Publication-Ye Lab - Laboratory of phospholipid biology and methionine metabolism

2026

42. Adaptive regulation of glycerophospholipid metabolism

Zhang T*, Wang Y*, Ye C#

Journal of Cell Science, 139(3):jcs264300

2025

41. Dietary methionine deprivation enhances renal resilience against ischemia-reperfusion injury through modulation of glucose oxidation

Peng X*, Xie Y*, Pan H, Ma T, Chen J, Jiang H#, Ye C#

Communications Biology, doi: 10.1038/s42003-025-09447-0.

微信图片_20260105214257_7_141.jpg Highlights

• Multi omics profiling identifies S-adenosylmethionine as a central dysregulated node

• The kidney is a major S-adenosylmethionine consuming organ

• Short term methionine deprivation diet for 7 days markedly mitigates renal IRI

• Methionine deprivation enhances PDH dependent pyruvate oxidation and TCA cycle flux in

IRI kidneys, and pharmacologic PDH activation recapitulates renal protection

40. Diet-induced RKIP downregulation disrupts PC/PE-ER homeostasis to drive MASLD

Li M, Ou Q, Qin Q, Chen J, Yang S, Zhao J, Meng H, Li X, Xu P, Ye C, Wang X

Nature Communications, 16(1):11092.

39. pORF-driven biogenesis of lipid droplets facilitates HEV infectivity

Xu LD, Zhang F, Miao C, Yu X, Zhu Y, Zhang MD, Liu S, Sridhar S, Sun Q, Neculai D, Zhang Q, Shen L, Liang T#, Ye C#, Huang YW#, Xu P#

Cell Reports, 44(10):116406.

38. Mevalonate metabolites boost aged oocyte quality through prenylation of small GTPases

Liu C, Zhang H, Mao J, Zhang S, Tian X, Zhu Y, Wang C, Fang J, Pan H, Kang N, Zhang Y, Zhou J, Zhen X, Yan G, Li C, Hu Y, Ye C, Xie R, So C, Sun H, Ding L

Nature Aging. 5(10), 2022-2038.

37. The roles of NHEJ and TLS pathways in genomic alterations and phenotypic evolution in the yeast Yarrowia lipolytica

Yan C, Wang YK, Xiong YR, Zhou XQ, Fang YC, Nie RT, Ye C, Zhang K, Zheng DQ

Applied Microbiology and Biotechnology, 109(1):183.

36. RIPK4 promotes epidermal differentiation through phase separation and activation of LATS1/2

Cao X, Lu Z, Fang Y, Huang F, Tang M, Wu B, Gao L, Zhao Y, Zhang T, Zhu Z, Si Y, Guo X, Liu J, Ye C, Song H, Lu H, Feng XH, Shen L, Li L, Zhao B

Developmental Cell, 60(20):2761-2776.e11.

35. An adaptive organelle triad houses lipid droplets for dynamic regulation

Qiu H*, Miao C*, Ye C#

Cell Reports, 44(6): 115813

CR 2025.png Highlights

• Lactate induces severe metabolic stress and vacuole deformation during nutrient deprivation

• Organelle triad: LDs encircling a nucleus, all enclosed in an enlarged vacuole

• Membrane tethers (NVJ and vCLIP) facilitate organelle triad formation

• This structure promotes efficient LD utilization and cellular adaptation

34. Temporal oscillation of phospholipids promotes metabolic efficiency

Yang S*, Wang Y*, Huang S, Zhang T, Xu P, Jiang C, Ye C#

Nature Chemical Biololgy, 21(10):1599-1610.

NCB ys.png Highlights

• Phospholipid levels oscillate temporally throughout the yeast metabolic cycle and cell division cycle

• The systematic segregation of phospholipid species over time corresponds logically with their physical properties

• The oscillatory rhythms in PE and PC require triacylglycerol as a lipid reservoir, with PI and PS synthesized primarily de novo

• The transcriptional regulation of metabolic enzymes in biosynthesis ensures phospholipid oscillations, ultimately promoting metabolic efficiency

33. Phospholipid biosynthesis: An unforeseen modulator of nuclear metabolism

Qiu H and Ye C#

Biology of the Cell, 117(3):e70002.

32. Zebrafish leg1a and leg1b double null mutant accumulates lipids in the liver

Wang J, Xie A, Fang W, Zhu H, Ye C, Peng J

Biochemical and Biophysical Research Communications. 751:151418.

