting that conventional lipid-measures insufficiently describe dyslipidemia that is present years before CAD. Identifying this hidden dyslipidemia may help motivate lifestyle and pharmacological interventions early enough to reach a substantial reduction in absolute risk.

Link: doi.org/10.1016/j.ijcard.2021.01.059

publications
data, human, blood, cardiovascular-disease, clinical-research, biomarker
148
EBioMedicine

Early signature in the blood lipidome associated with subsequent cognitive decline in the elderly: A case-control analysis nested within the Three-City cohort study

Sophie Lefèvre-Arbogast, Boris P Hejblum, Catherine Helmer, Christian Klose, Claudine Manach, Dorrain Y Low, Mireia Urpi-Sarda, Cristina Andres-Lacueva, Raúl González-Domínguez, Ludwig Aigner, Barbara Altendorfer, Paul J Lucassen, Silvie R Ruigrok, Chiara De Lucia, Andrea Du Preez, Cécile Proust-Lima, Sandrine Thuret, Aniko Korosi, Cécilia Samieri

Brain lipid metabolism appears critical for cognitive aging, but whether alterations in the lipidome relate to cognitive decline remains unclear at the system level. We studied participants from the Three-City study, a multicentric cohort of older persons, free of dementia at time of blood sampling, and who provided repeated measures of cognition over 12 subsequent years. We measured 189 serum lipids from 13 lipid classes using shotgun lipidomics in a case-control sample on cognitive decline (matched on age, sex and level of education) nested within the Bordeaux study center (discovery, n = 418). Associations with cognitive decline were investigated using bootstrapped penalized regression, and tested for validation in the Dijon study center (validation, n = 314). Among 17 lipids identified in the discovery stage, lower levels of the triglyceride TAG 50:5, and of four membrane lipids (sphingomyelin SM 40:2,2, phosphatidylethanolamine PE 38:5(18:1/20:4), ether-phosphatidylethanolamine PE O- 34:3(16:1/18:2), and ether-phosphatidylcholine PC O- 34:1(16:1/18:0)), and higher levels of PC O- 32:0(16:0/16:0), were associated with greater odds of cognitive decline, and replicated in our validation sample. These findings indicate that in the blood lipidome of non-demented older persons, a specific profile of lipids involved in membrane fluidity, myelination, and lipid rafts, is associated with subsequent cognitive decline.

Link: doi.org/10.1016/j.ebiom.2021.103216

publications
human, blood, neuroscience, clinical-research, biomarker, other-application
149
International Journal of Molecular Sciences

Influence of Antiplatelet Agents on the Lipid Composition of Platelet Plasma Membrane: A Lipidomics Approach with Ticagrelor and Its Active Metabolite

Jennifer Lagoutte-Renosi, Florentin Allemand, Christophe Ramseyer, Vahideh Rabani, Siamak Davani

Lipids contained in the plasma membrane of platelets play an important role in platelet function. Modifications in the lipid composition can fluidify or rigidify the environment around embedded receptors, in order to facilitate the access of the receptor by the drug. However, data concerning the lipid composition of platelet plasma membrane need to be updated. In addition, data on the impact of drugs on plasma membrane composition, in particular antiplatelet agents, remain sparse. After isolation of platelet plasma membrane, we assessed, using lipidomics, the effect of ticagrelor, a P2Y12 antagonist, and its active metabolite on the lipid composition of these plasma membranes. We describe the exact lipid composition of plasma membrane, including all sub-species. Ticagrelor and its active metabolite significantly increased cholesterol and phosphatidylcholine ether with short saturated acyl chains 16:0/16:0, and decreased phosphatidylcholine, suggesting overall rigidification of the membrane. Furthermore, ticagrelor and its active metabolite decreased some arachidonylated plasmalogens, suggesting a decrease in availability of arachidonic acid from the membrane phospholipids for synthesis of biologically active mediators. To conclude, ticagrelor and its active metabolite seem to influence the lipid environment of receptors embedded in the lipid bilayer and modify the behavior of the plasma membrane.

Link: doi.org/10.3390/ijms22031432

publications
human, blood, cardiovascular-disease, pharma, organelles
150
Cell Reports

Genome-wide CRISPR-Cas9 knockout library screening identified PTPMT1 in cardiolipin synthesis is crucial to survival in hypoxia in liver cancer

Macus H Bao, Chunxue Yang, Aki P Tse, Lai Wei, Derek Lee, Misty S Zhang, Chi C Goh, David K Chiu, Vincent W Yuen, Cheuk-Ting Law, Wai-Ching Chin, Noreen N Chui, Bowie P Wong, Cerise Y Chan, Irene O Ng, Clive Y Chung, Chun-Ming Wong, Carmen C Wong

Hypoxia, low oxygen (O2), is a key feature of all solid cancers, including hepatocellular carcinoma (HCC). Genome-wide CRISPR-Cas9 knockout library screening is used to identify reliable therapeutic targets responsible for hypoxic survival in HCC. We find that protein-tyrosine phosphatase mitochondrial 1 (PTPMT1), an important enzyme for cardiolipin (CL) synthesis, is the most significant gene and ranks just after hypoxia-inducible factor (HIF)-1α and HIF-1β as crucial to hypoxic survival. CL constitutes the mitochondrial membrane and ensures the proper assembly of electron transport chain (ETC) complexes for efficient electron transfer in respiration. ETC becomes highly unstable during hypoxia. Knockout of PTPMT1 stops the maturation of CL and impairs the assembly of ETC complexes, leading to further electron leakage and ROS accumulation at ETC in hypoxia. Excitingly, HCC cells, especially under hypoxic conditions, show great sensitivity toward PTPMT1 inhibitor alexidine dihydrochloride (AD). This study unravels the protective roles of PTPMT1 in hypoxic survival and cancer development.

