Publications

2024

• Lika J, Fan J. Metabolic regulation of neutrophil effector functions. (2024) Current Opinion in Immunology https://doi.org/10.1016/j.coi.2024.102497
• Gurel Z, Luy MS, Luo Q, Arp NL, Erbe AK, Kesarwala AH, Fan J, Kimple RJ. (2024) Metabolic Modulation of melanoma tumors expands the therapeutic potential of immune checkpoint inhibitors. Frontiers in Oncology DOI: https://doi.org/10.3389/fonc.2024.1428802
• Britt EC, Qing X, Votava JA, Lika J, Wagner A, Shen S, Arp NL, Khan H, Schieke SM, Fletcher CD, Huttenlocher A, Fan J. (2024) Activation-induced shift in nutrient preference and function-specific nutrient dependence in human neutrophils. Proceedings of the National Academy of Sciences, DOI:10.1073/pnas.2321212121
• Lancaster NM, Sinitcyn P, Forny P, Peters-Clarke TM, Fecher C, Smith AJ, Shishkova E, Arrey TN, Pashkova A, Robinson ML, Arp N, Fan J, Hansen J, Galmozzi A, Serrano LR, Westphall MS, Stewart H, Hock C, Damoc E, Pagliarini DJ, Zabrouskov V, Coon JJ. (2024) Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer. Nature Communications 15, 7016
• Steenberge LH, Sung AY, Fan J, Pagliarini DJ. (2024) Coenyzme Q4 is a functional substitute for coenyzme Q10 and can be targeted to the mitochondria. Journal of Biological Chemistry 300(5):107269
• Votava JA, John SV, Li Z, Chen S, Fan J, Parks BW. (2024) Systematically mining cholesterol metabolism genes from thousands of mouse livers identifies Aldolase C as a regulator of cholesterol biosynthesis. Journal of Lipid Research, doi: 10.1016/j.jlr.2024.100525

2023

• Arp NL, Seim GL, Votava JA, Josephson J, Fan J. (2023) Reactive nitrogen species inhibit branched chain alpha-ketoacid dehydrogenase complex and alter muscle cell metabolism. Journal of Biological Chemistry, 299 (11) 105333
• TeSlaa T, Ralser M, Fan J, Rabinowitz JD. (2023) The pentose phosphate pathway in health and disease.  Nature Metabolism 5, 1275–1289 
• Jiang J, Srivastava S, Liu S, Seim G, Zhong M, Cao S, Davé U, Kapur R, Mosley AL, Zhang C, Wan J, Fan J, Zhang J. (2023) Asparagine starvation suppresses histone demethylation through iron depletion. iScience  26 (4)
• Seim GL, John SV, Arp NL, Fang Z, Pagliarini DJ, Fan J. (2023) Nitric oxide-driven modifications of lipoic arm inhibit α-ketoacid dehydrogenases. Nature Chemical Biology,  19,  265–274

2022

• Srivastava S, Jiang J, Seim G, Misra J, Staschke K, Zhong M, Zhou L, Liu Y, Chen C, Dave U, Kapur R, Batra S, Zhang C, Zhou J, Fan J, Wek R, Zhang J. (2022) Asparagine bioavailability regulates the translation of MYC oncogene. Oncogene 41, 4855-4865
• Britt EC, Lika J, Giese MA, Schoen TJ, Seim GL, Huang Z, Lee PY, Huttenlocher A, Fan J. Switching to the cyclic pentose phosphate pathway powers the oxidative burst in activated neutrophils. Nature Metabolism 4, 389-403
• Seim GL, Fan, J. A matter of time: temporal structure and functional relevance of macrophage metabolic rewiring. Trends in Endocrinology and Metabolism 33(5):345-358
• Miskolci V, Tweed KE, Lasarev MR, Britt EC, Walsh AJ, Zimmerman LJ, McDougal CE, Cronan MR, Fan J, Sauer JD, Skala MC, Huttenlocher A. In vivo fluorescence lifetime imaging captures metabolic changes in macrophages during wound responses in zebrafish. eLife 11:e66080

2021

• Bae J, Salamon RJ, Brandt EB, Paltzer WG, Zhang Z, Britt EC, Hacker TA, Fan J, Mahmoud AI. Malonate Promotes Adult Cardiomyocyte Proliferation and Heart Regeneration. Circulation. 2021 Mar 5.
• Krautkramer KA, Fan J, Bäckhed F. Gut microbial metabolites as multi-kingdom intermediates. Nat Rev Microbiol. 2021 Feb;19(2):77-94.
• Fan J, Phelps EA. Career pathways, part 3. Nat Metab. 2021 Jan;3(1):2-4.

