Saravia, J., Raynor, J. L., Chapman, N. M., Lim, S. A. & Chi, H. Signaling networks in immunometabolism. Cell Res. 30, 328–342 (2020).
Zhang, D. et al. Metabolic regulation of gene expression by histone lactylation. Nature 574, 575–580 (2019).
Runtsch, M. C. et al. Itaconate and itaconate derivatives target JAK1 to suppress alternative activation of macrophages. Cell Metab. 34, 487–501 (2022).
Tong, Y. et al. SUCLA2-coupled regulation of GLS succinylation and activity counteracts oxidative stress in tumor cells. Mol. Cell 81, 2303–2316 (2021).
Cheng, J. et al. Cancer-cell-derived fumarate suppresses the anti-tumor capacity of CD8+ T cells in the tumor microenvironment. Cell Metab. 35, 961–978 (2023).
Yang, X., Stein, K. R. & Hang, H. C. Anti-infective bile acids bind and inactivate a Salmonella virulence regulator. Nat. Chem. Biol. 19, 91–100 (2023).
Borst, P. The malate-aspartate shuttle (Borst cycle): how it started and developed into a major metabolic pathway. IUBMB Life 72, 2241–2259 (2020).
Wang, Y. et al. Saturation of the mitochondrial NADH shuttles drives aerobic glycolysis in proliferating cells. Mol. Cell 82, 3270–3283 (2022).
Birsoy, K. et al. An essential role of the mitochondrial electron transport chain in cell proliferation is to enable aspartate synthesis. Cell 162, 540–551 (2015).
Wang, Y. P. et al. Arginine methylation of MDH1 by CARM1 inhibits glutamine metabolism and suppresses pancreatic cancer. Mol. Cell 64, 673–687 (2016).
Wiese, E. K. et al. Enzymatic activation of pyruvate kinase increases cytosolic oxaloacetate to inhibit the Warburg effect. Nat. Metab. 3, 954–968 (2021).
Zhang, Y. et al. A single-cell atlas of the peripheral immune response in patients with influenza A virus infection. iScience 26, 108507 (2023).
Castro-Mondragon, J. A. et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 50, 165–173 (2022).
Yu, L. & Sivitz, W. I. Oxaloacetate mediates mitochondrial metabolism and function. Curr. Metabolomics Syst. Biol. 7, 11–23 (2020).
Yang, Y. Enhancing doxorubicin efficacy through inhibition of aspartate transaminase in triple-negative breast cancer cells. Biochem. Biophys. Res. Commun. 473, 1295–1300 (2016).
Lee, S. M., Kim, J. H., Cho, E. J. & Youn, H. D. A nucleocytoplasmic malate dehydrogenase regulates p53 transcriptional activity in response to metabolic stress. Cell Death Differ. 16, 738–748 (2009).
McCue, W. M. & Finzel, B. C. Structural characterization of the human cytosolic malate dehydrogenase I. ACS Omega 7, 207–214 (2022).
Agudo-Canalejo, J., Illien, P. & Golestanian, R. Cooperatively enhanced reactivity and ‘stabilitaxis’ of dissociating oligomeric proteins. Proc. Natl Acad. Sci. USA 117, 11894–11900 (2020).
Broeks, M. H. et al. MDH1 deficiency is a metabolic disorder of the malate-aspartate shuttle associated with early onset severe encephalopathy. Hum. Genet. 138, 1247–1257 (2019).
Sizemore, G. M., Pitarresi, J. R., Balakrishnan, S. & Ostrowski, M. C. The ETS family of oncogenic transcription factors in solid tumours. Nat. Rev. Cancer 17, 337–351 (2017).
Alkan, H. F. et al. Cytosolic aspartate availability determines cell survival when glutamine is limiting. Cell Metab. 28, 706–720 (2018).
Agathocleous, M. et al. Ascorbate regulates haematopoietic stem cell function and leukaemogenesis. Nature 549, 476–481 (2017).
Meacham, C. E., DeVilbiss, A. W. & Morrison, S. J. Metabolic regulation of somatic stem cells in vivo. Nat. Rev. Mol. Cell Biol. 23, 428–443 (2022).
Guo, H. et al. Multi-omics analyses reveal that HIV-1 alters CD4+ T cell immunometabolism to fuel virus replication. Nat. Immunol. 22, 423–433 (2021).
Zhang, W. et al. Lactate is a natural suppressor of RLR signaling by targeting MAVS. Cell 178, 176–189 (2019).
Fitzgerald, K. A. et al. IKKε and TBK1 are essential components of the IRF3 signaling pathway. Nat. Immunol. 4, 491–496 (2003).
Taft, J. et al. Human TBK1 deficiency leads to autoinflammation driven by TNF-induced cell death. Cell 184, 4447–4463 (2021).
Prabakaran, T. et al. Attenuation of cGAS-STING signaling is mediated by a p62/SQSTM1-dependent autophagy pathway activated by TBK1. EMBO J. 37, e97858 (2018).
Xie, W. et al. ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1. Autophagy 19, 2853–2868 (2023).
Li, X. et al. Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity. Nat. Immunol. 17, 806–815 (2016).
Wang, Y. et al. Decreased expression of the host long-noncoding RNA-GM facilitates viral escape by inhibiting the kinase activity TBK1 via S-glutathionylation. Immunity 53, 1168–1181 (2020).
Gielisch, I. & Meierhofer, D. Metabolome and proteome profiling of complex I deficiency induced by rotenone. J. Proteome Res. 14, 224–235 (2015).
Ying, P. et al. Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk. Nat. Commun. 14, 5958 (2023).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 16, 284–287 (2012).
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, 160–165 (2016).
Sundaram, B. et al. NLRC5 senses NAD+ depletion, forming a PANoptosome and driving PANoptosis and inflammation. Cell 187, 4061–4077 (2024).