Link: doi.org/10.1016/j.celrep.2020.108676

publications
human, mouse-rat, cell, oncology, tissue-organ, organelles, multiomics
151
Article

Multiomics in cardiovascular disease research

Henri M Deda

Cardiovascular diseases are the leading cause of death worldwide. This group of conditions – which includes arrhythmia and heart failure – are indicated by a reduced ability of the heart and blood vessels to move blood throughout the body. Risk factors for cardiovascular disease include genetics, diet, and physical inactivity; symptoms include stroke and heart attack. Plasma lipids such as cholesterols, triglycerides, and lipoproteins are often used to estimate an individual’s risk of developing cardiovascular diseases. While informative, a more comprehensive picture of the plasma lipidome – especially if combined with other omic endpoints – may improve prediction of and inform therapies for cardiovascular diseases.

Link: lipotype.com/multiomics-in-cardiovascular-research

articles
human, blood, cardiovascular-disease, biomarker, multiomics
152
Cell Chemical Biology

Investigating the mechanism of action of aggregation-inducing antimicrobial Pept-ins

Guiqin Wu, Laleh Khodaparast, Ladan Khodaparast, Matthias De Vleeschouwer, Joëlle Housmans, Bert Houben, Joost Schymkowitz, Frederic Rousseau

Aggregation can be selectively induced by aggregation-prone regions (APRs) contained in the target proteins. Aggregation-inducing antimicrobial peptides (Pept-ins) contain sequences homologous to APRs of target proteins and exert their bactericidal effect by causing aggregation of a large number of proteins. To better understand the mechanism of action of Pept-ins and the resistance mechanisms, we analyzed the phenotypic, lipidomic, and transcriptomic as well as genotypic changes in laboratory-derived Pept-in-resistant E. coli mutator cells. The analysis showed that the Pept-in resistance mechanism is dominated by a decreased Pept-in uptake, in both laboratory-derived mutator cells and clinical isolates. Our data indicate that Pept-in uptake involves an electrostatic attraction between the Pept-in and the bacterial membrane and follows a complex mechanism potentially involving many transporters. Furthermore, it seems more challenging for bacteria to become resistant toward Pept-ins that are less dependent on electrostatic attraction for uptake, suggesting that future Pept-ins should be selected for this property.

Link: doi.org/10.1016/j.chembiol.2020.12.008

publications
cell, bacterium, pharma, organelles, microbiology, multiomics
153
Cell Reports Medicine

A 4-Aminoquinoline Inhibits the Trained Innate Immune Response to Interferons

Nils Rother, Cansu Yanginlar, Rik G H Lindeboom, Siroon Bekkering, Mandy M T van Leent, Baranca Buijsers, Inge Jonkman, Mark de Graaf, Marijke Baltissen, Lieke A Lamers, Niels P Riksen, Zahi A Fayad, Willem J M Mulder, Luuk B Hilbrands, Leo A B Joosten, Mihai G Netea, Michiel Vermeulen, Johan van der Vlag, Raphaël Duivenvoorden

A commercially available 4-aminoquinoline is being investigated for a potential prophylactic effect in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but its mechanism of action is poorly understood. Circulating leukocytes from the blood of coronavirus disease 2019 (COVID-19) patients show increased responses to Toll-like receptor ligands, suggestive of trained immunity. By analyzing interferon responses of peripheral blood mononuclear cells from healthy donors conditioned with heat-killed Candida, trained innate immunity can be modeled in vitro. In this model, the 4-aminoquinoline inhibits the responsiveness of these innate immune cells to virus-like stimuli and interferons. This is associated with a suppression of histone 3 lysine 27 acetylation and histone 3 lysine 4 trimethylation of inflammation-related genes, changes in the cellular lipidome, and decreased expression of interferon-stimulated genes. Our findings indicate that the 4-aminoquinoline inhibits trained immunity in vitro, which may not be beneficial for the antiviral innate immune response to SARS-CoV-2 infection in patients.

Link: doi.org/10.1016/j.xcrm.2020.100146

publications
human, cell, pharma, clinical-research, other-application
154
Article

Skin pigmentation and ceramide content

Olga (Olya) Vvedenskaya, Henri M Deda

Moisturization has taken center stage in skin care research and product development for decades. New remedies for dry skin have entered and left the shelves of drugstores. Still, dry facial skin remains a major concern for consumers. Though skin biology is central to develop reliable moisturizers, researching the impact of the skin’s molecular profile has been lacking. Skin lipidomics is changing this.

