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Lipidomics for studying metabolism

Lipidomics uses the principles of analytical chemistry to reveal the total lipid content and composition in a cell. In this Review, Xianlin Han provides an overview of lipidomics as applied to the study of metabolic pathways and how this technique can help in the understanding of metabolic diseases.

Xianlin Han
Reviews29 Jul 2016
Nature Reviews Endocrinology

Volume: 12, P: 668-679
GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau

The relationship between lipid dyshomeostasis and tau pathology in FTLD and AD remains unclear. Here, the authors demonstrate that GRAMD1B contributes to lipid dyshomeostasis, autophagy impairment, and tau hyperphosphorylation in neurons.

Diana Acosta Ingram
Emir Turkes
Hongjun Fu
ResearchOpen Access09 Apr 2025
Nature Communications

Volume: 16, P: 1-24
Author Correction: Lipocalin 2 regulates mitochondrial phospholipidome remodeling, dynamics, and function in brown adipose tissue in male mice

Hongming Su
Hong Guo
Xiaoli Chen
Amendments and CorrectionsOpen Access12 Dec 2023
Nature Communications

Volume: 14, P: 1-2
Relic2Contour: Salient contour detection in relics using semi-supervised generative adversarial networks based on knowledge sharing

Zhe Yu
Qingqing Kang
Xianlin Peng
ResearchOpen Access24 Mar 2025
npj Heritage Science

Volume: 13, P: 1-17
Publisher Correction: Dynamic changes to lipid mediators support transitions among macrophage subtypes during muscle regeneration

Nikolas Giannakis
Brian E. Sansbury
Laszlo Nagy
Amendments and Corrections02 May 2019
Nature Immunology

Volume: 20, P: 765-767
Quality control requirements for the correct annotation of lipidomics data

Harald C. Köfeler
Thomas O. Eichmann
Kim Ekroos
ResearchOpen Access06 Aug 2021
Nature Communications

Volume: 12, P: 1-4
PNPLA3 is a triglyceride lipase that mobilizes polyunsaturated fatty acids to facilitate hepatic secretion of large-sized very low-density lipoprotein

The PNPLA3 gene is associated with fatty liver disease. Here, the authors define a role for PNPLA3 as a polyunsaturated triglyceride lipase that maintains the balance between hepatic triglyceride storage and secretion.

Scott M. Johnson
Hanmei Bao
Jun Liu
ResearchOpen Access06 Jun 2024
Nature Communications

Volume: 15, P: 1-18
Reduced progranulin increases tau and α-synuclein inclusions and alters mouse tauopathy phenotypes via glucocerebrosidase

Neurodegenerative diseases often co-accumulate several disease-associated proteins. Here, the authors show that reduction of progranulin, a protein associated with TDP-43, also increases accumulation of tau and a-synuclein via glucocerebrosidase.

Hideyuki Takahashi
Sanaea Bhagwagar
Stephen M. Strittmatter
ResearchOpen Access16 Feb 2024
Nature Communications

Volume: 15, P: 1-23
Deep learning HRNet FCN for blood vessel identification in laparoscopic pancreatic surgery

Jile Shi
Ruohan Cui
Wenming Wu
ResearchOpen Access01 May 2025
npj Digital Medicine

Volume: 8, P: 1-8
De novo lipogenesis fuels adipocyte autophagosome and lysosome membrane dynamics

The function of de novo lipogenesis (DNL) in adipocytes has been a mystery as it contributes little to fat storage in these cells. Here, the authors show that DNL is a critical source of fatty acids for membrane-expanding processes like autophagy.

Leslie A. Rowland
Adilson Guilherme
Michael P. Czech
ResearchOpen Access13 Mar 2023
Nature Communications

Volume: 14, P: 1-14
Controllable field-free switching of perpendicular magnetization through bulk spin-orbit torque in symmetry-broken ferromagnetic films

A major challenge of spintronics is achieving magnetic field free electrical control of magnetisation. Here, Xie et al. achieve perpendicular magnetisation switching in a CoPt alloy, breaking inversion symmetry by varying the composition of the alloy in the growth direction.