2020

• Seim GL., John SV, Fan J. Metabolomic and Lipidomic Analysis of Bone Marrow Derived Macrophages. Bio-Protocol.
• Liao R, Zheng Y, Liu X, Zhang Y, Seim GL, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH. Heme-omics: How Heme Controls Genome Function. Cell Report  31(13):107832
• Ghergurovich JM, García-Cañaveras JC, Wang J, Schmidt E, Zhang Z, TeSlaa T, Patel H, Chen L, Britt EC, Piqueras-Nebot M, Gomez-Cabrera MC, Lahoz A, Fan J, Beier UH, Kim H, Rabinowitz JD (2020) A small molecule G6PD inhibitor reveals immune dependence on pentose phosphate pathway. Nature Chemical Biology  16(7): 731-739
• Baeza J, Lawton AJ, Fan J, Smallegan MJ, Lienert I, Gandhi T, Bernhardt OM, Reiter L, Denu JM. Revealing Dynamic Protein Acetylation across Subcellular Compartments. J Proteome Res. 19(6):2404-2418.
• Britt EC, John SV, Locasale JW, Fan J.(2020) Metabolic regulation of epigenetic remodeling in immune cells. Current Opinion in Biotechnology; 63:111-117

2019

• Jiang J, Srivastava S, Seim G, Pavlova NN, King B, Zou L, Zhang C, Zhong M, Feng H, Kapur R, Wek RC, Fan J, Zhang J. (2019)  Promoter demethylation of the asparagine synthetase gene is required for an ATF4-dependent adaptation to asparagine depletion. Journal of Biological Chemistry
• Seim GL, Britt EC, John SV, Yeo FJ, Johnson AR, Eisenstein RS, Pagliarini DJ, Fan J. (2019) Two-stage metabolic remodelling in macrophages in response to LPS and interferon-γ stimulation. Nature Metabolism 1, 731–742
• Seim GL, Britt EC, Fan J. (2019) Analysis of Arginine Metabolism Using LC-MS and Isotopic Labeling. Methods in Molecular Biology 1978:199-217.

2018

• Pavlova NN, Hui S, Ghergurovich JM, Fan J, Intlekofer AM, White RM, Rabinowitz JD, Thompson CB, Zhang J. As extracellular glutamine levels decline, asparagine becomes an essential amino acid (2018). Cell Metabolism 27(2):428-438.e5