Link: lipotype.com/skin-lipidomics-for-moisturizer-research

articles
human, dermatology, skin, clinical-research, multiomics
155
Frontiers in Immunology

Maturation of Monocyte-Derived DCs Leads to Increased Cellular Stiffness, Higher Membrane Fluidity, and Changed Lipid Composition

Jennifer J Lühr, Nils Alex, Lukas Amon, Martin Kräter, Markéta Kubánková, Erdinc Sezgin, Christian H K Lehmann, Lukas Heger, Gordon F Heidkamp, Ana-Sunčana Smith, Vasily Zaburdaev, Rainer A Böckmann, Ilya Levental, Michael L Dustin, Christian Eggeling, Jochen Guck, Diana Dudziak

Dendritic cells (DCs) are professional antigen-presenting cells of the immune system. Upon sensing pathogenic material in their environment, DCs start to mature, which includes cellular processes, such as antigen uptake, processing and presentation, as well as upregulation of costimulatory molecules and cytokine secretion. During maturation, DCs detach from peripheral tissues, migrate to the nearest lymph node, and find their way into the correct position in the net of the lymph node microenvironment to meet and interact with the respective T cells. We hypothesize that the maturation of DCs is well prepared and optimized leading to processes that alter various cellular characteristics from mechanics and metabolism to membrane properties. Here, we investigated the mechanical properties of monocyte-derived dendritic cells (moDCs) using real-time deformability cytometry to measure cytoskeletal changes and found that mature moDCs were stiffer compared to immature moDCs. These cellular changes likely play an important role in the processes of cell migration and T cell activation. As lipids constitute the building blocks of the plasma membrane, which, during maturation, need to adapt to the environment for migration and DC-T cell interaction, we performed an unbiased high-throughput lipidomics screening to identify the lipidome of moDCs. These analyses revealed that the overall lipid composition was significantly changed during moDC maturation, even implying an increase of storage lipids and differences of the relative abundance of membrane lipids upon maturation. Further, metadata analyses demonstrated that lipid changes were associated with the serum low-density lipoprotein (LDL) and cholesterol levels in the blood of the donors. Finally, using lipid packing imaging we found that the membrane of mature moDCs revealed a higher fluidity compared to immature moDCs. This comprehensive and quantitative characterization of maturation associated changes in moDCs sets the stage for improving their use in clinical application.

Link: doi.org/10.3389/fimmu.2020.590121

publications
human, cell, organelles, other-application
156
European Journal of Pharmaceutics and Biopharmaceutics

Evaluation of Bovine Milk Extracellular Vesicles for the Delivery of Locked Nucleic Acid Antisense Oligonucleotides

Philip Grossen, Michaela Portmann, Erich Koller, Martina Duschmalé, Tanja Minz, Sabine Sewing, Nikhil J Pandya, Sabine Kux van Geijtenbeek, Axel Ducret, Eric-André Kusznir, Sylwia Huber, Marco Berrera, Matthias E Lauer, Philippe Ringler, Bettina Nordbo, Marianne Lerbech Jensen, Filippo Sladojevich, Ravi Jagasia, Rainer Alex, Remo Gamboni, Michael Keller

The natural capacity of extracellular vesicles (EVs) to transport their payload to recipient cells has raised big interest to repurpose EVs as delivery vehicles for xenobiotics. In the present study, bovine milk-derived EVs (BMEVs) were investigated for their potential to shuttle locked nucleic acid-modified antisense oligonucleotides (LNA ASOs) into the systemic circulation after oral administration. To this end, a broad array of analytical methods including proteomics and lipidomics were used to thoroughly characterize BMEVs. We found that additional purification by density gradients efficiently reduced levels of non-EV associated proteins. The potential of BMEVs to functionally transfer LNA ASOs was tested using advanced in vitro systems (i.e. hPSC-derived neurons and primary human cells). A slight increase in cellular LNA ASO internalization and target gene reduction was observed when LNA ASOs were delivered using BMEVs. When dosed orally in mice, only a small fraction (about 1 % of total administered dose) of LNA ASOs was recovered in the peripheral tissues liver and kidney, however, no significant reduction in target gene expression (i.e. functional knockdown) was observed.

Link: doi.org/10.1016/j.ejpb.2020.11.012

publications
exosome, other-organism, pharma, organelles, other-application
157
nature communications

ETNK1 mutations induce a mutator phenotype that can be reverted with phosphoethanolamine

Diletta Fontana, Mario Mauri, Rossella Renso, Mattia Docci, Ilaria Crespiatico, Lisa M Røst, Mi Jang, Antonio Niro, Deborah D’Aliberti, Luca Massimino, Mayla Bertagna, Giovanni Zambrotta, Mario Bossi, Stefania Citterio, Barbara Crescenzi, Francesca Fanelli, Valeria Cassina, Roberta Corti, Domenico Salerno, Luca Nardo, Clizia Chinello, Francesco Mantegazza, Cristina Mecucci, Fulvio Magni, Guido Cavaletti, Per Bruheim, Delphine Rea, Steen Larsen, Carlo Gambacorti-Passerini, Rocco Piazza

Recurrent somatic mutations in ETNK1 (Ethanolamine-Kinase-1) were identified in several myeloid malignancies and are responsible for a reduced enzymatic activity. Here, we demonstrate in primary leukemic cells and in cell lines that mutated ETNK1 causes a significant increase in mitochondrial activity, ROS production, and Histone H2AX phosphorylation, ultimately driving the increased accumulation of new mutations. We also show that phosphoethanolamine, the metabolic product of ETNK1, negatively controls mitochondrial activity through a direct competition with succinate at mitochondrial complex II. Hence, reduced intracellular phosphoethanolamine causes mitochondria hyperactivation, ROS production, and DNA damage. Treatment with phosphoethanolamine is able to counteract complex II hyperactivation and to restore a normal phenotype.