2024

31. Lysosomal catabolic activity promotes the exit of murine totipotent 2-cell state by silencing early-embryonic retrotransposons

Wu H, Cao R, Wen X, Fan J, Wang Y, Hu H, Ji S, Zhang Y, Ye C, Xie W, Zhang J, Xu H, Fu X

Developmental Cell, 60(4):512-523.e7.

30. Ginsenoside Rg3 restores mitochondrial cardiolipin homeostasis via GRB2 to prevent Parkinson's disease

Qi LF, Liu S, Fang Q, Qian C, Peng C, Liu Y, Yang P, Wu P, Shan L, Cui Q, Hua Q, Yang S, Ye C, Yang W, Li P, Xu X

Advanced Science, 11(39):e2403058.

29. Placental and fetal enrichment of microplastics from disposable paper cups: Implications for metabolic and reproductive health druing pregnancy

Chen Q, Peng C, Xie R, Xu H, Su Z, Yilihan G, Wei X, Yang S, Shen Y, Ye C, Jiang C

Journal of Hazardours Materials, 478:135527.

28. Phospholipid biosynthesis modulates nucleotide metabolism and reductive capacity

Zhu Y*, Tong X*, Xue J*, Qiu H, Zheng D, Zheng DQ, Tu ZC, Ye C#

Nature Chemical Biololgy, 21 (1).

Highlights

• Deficiencies in Kennedy pathway for phospholipid synthesis limit nucleotide salvage while promoting de novo synthesis

• Kennedy pathway deficiencies elevate antioxidant levels, such as NADPH and glutathione, via the pentose phosphate pathway

• The activity of the Kennedy pathway is sensitive to choline availability and oxidative stress

• Attenuation of the Kennedy pathway during aging enhances antioxidative defense

27. The role of lipoylation in mitochondrial adaptation to methionine restriction

Xue J and Ye C#

BioEssays, 46(6):e2300218.

26. Low-input lipidomics reveals lipid metabolism remodeling during early mammalian embryo development

Zhang L, Zhao J, Lam SM, Chen L, Gao Y, Wang W, Xu Y, Tan T, Yu H, Zhang M, Liao X, Wu M, Zhang T, Huang J, Li B, Zhou QD, Shen N, Lee HJ, Ye C, Li D, Shui G, Zhang J

Nature Cell Biology, 26(2):278-293.

25. Innate immunity sensing of lysosomal dysfunction drives multiple lysosomal storage disorders

Wang A, Chen C, Mei C, Liu S, Xiang C, Fang W, Zhang F, Xu Y, Chen S, Zhang Q, Bai X, Lin A, Neculai D, Xia B, Ye C, Zou J, Liang T, Feng XH, Li X, Shen C, Xu P

Nature Cell Biololgy, 26(2):219-234.

24. Ethanolamine as a biomarker and biomarker-based therapy for diabetic retinopathy in glucose-well-controlled diabetic patients

Hu G, Gu L, Wang R, Jian Q, Lv K, Xia M, Lai M, Shen T, Hu J, Yang S, Ye C, Zhang X, Wang Y, Xu X, Zhang F

Science Bulletin, 69(12):1920-1935.

23. MAPK1 mediates MAM disruption and mitochondrial dysfunction in diabetic kidney disease via the PACS-2-dependent mechanism

Liu S, Han S, Wang C, Chen H, Xu Q, Feng S, Wang Y, Yao J, Zhou Q, Tang X, Lin L, Hu L, Davidson AJ, Yang B, Ye C, Yang F, Mao J, Tong C, Chen J, Jiang H

International Journal of Biological Sciences, 20(2):569-584.

2023

22. Methionine restriction constrains lipoylation and activates mitochondria for nitrogenic synthesis of amino acids

Fang W*, Jiang L*, Zhu Y*, Yang S, Qiu H, Cheng J, Liang Q, Tu ZC, Ye C#

Nature Communications, 14:2504.

Highlights

• Methionine restriction adapts bioenergetic mitochondria to prioritize nitrogenic anabolism

• Decreases in cellular S-adenosylmethionine constrain lipoate metabolism

• Lipoylation deficiency leads to incomplete glucose oxidation within the TCA cycle

• The exit of acetyl-CoA and α-ketoglutarate from TCA cycle promotes arginine synthesis

21. Spatial sterol metabolism unveiled by stimulated Raman imaging

Zhang Y*, Zhou Y*, Fang W*, Zhu H, Cao W, Ye C#, Zhang D#, Lee HJ#

Frontiers in Chemistry, 11:1166313.