Pre-2017

• Morris B, Burkel B*, Ponik SM*, Fan J*, Eliceiri K, Condeelis J, Aquire-Ghiso J, Castracane J, Denu JM, Keely PJ. (2016) Changes in collagen matrix density alters the metabolic profile of breast cancer cells. EBioMedicine 13:146-156
• Wang X, Yuan Z, Fan J, Karch KR, Denu JM, Garcia BA. (2016) A novel quantitative mass spectrometry platform for determining site-specific protein O-GlcNAcylation dynamics. Mol. Cell. Proteomics. 15(7):2462-75
• Fan J, Baeza J, Denu JM. Investigating histone acetylation stoichiometry and turnover rate (2016). Methods Enzymol.
• Liu L, Shah S, Fan J, Park JO, Wellen KE, Rabinowitz JD.(2016) Tracers for malic enzyme reveal a hypoxia-induced switch in adipocyte NADPH production. Nat. Chem. Biol. 12(5):345-52
• Park JO, Rubin SA, Xu YF, Amador-Noguez D, Fan J, Shlomi T, Rabinowitz JD. (2016) Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat. Chem. Biol. 12(7):482-9
• Fan J, Krautkramer KA, Feldman JL, Denu JM. (2015) Metabolic regulation of histone post-translational modifications. ACS Chem. Biol. 10(1):95-108
• Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Siahpirani AF, Kemmerery ZA, Prolla TA, Roy S, Coon JJ, Denu JM. (2015) SIRT3 mediates multi-tissue coupling for metabolic fuel switching. Cell Metab. 21(4):637-46
• Fan J, Teng X, Liu L, Mattaini KR, Looper RE, Vander Heiden MG, Rabinowitz JD. Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate. (2015) ACS Chem. Biol. 10(2):510-6.
• Baeza J, Dowell JA, Smallegan MJ, Fan J, Amador-Noguez D, Khan Z, Denu JM, (2014) Stoichiometry of site-specific lysine acetylation in an entire proteome. J Biol. Chem. 289(31):21326-38
• Fan J*, Ye J*, Kamphorst JJ, Shlomi T, Thompson CB, Rabinowitz JD. (2014) Quantitative flux analysis reveals folate-dependent NADPH production. Nature. 510(7504):298-302.
• Zhang J, Fan J, Venneti S, Cross JR, Takagi T, Bhinder B, Djaballah H, Kanai M, Cheng EH, Judkins AR, Pawel B, Baggs J, Cherry S, Rabinowitz JD, Thompson CB. (2014) Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion. Mol.Cell. 56(2):205-18
• Kamphorst JJ, Chung MK, Fan J, Rabinowitz JD. (2014) Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate. Cancer Metab. 2:23
• Shlomi T, Fan J, Tang B, Kruger W, Rabinowitz JD. (2014) An analytical approach for quantifying methionine metabolism in cancer cells. Anal. Chem. 86(3):1583-91
• Ye J*, Fan J*, Venneti S, Wan YW, Pawel BR, Zhang J, Finley LW, Lu C, Lindsten T, Cross JR, Qing G, Liu Z, Simon MC, Rabinowitz JD, Thompson CB. (2014) Serine catabolism regulates mitochondrial redox control during hypoxia. Cancer Discov. 4(12):1406-17
• Fan J, Kamphorst JJ, Mathew R, Cheung MK., White E, Shlomi T, Rabinowitz JD. (2013) Simultaneous aerobic glycolysis and glutamine-supported oxidative ATP production in oncogene-driven renal epithelial cells. Mol. Syst. Biol. 9: 712.
• Fan J, Kamphorst JJ, Rabinowitz JD, Shlomi T. (2013) Fatty acid labeling from glutamine in hypoxia can be explained by isotope exchange without net reductive IDH flux. J. Biol.Chem. 288(43):31363-9
• Kamphorst JJ, Cross JR, Fan J, De Stanchina E, Mathew R, White E, Thompson CB, Rabinowitz JD. (2013) Hypoxia and oncogenic Ras trigger scavenging of fatty acids from lysophospholipids. Proc. Nat. Acad. Sci. 110(22):8882-7
• Bray K, Mathew R, Lau A, Kamphorst JJ, Fan J, Chen J, Chen HY, Ghavami A, Stein M, Dipaola RS, Zhang D, Rabinowitz JD, White E. (2012) Autophagy suppresses RIP kinase-dependent necrosis enabling survival to mTOR inhibition. PLoS One 7(7): e41831
• Ye J, Mancuso A, Tong X, Ward PS, Fan J, Rabinowitz JD, Thompson CB (2012). Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation. Proc. Nat. Acad. Sci. 109(18):6904-9
• Guo JX*, Chen HY*, Mathew R*, Fan J*, Strohecker AM, Karsli-Uzunbas G, Kamphorst JJ, Chen G, Lemmons JM, Karantza V, Coller HA, DiPaola RS, Gelinase C, Rabinowitz, JD, White E. (2011) Activated Ras Requires Autophagy to Maintain Oxidative Metabolism and Tumorigenesis. Genes Dev. 25(5):460-70
• Kamphorst JJ, Fan J, Lu W, White E, Rabinowitz JD. (2011). Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism. Anal. Chem. 83 (23): 9114-22
• Amador-Noguez D, Feng XJ, Fan J, Roquet N, Rabitz H, Rabinowitz JD. (2010) Systems-level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum. J. Bacteriol. 192 (17): 4452-4461

* authors contributed equally to this work