Link: doi.org/10.1038/s41467-020-19721-w

publications
human, cell, subcellular, oncology, organelles
158
BBA Molecular and Cell Biology of Lipids

LAPTM4B controls the sphingolipid and ether lipid signature of small extracellular vesicles

Andrea Dichlberger, Kecheng Zhou, Nils Bäck, Thomas Nyholm, Anders Backman, Peter Mattjus, Elina Ikonen, Tomas Blom

Lysosome Associated Protein Transmembrane 4B (LAPTM4B) is a four-membrane spanning ceramide interacting protein that regulates mTORC1 signaling. Here, we show that LAPTM4B is sorted into intraluminal vesicles (ILVs) of multivesicular endosomes (MVEs) and released in small extracellular vesicles (sEVs) into conditioned cell culture medium and human urine. Efficient sorting of LAPTM4B into ILV membranes depends on its third transmembrane domain containing a sphingolipid interaction motif (SLim). Unbiased lipidomic analysis reveals a strong enrichment of glycosphingolipids in sEVs secreted from LAPTM4B knockout cells and from cells expressing a SLim-deficient LAPTM4B mutant. The altered sphingolipid profile is accompanied by a distinct SLim-dependent co-modulation of ether lipid species. The changes in the lipid composition of sEVs derived from LAPTM4B knockout cells is reflected by an increased stability of membrane nanodomains of sEVs. These results identify LAPTM4B as a determinant of the glycosphingolipid profile and membrane properties of sEVs.

Link: doi.org/10.1016/j.bbalip.2020.158855

publications
human, cell, exosome, organelles, other-application
159
Annals of Clinical and Translational Neurology

Plasma lipidomics of monozygotic twins discordant for multiple sclerosis

Horst Penkert, Chris Lauber, Mathias J Gerl, Christian Klose, Markus Damm, Dirk Fitzner, Andrea Flierl‐Hecht, Tania Kümpfel, Martin Kerschensteiner, Reinhard Hohlfeld, Lisa A Gerdes, Mikael Simons

Blood biomarkers of multiple sclerosis (MS) can provide a better understanding of pathophysiology and enable disease monitoring. Here, we performed quantitative shotgun lipidomics on the plasma of a unique cohort of 73 monozygotic twins discordant for MS. We analyzed 243 lipid species, evaluated lipid features such as fatty acyl chain length and number of acyl chain double bonds, and detected phospholipids that were significantly altered in the plasma of co‐twins with MS compared to their non‐affected siblings. Strikingly, changes were most prominent in ether phosphatidylethanolamines and ether phosphatidylcholines, suggesting a role for altered lipid signaling in the disease.

Link: doi.org/10.1002/acn3.51216

publications
data, human, blood, neuroscience, clinical-research, biomarker
160
Frontiers in Cell and Developmental Biology

Fluidity and Lipid Composition of Membranes of Peroxisomes, Mitochondria and the ER From Oleic Acid-Induced Saccharomyces cerevisiae

Katharina Reglinski, Laura Steinfort-Effelsberg, Erdinc Sezgin, Christian Klose, Harald W Platta, Wolfgang Girzalsky, Christian Eggeling, Ralf Erdmann

The maintenance of a fluid lipid bilayer is key for organelle function and cell viability. Given the critical role of lipid compositions in determining membrane properties and organelle identity, it is clear that cells must have elaborate mechanism for membrane maintenance during adaptive responses to environmental conditions. Emphasis of the presented study is on peroxisomes, oleic acid-inducible organelles that are essential for the growth of yeast under conditions of oleic acid as single carbon source. Here, we isolated peroxisomes, mitochondria and ER from oleic acid-induced Saccharomyces cerevisiae and determined the lipid composition of their membranes using shotgun lipidomics and compared it to lipid ordering using fluorescence microscopy. In comparison to mitochondrial and ER membranes, the peroxisomal membranes were slightly more disordered and characterized by a distinct enrichment of phosphaditylinositol, indicating an important role of this phospholipid in peroxisomal membrane associated processes.

Link: doi.org/10.3389/fcell.2020.574363

publications
subcellular, yeast, organelles, other-application
161
PNAS

Myelination of peripheral nerves is controlled by PI4KB through regulation of Schwann cell Golgi function

Takashi Baba, Alejandro Alvarez-Prats, Yeun Ju Kim, Daniel Abebe, Steve Wilson, Zane Aldworth, Mark A Stopfer, John Heuser, Tamas Balla

Better understanding myelination of peripheral nerves would benefit patients affected by peripheral neuropathies, including Charcot–Marie–Tooth disease. Little is known about the role the Golgi compartment plays in Schwann cell (SC) functions. Here, we studied the role of Golgi in myelination of peripheral nerves in mice through SC-specific genetic inactivation of phosphatidylinositol 4-kinase beta (PI4KB), a Golgi-associated lipid kinase. Sciatic nerves of such mice showed thinner myelin of large diameter axons and gross aberrations in myelin organization affecting the nodes of Ranvier, the Schmidt–Lanterman incisures, and Cajal bands. Nonmyelinating SCs showed a striking inability to engulf small diameter nerve fibers. SCs of mutant mice showed a distorted Golgi morphology and disappearance of OSBP at the cis-Golgi compartment, together with a complete loss of GOLPH3 from the entire Golgi. Accordingly, the cholesterol and sphingomyelin contents of sciatic nerves were greatly reduced and so was the number of caveolae observed in SCs. Although the conduction velocity of sciatic nerves of mutant mice showed an 80% decrease, the mice displayed only subtle impairment in their motor functions. Our analysis revealed that Golgi functions supported by PI4KB are critically important for proper myelination through control of lipid metabolism, protein glycosylation, and organization of microvilli in the nodes of Ranvier of peripheral nerves.