2022

20. Energy sensor AMPK gamma regulates translation via phosphatase PPP6C independent of AMPK alpha

Zhou Q, Hao B, Cao X, Gao L, Yu Z, Zhao Y, Zhu M, Zhong G, Chi F, Dai X, Mao J, Zhu Y, Rong P, Chen L, Bai X, Ye C, Chen S, Liang T, Li L, Feng XH, Tan M, Zhao B

Molecular Cell, 82(24):4700-4711.

19. Protocol for rapid and accurate quantification of phospholipids using LC-MS

Yang S, Xue J, Ye C#

STAR Protocols, 3(4):101769.

18. FUNDC2 promotes liver tumorigenesis by inhibiting MFN1-mediated mitochondrial fusion

Li S*, Han S*, Zhang Q, Zhu Y, Zhang H, Wang J, Zhao Y, Zhao J, Su L, Li L, Zhou D, Ye C, Feng XH, Liang T, Zhao B

Nature Communications, 13(1):3486.

17. Serum Metabolomics Benefits Discrimination Kidney Disease Development in Type 2 Diabetes Patients

Peng X, Wang X, Shao X, Wang Y, Feng S, Wang C, Ye C, Chen J, Jiang H

Frontiers in Medicine, 9:819311.

16. Reciprocal regulation of phosphatidylcholine synthesis and H3K36 methylation programs metabolic adaptation

Fang W*, Zhu Y*, Yang S, Tong X, Ye C#

Cell Reports, 39(2):11067

Highlights

• H3K36me deficiency sensitizes respiring cells to loss of viability under starvation

• Loss of H3K36me leads to membrane defects with aberrant phospholipid compositions

• The methyl sink function for H3K36 affects phospholipid and pyrimidine metabolism

• Rewiring phosphatidylcholine synthesis necessitates metabolic coordination

15. Glutamine synthetase licenses APC/C-mediated mitotic progression to drive cell growth

Zhao JS#, Shi S, Qu HY, Keckesova Z, Cao ZJ, Yang LX, Yu X, Feng L, Shi Z, Krakowiak J, Mao RY, Shen YT, Fan YM, Fu TM, Ye C, Xu D, Gao X, You J, Li W, Liang T#, Lu Z#, Feng YX#

Nature Metabolism, 4(2):239-253.

2021

14. Multiomics analyses reveal a critical role of selenium in controlling T cell differentiation in Crohn's disease

Huang LJ, Mao XT, Li YY, Liu DD, Fan KQ, Liu RB, Wu TT, Wang HL, Zhang Y, Yang B, Ye C, Zhong JY, Chai RJ, Cao Q, Jin J

Immunity, 54(8):1728-1744.

13. Inhibition of Syk promotes chemical reprogramming of fibroblasts via metabolic rewiring and H2S production

Wang W, Ren S, Lu Y, Chen X, Qu J, Ma X, Deng Q, Hu Z, Jin Y, Zhou Z, Ge W, Zhu Y, Yang N, Li Q, Pu J, Chen G, Ye C, Wang H, Zhao X, Liu Z, Zhu S

The EMBO Journal, 40 (11) e106771.

2020

12. Cardiolipin-deficient cells have decreased levels of the iron-sulfur biogenesis protein frataxin

Li Y, Lou W, Grevel A, Böttinger L, Liang Z, Ji J, Patil VA, Liu J, Ye C, Hüttemann M, Becker T, Greenberg ML

Journal of Biological Chemistry, 295(33):11928-11937.

11. Methyl-metabolite depletion elicits adaptive responses to support heterochromatin stability and epigenetic persistence

Haws SA, Yu D, Ye C, Wille CK, Nguyen LC, Krautkramer KA, Tomasiewicz JL, Yang SE, Miller BR, LiuWH, Igarashi K, Sridharan R, Tu BP, Cryns VL, Lamming DW, Denu JM

Molecular Cell, 78(2):210-223.

2013-2019 (before joining the LSI)

10. The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3 (2019)

Kuang Z, Wang Y, Li Y, Ye C, Ruhn KA, BehrendtCL, Olson EN, Hooper LV

Science, 365(6460):1428-1434.

9. Demethylation of the protein phosphatase PP2A promotes demethylation of histones to enable their function as a methyl group sink (2019)

Ye C, Sutter BM, Wang Y, Kuang Z, Zhao X, Yu Y, Tu BP

Molecular Cell, 73(6):1115-1126.

8. Sink into the Epigenome: Histones as repositories that influence cellular metabolism (2018)

Ye C and Tu BP

Trends in Endocrinology & Metabolism, 29(9):626-637.

7. A metabolic function for phospholipid and histone methylation (2017)