Xuejie Xie
Xiaonan Zhao
Shishen Yan
ResearchOpen Access30 Apr 2021
Nature Communications

Volume: 12, P: 1-10
Lipocalin 2 regulates mitochondrial phospholipidome remodeling, dynamics, and function in brown adipose tissue in male mice

Mitochondrial function is essential for energy metabolism in brown adipocytes. Here, the authors show that LCN2 plays a critical role as a phosphatidic acid binding protein in phospholipid acyl chain remodeling and mitochondrial bioenergetics, influencing signaling pathway activation.

Hongming Su
Hong Guo
Xiaoli Chen
ResearchOpen Access23 Oct 2023
Nature Communications

Volume: 14, P: 1-19
Comprehensive genetic analysis of the human lipidome identifies loci associated with lipid homeostasis with links to coronary artery disease

Dysregulation of lipid metabolism is associated with coronary artery disease (CAD). Here, the authors perform GWAS of the serum lipidome to identify variants associated with lipid species that are putatively in the mechanistic pathway to CAD.

Gemma Cadby
Corey Giles
Eric K. Moses
ResearchOpen Access06 Jun 2022
Nature Communications

Volume: 13, P: 1-17
RORγt-Raftlin1 complex regulates the pathogenicity of Th17 cells and colonic inflammation

IL-17 secreting Th17 cells have established roles in numerous immune-pathologies but paradoxically are required homeostatically in the maintenance of the intestinal barrier. Here the authors establish Raftlin-1 in the recruitment of phospholipids that are linked to the emergence of pathogenic Th17 cells in animal models of bowel inflammation.

Amir Kumar Singh
Ritesh Kumar
K. Venuprasad
ResearchOpen Access17 Aug 2023
Nature Communications

Volume: 14, P: 1-15
Concordant peripheral lipidome signatures in two large clinical studies of Alzheimer’s disease

The onset and pathology of Alzheimer’s disease (AD) is associated with changes to lipid metabolism. Here, the authors analysed 569 lipids from 32 classes and subclasses in two independent patient cohorts to identify key lipid pathways to link the plasma lipidome with AD and the future onset of AD.

Kevin Huynh
Wei Ling Florence Lim
Peter J. Meikle
ResearchOpen Access10 Nov 2020
Nature Communications

Volume: 11, P: 1-11
Phospholipids of APOE lipoproteins activate microglia in an isoform-specific manner in preclinical models of Alzheimer’s disease

Microglia can clear amyloid plaques in Alzheimer’s disease. Here, the authors show that specific isoforms of the phospholipid forming APOE lipoproteins activate microglia in pre-clinical mouse models of Alzheimer’s disease.

Nicholas F. Fitz
Kyong Nyon Nam
Radosveta Koldamova
ResearchOpen Access07 Jun 2021
Nature Communications

Volume: 12, P: 1-18
High-fat diet-induced upregulation of exosomal phosphatidylcholine contributes to insulin resistance

High-fat diet plays a role in development of insulin resistance. Here, the authors report a mechanism that underlies the development of diet induced insulin resistance through the activation of an aryl hydrocarbon receptor mediated signalling pathway in the liver by faecal exosomes derived from intestinal cells.

Anil Kumar
Kumaran Sundaram
Huang-Ge Zhang
ResearchOpen Access11 Jan 2021
Nature Communications

Volume: 12, P: 1-21
Phosphatidylethanolamine made in the inner mitochondrial membrane is essential for yeast cytochrome bc₁ complex function

Phosphatidylethanolamine (PE) is synthesized by four separate pathways, although surprisingly, perturbing mitochondrial PE synthesis compromises mitochondrial function. Here, the authors show that mitochondrial PE synthesis is required for Complex III function and challenge PE trafficking dogma.

Elizabeth Calzada
Erica Avery
Steven M. Claypool
ResearchOpen Access29 Mar 2019
Nature Communications

Volume: 10, P: 1-17
Sex and APOE ε4 genotype modify the Alzheimer’s disease serum metabolome

Sex and the APOE ε4 genotype are important risk factors for late-onset Alzheimer’s disease. In the current study, the authors investigate how sex and APOE ε4 genotype modify the association between Alzheimer’s disease biomarkers and metabolites in serum.