Link: doi.org/10.1073/pnas.2007432117

publications
mouse-rat, neuroscience, tissue-organ, organelles
162
Patent

Methods and Compositions Relating to Chondrisomes from Cultured Cells

Geoffrey A Von Maltzahn, John M Milwid, Michael T Mee, Jacob Rosenblum-Rubens, David Chess, Kyle M Trudeau, Kiana Mahdaviani, Jacob Feala

Mitochondria are membrane bound subcellular structures found in eukaryotic cells. Sometimes described as the power plants of cells, mitochondria generate most of the energy of the cell in the form of adenosine triphosphate (ATP) through respiration. Damage and subsequent dysfunction of mitochondria are important factors in a range of human diseases. Described herein are novel preparations of chondrisomes derived from mitochondria, and related methods, that have advantageous and surprising qualities for use in human pharmaceutical and in veterinary applications. Chondrisome preparations and methods described herein have beneficial structural characteristics, yield, concentration, stability, viability, integrity, or function, e.g., a bioenergetic or biological function, for use in therapeutic applications. Accordingly, in one aspect, the invention features a pharmaceutical composition comprising a preparation of isolated chondrisomes, derived from cultured cells, and a pharmaceutically acceptable carrier.

Link: freepatentsonline.com/y2020/0306315.html

patents
pharma
163
Patent

Methods and Compositions Relating to Chondrisomes from Blood Products

Geoffrey A Von Maltzahn, John M Milwid, Michael T Mee, Jacob Rosenblum-Rubens, David Chess, Kyle M Trudeau, Kiana Mahdaviani, Jacob Feala

Mitochondria are membrane bound subcellular structures found in eukaryotic cells. Sometimes described as the power plants of cells, mitochondria generate most of the energy of the cell in the form of adenosine triphosphate (ATP) through respiration. Damage and subsequent dysfunction of mitochondria are important factors in a range of human diseases. Described herein are novel preparations of chondrisomes derived from blood or blood products, and related methods, that have advantageous and surprising qualities for use in human pharmaceutical and in veterinary applications. Chondrisome and mitoparticle preparations and methods described herein have beneficial structural characteristics, yield, concentration, stability, viability, integrity, or function, e.g., a bioenergetic or biological function, for use in therapeutic applications. Accordingly, in one aspect, the invention features a pharmaceutical composition comprising a preparation of isolated chondrisomes and/or mitoparticles, derived from blood or a blood product, and a pharmaceutically acceptable carrier.

Link: freepatentsonline.com/y2020/0306316.html

patents
pharma
164
eLife

Phosphatidylcholines from Pieris brassicae eggs activate an immune response in Arabidopsis

Elia Stahl, Théo Brillatz, Emerson Ferreira Queiroz, Laurence Marcourt, André Schmiesing, Olivier Hilfiker, Isabelle Riezman, Howard Riezman, Jean-Luc Wolfender, Philippe Reymond

Recognition of conserved microbial molecules activates immune responses in plants, a process termed pattern-triggered immunity (PTI). Similarly, insect eggs trigger defenses that impede egg development or attract predators, but information on the nature of egg-associated elicitors is scarce. We performed an unbiased bioactivity-guided fractionation of eggs of the butterfly Pieris brassicae. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry of active fractions led to the identification of phosphatidylcholines (PCs). PCs are released from insect eggs, and they induce salicylic acid and H2O2 accumulation, defense gene expression and cell death in Arabidopsis, all of which constitute a hallmark of PTI. Active PCs contain primarily C16 to C18-fatty acyl chains with various levels of desaturation, suggesting a relatively broad ligand specificity of cell-surface receptor(s). The finding of PCs as egg-associated molecular patterns (EAMPs) illustrates the acute ability of plants to detect conserved immunogenic patterns from their enemies, even from seemingly passive structures such as eggs.

Link: doi.org/10.7554/eLife.60293

publications
cell, insect, other-application
165
Cell Reports

Cell-Type- and Brain-Region-Resolved Mouse Brain Lipidome

Dirk Fitzner, Jakob M Bader, Horst Penkert, Caroline G Bergner, Minhui Su, Marie-Theres Weil, Michal A Surma, Matthias Mann, Christian Klose, Mikael Simons

Gene and protein expression data provide useful resources for understanding brain function, but little is known about the lipid composition of the brain. Here, we perform quantitative shotgun lipidomics, which enables a cell-type-resolved assessment of the mouse brain lipid composition. We quantify around 700 lipid species and evaluate lipid features including fatty acyl chain length, hydroxylation, and number of acyl chain double bonds, thereby identifying cell-type- and brain-region-specific lipid profiles in adult mice, as well as in aged mice, in apolipoprotein-E-deficient mice, in a model of Alzheimer’s disease, and in mice fed different diets. We also integrate lipid with protein expression profiles to predict lipid pathways enriched in specific cell types, such as fatty acid β-oxidation in astrocytes and sphingolipid metabolism in microglia. This resource complements existing brain atlases of gene and protein expression and may be useful for understanding the role of lipids in brain function.

Link: doi.org/10.1016/j.celrep.2020.108132

publications
mouse-rat, diet, cell, neuroscience, model-systems
166
International Journal of Molecular Sciences

Tolerance of Stored Boar Spermatozoa to Autologous Seminal Plasma: A Proteomic and Lipidomic Approach

Lisa Höfner, Anne-Marie Luther, Alessandra Palladini, Thomas Fröhlich, Dagmar Waberski

Long-term exposure of liquid preserved boar spermatozoa to seminal plasma (SP) can cause dramatic sperm injury. This study examined whether boar specificity exists in the sensitivity of spermatozoa to SP and whether correspondent biomarkers can be identified. Consecutive ejaculates (n = 4–5) collected from 19 boars were centrifuged, diluted with a pH-stablising extender with 10% (v/v) autologous SP and evaluated by computer-assisted semen analysis and flow cytometry. Up until 144 h storage, four boars showed consistently high sperm motility, viability and mitochondria activity, and one boar showed consistently low values. Intra-boar variability was high in the other boars. Screening of SP (n = 12 samples) for protein markers using mass spectrometry identified three protein candidates of which the granulin precursor, legumain and AWN were 0.5 to 0.9 log2-fold less abundant (p < 0.05) in SP-resistant compared to SP-sensitive samples. Lipidome analysis by mass spectrometry revealed 568 lipids showing no difference between the SP-groups. The most abundant lipids were cholesterol (42,442 pmol), followed by phosphatidylserine (20,956 pmol) and ether-linked phosphatidylethanolamine (13,039 pmol). In conclusion, three candidate proteins were identified which might be indicative of SP-tolerance of sperm during long-term storage. Noteworthy, a first lipidomic profile of boar SP is presented.

Link: doi.org/10.3390/ijms21186474

publications
other-sample-type, other-organism, other-application
167
PNAS

Human epidermal stem cell differentiation is modulated by specific lipid subspecies

Matteo Vietri Rudan, Ajay Mishra, Christian Klose, Ulrike S Eggert, Fiona M Watt

While the lipids of the outer layers of mammalian epidermis and their contribution to barrier formation have been extensively described, the role of individual lipid species in the onset of keratinocyte differentiation remains unknown. A lipidomic analysis of primary human keratinocytes revealed accumulation of numerous lipid species during suspension-induced differentiation. A small interfering RNA screen of 258 lipid-modifying enzymes identified two genes that on knockdown induced epidermal differentiation: ELOVL1, encoding elongation of very long-chain fatty acids protein 1, and SLC27A1, encoding fatty acid transport protein 1. By intersecting lipidomic datasets from suspension-induced differentiation and knockdown keratinocytes, we pinpointed candidate bioactive lipid subspecies as differentiation regulators. Several of these—ceramides and glucosylceramides—induced differentiation when added to primary keratinocytes in culture. Our results reveal the potential of lipid subspecies to regulate exit from the epidermal stem cell compartment.

Link: doi.org/10.1073/pnas.2011310117

publications
human, cell, dermatology, skin, other-application, multiomics
168
Frontiers in Cell and Developmental Biology

A Quantitative Analysis of Cellular Lipid Compositions During Acute Proteotoxic ER Stress Reveals Specificity in the Production of Asymmetric Lipids

John Reinhard, Carsten Mattes, Kristina Väth, Toni Radanović, Michal A Surma, Christian Klose, Robert Ernst

The unfolded protein response (UPR) is central to endoplasmic reticulum (ER) homeostasis by controlling its size and protein folding capacity. When activated by unfolded proteins in the ER-lumen or aberrant lipid compositions, the UPR adjusts the expression of hundreds of target genes to counteract ER stress. The proteotoxic drugs dithiothreitol (DTT) and tunicamycin (TM) are commonly used to induce misfolding of proteins in the ER and to study the UPR. However, their potential impact on the cellular lipid composition has never been systematically addressed. Here, we report the quantitative, cellular lipid composition of Saccharomyces cerevisiae during acute, proteotoxic stress in both rich and synthetic media. We show that DTT causes rapid remodeling of the lipidome when used in rich medium at growth-inhibitory concentrations, while TM has only a marginal impact on the lipidome under our conditions of cultivation. We formulate recommendations on how to study UPR activation by proteotoxic stress without interferences from a perturbed lipid metabolism. Furthermore, our data suggest an intricate connection between the cellular growth rate, the abundance of the ER, and the metabolism of fatty acids. We show that Saccharomyces cerevisiae can produce asymmetric lipids with two saturated fatty acyl chains differing substantially in length. These observations indicate that the pairing of saturated fatty acyl chains is tightly controlled and suggest an evolutionary conservation of asymmetric lipids and their biosynthetic machineries.

Link: doi.org/10.3389/fcell.2020.00756

publications
cell, yeast, model-systems, organelles, microbiology, other-application
169
Article

Multi resistant bacteria & phospholipids

Henri M Deda

The discovery and description of the first antibiotic compound in 1928 was a milestone in pharma research, and the development of further antibiotics helped modern medicine thrive and flourish. Antibiotics prevent infections from spreading and help the immune system fight off invading pathogens like bacteria. Their wide-spread use comes with a downside: many bacteria evolved strategies to resist antibiotics thus rendering them ineffective. The development of new antibiotics alone is not believed to stop multi resistant bacteria. A new strategy is emerging.

Link: lipotype.com/lipidomics-of-multi-resistant-bacteria

articles
cell, bacterium, pharma, microbiology
170
Article

Lipid-based adjuvants in vaccine development

Henri M Deda, Olga (Olya) Vvedenskaya

Vaccines train the immune system to recognize pathogens. To achieve that, they introduce antigens to the body to trigger an immune response. Vaccine development can count on agents that enhance the impact of the antigens in the human body by triggering a stronger immune reaction with fewer antigen. These vaccine components are called adjuvants, they are the magic sauce of modern vaccines. Adjuvants are added to vaccines to boost their efficiency, but the underlying molecular mechanisms used to be poorly understood.