Matthias Arnold
Kwangsik Nho
Gabi Kastenmüller
ResearchOpen Access02 Mar 2020
Nature Communications

Volume: 11, P: 1-12
Introducing the Lipidomics Minimal Reporting Checklist

The rapid increase in lipidomic data has triggered a community-based movement to develop guidelines and minimum requirements for generating, reporting and publishing lipidomic data. The creation of a dynamic checklist summarizing key details of lipidomic analyses using a common language has the potential to harmonize the field by improving both traceability and reproducibility.

Jeffrey G. McDonald
Christer S. Ejsing
Kim Ekroos
Comments & Opinion08 Aug 2022
Nature Metabolism

Volume: 4, P: 1086-1088
The emerging role of lipidomics in prediction of diseases

A recent paper published in PLoS Biology reported the application of lipidomics in predicting the incidence of type 2 diabetes mellitus and cardiovascular diseases in a population cohort. The study demonstrates the role of lipidomics in prediction of diseases and translational research, which could herald the beginning of an era of quantitative lipidomics.

Xianlin Han
News & Views07 Apr 2022
Nature Reviews Endocrinology

Volume: 18, P: 335-336
Consuming a modified Mediterranean ketogenic diet reverses the peripheral lipid signature of Alzheimer’s disease in humans

Neth, Huynh et al. evaluate whether consuming a modified Mediterranean ketogenic diet alters parts of the plasma lipidome associated with development of Alzheimer’s disease (AD). Consuming the ketogenic diet alters the plasma lipidome, with changes inversely linked to Alzheimer’s disease (AD) biomarkers and lipidomic signatures.

Bryan J. Neth
Kevin Huynh
Rima Kaddurah-Daouk
ResearchOpen Access09 Jan 2025
Communications Medicine

Volume: 5, P: 1-15
Fasting induces a subcutaneous-to-visceral fat switch mediated by microRNA-149-3p and suppression of PRDM16

Visceral adiposity is associated with metabolic diseases, whereas subcutaneous adiposity is comparatively benign. Here, the authors report that subcutaneous adipose tissue adopts visceral-like characteristics in response to prolonged fasting, and show this is mediated by miR-149-3p and its target, PRDM16.

Hanying Ding
Shasha Zheng
Xiaohong Jiang
ResearchOpen Access31 May 2016
Nature Communications

Volume: 7, P: 1-17
Dynamic changes to lipid mediators support transitions among macrophage subtypes during muscle regeneration

Muscle damage elicits a sterile immune response that facilitates complete regeneration. Nagy and colleagues map the mediator lipidome during the transition from inflammation to resolution in skeletal muscle injury.

Nikolas Giannakis
Brian E. Sansbury
Laszlo Nagy
Research01 Apr 2019
Nature Immunology

Volume: 20, P: 626-636
Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression

Siamak MahmoudianDehkordi
Ahmed T. Ahmed
Ranga Krishnan
ResearchOpen Access02 Mar 2021
Translational Psychiatry

Volume: 11, P: 1-14
Lysosomal TMEM106B interacts with galactosylceramidase to regulate myelin lipid metabolism

Unbiased lipidomic and proteomic analyses reveal that TMEM106B, an endolysosomal protein associated with many neurological disorders including frontotemporal dementia, regulates myelin lipid metabolism by interacting with galactosylceramidase.

Hideyuki Takahashi
Azucena Perez-Canamas
Stephen M. Strittmatter
ResearchOpen Access05 Sept 2024
Communications Biology

Volume: 7, P: 1-11
The metabolome-wide signature of major depressive disorder

Rick Jansen
Yuri Milaneschi
Brenda W. J. H. Penninx
Research07 Jun 2024
Molecular Psychiatry

Volume: 29, P: 3722-3733
Restoring mitochondrial cardiolipin homeostasis reduces cell death and promotes recovery after spinal cord injury

Nai-Kui Liu
Ling-Xiao Deng
Xiao-Ming Xu
ResearchOpen Access20 Dec 2022
Cell Death & Disease

Volume: 13, P: 1-16
ABCA7 deficiency causes neuronal dysregulation by altering mitochondrial lipid metabolism

Keiji Kawatani
Marie-Louise Holm
Takahisa Kanekiyo
ResearchOpen Access22 Dec 2023
Molecular Psychiatry

Volume: 29, P: 809-819
Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer’s disease

Complementary multi-omics approach, in silico metabolic flux, and neuroimaging analyses link the sphingolipid pathway to Alzheimer’s disease pathogenesis with therapeutic targets validated using behavioral assessments in amyloidogenic APP/PS1 mice.