Link: lipotype.com/lipidomics-in-vaccine-research

articles
mouse-rat, cell, pharma, organelles, other-application
171
Translational Oncology

Mass Spectrometry–Based Lipidomics of Oral Squamous Cell Carcinoma Tissue Reveals Aberrant Cholesterol and Glycerophospholipid Metabolism — A Pilot Study

Amy Dickinson, Mayank Saraswat, Sakari Joenväärä, Rahul Agarwal, Daniel Jyllikoski, Tommy Wilkman, Antti Mäkitie, Suvi Silén

Lipid metabolic reprogramming is one hallmark of cancer. Lipid metabolism is regulated by numerous enzymes, many of which are targeted by several drugs on the market. We aimed to characterize the lipid alterations in oral squamous cell carcinoma (OSCC) as a basis for understanding its lipid metabolism, thus identifying potential therapeutic targets. We compared lipid species, classes, and glycerophospholipid (GPL) fatty acid species between paired tumor tissue and healthy oral tongue mucosa samples from 10 OSCC patients using a QExactive mass spectrometer. After filtering the 1370 lipid species identified, we analyzed 349 species: 71 were significantly increased in OSCC. The GPL metabolism pathway was most represented by the lipids differing in OSCC (P = .005). Cholesterol and the GPLs phosphatidylcholines, phosphatidylethanolamines, and phosphatidylinositols were most significantly increased in OSCC tissue (FC 1.8, 2.0, 2.1, and 2.3 and, P = .003, P = .005, P = .002, P = .007). In conclusion, we have demonstrated a shift in the lipid metabolism in these OSCC samples by characterizing the detailed landscape. Predominantly, cholesterol and GPL metabolism were altered, suggesting that interactions with sterol regulatory binding proteins may be involved. The FA composition changes of the GPLs suggest increased de novo lipogenesis.

Link: doi.org/10.1016/j.tranon.2020.100807

publications
human, oncology, tissue-organ, clinical-research
172
Journal of Cellular and Molecular Medicine

Targeting lipid droplet lysophosphatidylcholine for cisplatin chemotherapy

Lumin Chen, Wen-Lung Ma, Wei-Chung Cheng, Juan-Cheng Yang, Hsiao-Ching Wang, Yu‐Ting Su, Azaj Ahmad, Yao‐Ching Hung, Wei‐Chun Chang

This study aims to explore lipidic mechanism towards low‐density lipoprotein receptor (LDLR)‐mediated platinum chemotherapy resistance. By using the lipid profiling technology, LDLR knockdown was found to increase lysosomal lipids and decrease membranous lipid levels in EOC cells. LDLR knockdown also down‐regulated ether‐linked phosphatidylethanolamine (PE‐O, lysosomes or peroxisomes) and up‐regulated lysophosphatidylcholine [LPC, lipid droplet (LD)]. This implies that the manner of using Lands cycle (conversion of lysophospholipids) for LDs might affect cisplatin sensitivity. The bioinformatics analyses illustrated that LDLR‐related lipid entry into LD, rather than an endogenous lipid resource (eg Kennedy pathway), controls the EOC prognosis of platinum chemotherapy patients. Moreover, LDLR knockdown increased the number of platinum‐DNA adducts and reduced the LD platinum amount. By using a manufactured LPC‐liposome‐cisplatin (LLC) drug, the number of platinum‐DNA adducts increased significantly in LLC‐treated insensitive cells. Moreover, the cisplatin content in LDs increased upon LLC treatment. Furthermore, lipid profiles of 22 carcinoma cells with differential cisplatin sensitivity (9 sensitive vs 13 insensitive) were acquired. These profiles revealed low storage lipid levels in insensitive cells. This result recommends that LD lipidome might be a common pathway in multiple cancers for platinum sensitivity in EOC. Finally, LLC suppressed both cisplatin‐insensitive human carcinoma cell training and testing sets. Thus, LDLR‐platinum insensitivity can be due to a defective Lands cycle that hinders LPC production in LDs. Using lipidome assessment with the newly formulated LLC can be a promising cancer chemotherapy method.

Link: doi.org/10.1111/jcmm.15218

publications
human, cell, oncology, pharma
173
Brain

Excess Lipin enzyme activity contributes to TOR1A recessive disease and DYT-TOR1A dystonia

Ana Cascalho, Joyce Foroozandeh, Lise Hennebel, Jef Swerts, Christine Klein, Stef Rous, Beatriz Dominguez Gonzalez, Antonio Pisani, Maria Meringolo, Sandra F Gallego, Patrik Verstreken, Philip Seibler, Rose E Goodchild

TOR1A/TorsinA mutations cause two incurable diseases: a recessive congenital syndrome that can be lethal, and a dominantly-inherited childhood-onset dystonia (DYT-TOR1A). TorsinA has been linked to phosphatidic acid lipid metabolism in Drosophila melanogaster. Here we evaluate the role of phosphatidic acid phosphatase (PAP) enzymes in TOR1A diseases using induced pluripotent stem cell-derived neurons from patients, and mouse models of recessive Tor1a disease. We find that Lipin PAP enzyme activity is abnormally elevated in human DYT-TOR1A dystonia patient cells and in the brains of four different Tor1a mouse models. Its severity also correlated with the dosage of Tor1a/TOR1A mutation. We assessed the role of excess Lipin activity in the neurological dysfunction of Tor1a disease mouse models by interbreeding these with Lpin1 knock-out mice. Genetic reduction of Lpin1 improved the survival of recessive Tor1a disease-model mice, alongside suppressing neurodegeneration, motor dysfunction, and nuclear membrane pathology. These data establish that TOR1A disease mutations cause abnormal phosphatidic acid metabolism, and suggest that approaches that suppress Lipin PAP enzyme activity could be therapeutically useful for TOR1A diseases.

Link: doi.org/10.1093/brain/awaa139

publications
mouse-rat, neuroscience, tissue-organ
174
MDPI Cells

Phosphoinositide Profile of the Mouse Retina

Stella Finkelstein, Sidney M Gospe III, Kai Schuhmann, Andrej Shevchenko, Vadim Y Arshavsky, Ekaterina S Lobanova

Phosphoinositides are known to play multiple roles in eukaryotic cells. Although dysregulation of phosphoinositide metabolism in the retina has been reported to cause visual dysfunction in animal models and human patients, our understanding of the phosphoinositide composition of the retina is limited. Here, we report a characterization of the phosphoinositide profile of the mouse retina and an analysis of the subcellular localization of major phosphorylated phosphoinositide forms in light-sensitive photoreceptor neurons. Using chromatography of deacylated phosphatidylinositol headgroups, we established PI(4,5)P2 and PI(4)P as two major phosphorylated phosphoinositides in the retina. Using high-resolution mass spectrometry, we revealed 18:0/20:4 and 16:0/20:4 as major fatty-acyl chains of retinal phosphoinositides. Finally, analysis of fluorescent phosphoinositide sensors in rod photoreceptors demonstrated distinct subcellular distribution patterns of major phosphoinositides. The PI(4,5)P2 reporter was enriched in the inner segments and synapses, but was barely detected in the light-sensitive outer segments. The PI(4)P reporter was mostly found in the outer and inner segments and the areas around nuclei, but to a lesser degree in the synaptic region. These findings provide support for future mechanistic studies defining the biological significance of major mono- (PI(4)P) and bisphosphate (PI(4,5)P2) phosphatidylinositols in photoreceptor biology and retinal health.

Link: doi.org/10.3390/cells9061417

publications
mouse-rat, cell, neuroscience, model-systems
175
Scientific Reports

Avicin G is a potent sphingomyelinase inhibitor and blocks oncogenic K- and H-Ras signaling

Christian M Garrido, Karen M Henkels, Kristen M Rehl, Hong Liang, Yong Zhou, Jordan U Gutterman, Kwang-Jin Cho

K-Ras must interact primarily with the plasma membrane (PM) for its biological activity. Therefore, disrupting K-Ras PM interaction is a tractable approach to block oncogenic K-Ras activity. Here, we found that avicin G, a family of natural plant-derived triterpenoid saponins from Acacia victoriae, mislocalizes K-Ras from the PM and disrupts PM spatial organization of oncogenic K-Ras and H-Ras by depleting phosphatidylserine (PtdSer) and cholesterol contents, respectively, at the inner PM leaflet. Avicin G also inhibits oncogenic K- and H-Ras signal output and the growth of K-Ras-addicted pancreatic and non-small cell lung cancer cells. We further identified that avicin G perturbs lysosomal activity, and disrupts cellular localization and activity of neutral and acid sphingomyelinases (SMases), resulting in elevated cellular sphingomyelin (SM) levels and altered SM distribution. Moreover, we show that neutral SMase inhibitors disrupt the PM localization of K-Ras and PtdSer and oncogenic K-Ras signaling. In sum, this study identifies avicin G as a new potent anti-Ras inhibitor, and suggests that neutral SMase can be a tractable target for developing anti-K-Ras therapeutics.

Link: doi.org/10.1038/s41598-020-65882-5

publications
cell, oncology, other-organism, pharma, organelles, other-application
176
The EMBO Journal

Dysfunctional oxidative phosphorylation shunts branched‐chain amino acid catabolism onto lipogenesis in skeletal muscle

Cristina Sánchez‐González, Cristina Nuevo‐Tapioles, Juan C Herrero Martín, Marta P Pereira, Sandra Serrano Sanz, Ana Ramírez de Molina, José M Cuezva, Laura Formentini

It is controversial whether mitochondrial dysfunction in skeletal muscle is the cause or consequence of metabolic disorders. Herein, we demonstrate that in vivo inhibition of mitochondrial ATP synthase in muscle alters whole‐body lipid homeostasis. Mice with restrained mitochondrial ATP synthase activity presented intrafiber lipid droplets, dysregulation of acyl‐glycerides, and higher visceral adipose tissue deposits, poising these animals to insulin resistance. This mitochondrial energy crisis increases lactate production, prevents fatty acid β‐oxidation, and forces the catabolism of branched‐chain amino acids (BCAA) to provide acetyl‐CoA for de novo lipid synthesis. In turn, muscle accumulation of acetyl‐CoA leads to acetylation‐dependent inhibition of mitochondrial respiratory complex II enhancing oxidative phosphorylation dysfunction which results in augmented ROS production. By screening 702 FDA‐approved drugs, we identified edaravone as a potent mitochondrial antioxidant and enhancer. Edaravone administration restored ROS and lipid homeostasis in skeletal muscle and reinstated insulin sensitivity. Our results suggest that muscular mitochondrial perturbations are causative of metabolic disorders and that edaravone is a potential treatment for these diseases.

Link: doi.org/10.15252/embj.2019103812

publications
metabolic-disorders, mouse-rat, cell, tissue-organ, pharma
177