Priyanka Baloni
Matthias Arnold
Rima Kaddurah-Daouk
ResearchOpen Access08 Oct 2022
Communications Biology

Volume: 5, P: 1-13
The cardiolipin-binding peptide elamipretide mitigates fragmentation of cristae networks following cardiac ischemia reperfusion in rats

Allen and Pennington et al. show that the cardiolipin-binding peptide elamipretide mitigates disease-induced fragmentation of cristae networks following cardiac ischemia reperfusion in rats. This study suggests that elamipretide targets mitochondrial membranes to sustain cristae networks, improving their bioenergetic function.

Mitchell E. Allen
Edward Ross Pennington
Saame Raza Shaikh
ResearchOpen Access17 Jul 2020
Communications Biology

Volume: 3, P: 1-12
Peripheral serum metabolomic profiles inform central cognitive impairment

Jingye Wang
Runmin Wei
Wei Jia
ResearchOpen Access20 Aug 2020
Scientific Reports

Volume: 10, P: 1-14
Effect of high fat diet on phenotype, brain transcriptome and lipidome in Alzheimer’s model mice

Kyong Nyon Nam
Anais Mounier
Radosveta Koldamova
ResearchOpen Access27 Jun 2017
Scientific Reports

Volume: 7, P: 1-13
Cytochrome b₅ reductase and the control of lipid metabolism and healthspan

Alejandro Martin-Montalvo
Yaning Sun
Rafael de Cabo
ResearchOpen Access12 May 2016
npj Aging and Mechanisms of Disease

Volume: 2, P: 1-12
Natural hazard triggered technological risks in the Yangtze River Economic Belt, China

Yue Gao
Guozhi Cao
Zongwei Ma
ResearchOpen Access05 Jul 2021
Scientific Reports

Volume: 11, P: 1-14
Peripheral inflammation is associated with brain atrophy and cognitive decline linked to mild cognitive impairment and Alzheimer’s disease

Nuanyi Liang
Kwangsik Nho
Frank Sacks
ResearchOpen Access29 Jul 2024
Scientific Reports

Volume: 14, P: 1-14
Dopamine D2 receptor restricts astrocytic NLRP3 inflammasome activation via enhancing the interaction of β-arrestin2 and NLRP3

Jialei Zhu
Zhaoli Hu
Gang Hu
Research21 May 2018
Cell Death & Differentiation

Volume: 25, P: 2037-2049
Matrine inhibits itching by lowering the activity of calcium channel

Xiao Geng
Hao Shi
Zongxiang Tang
ResearchOpen Access27 Jul 2018
Scientific Reports

Volume: 8, P: 1-13
Bile acids targeted metabolomics and medication classification data in the ADNI1 and ADNIGO/2 cohorts

Lisa St. John-Williams
Siamak Mahmoudiandehkordi
Rima Kaddurah-Daouk
ResearchOpen Access17 Oct 2019
Scientific Data

Volume: 6, P: 1-8
Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature

Christopher R. Brydges
Oliver Fiehn
Piero Rinaldo
ResearchOpen Access25 Oct 2021
Scientific Reports

Volume: 11, P: 1-14
M6A RNA methylation in biliary tract cancer: the function roles and potential therapeutic implications

Xuesong Bai
Jianhao Huang
Xiaodong He
ReviewsOpen Access16 Feb 2024
Cell Death Discovery

Volume: 10, P: 1-11
A blood-based signature of cerebrospinal fluid Aβ_1–42 status

Benjamin Goudey
Bowen J. Fung
Brenda Plassman
ResearchOpen Access11 Mar 2019
Scientific Reports

Volume: 9, P: 1-12
Targeted metabolomics and medication classification data from participants in the ADNI1 cohort

Lisa St John-Williams
Colette Blach
Rima Kaddurah-Daouk
ResearchOpen Access17 Oct 2017
Scientific Data

Volume: 4, P: 1-11

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