A non-canonical tricarboxylic acid cycle underlies cellular identity
Open accessAbstract
The tricarboxylic acid (TCA) cycle is a central hub of cellular metabolism, oxidizing nutrients to generate reducing equivalents for energy production and critical metabolites for biosynthetic reactions. Despite the importance of the products of the TCA cycle for cell viability and proliferation, mammalian cells display diversity in TCA-cycle activity 1,2. How this diversity is achieved, and whether it is critical for establishing cell fate, remains poorly understood. Here we identify a non-canonical TCA cycle that is required for changes in cell state. Genetic co-essentiality mapping revealed a cluster of genes that is sufficient to compose a biochemical alternative to the canonical TCA cycle, wherein mitochondrially derived citrate exported to the cytoplasm is metabolized by ATP citrate lyase, ultimately regenerating mitochondrial oxaloacetate to complete this non-canonical TCA cycle. Manipulating the expression of ATP citrate lyase or the canonical TCA-cycle enzyme aconitase 2 in mouse myoblasts and embryonic stem cells revealed that changes in the configuration of the TCA cycle accompany cell fate transitions. During exit from pluripotency, embryonic stem cells switch from canonical to non-canonical TCA-cycle metabolism. Accordingly, blocking the non-canonical TCA cycle prevents cells from exiting pluripotency. These results establish a context-dependent alternative to the traditional TCA cycle and reveal that appropriate TCA-cycle engagement is required for changes in cell state.
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The citrate-malate shuttle performs functions beyond electron shuttling and supports continuous citrate regeneration and TCA cycle intermediate homeostasis.
“More recently, it was demonstrated that the citrate–malate shuttle performs functions beyond that of an electron shuttle and, in fact, supports continuous citrate regeneration and TCA cycle intermediate homeostasis (119, 121).”
From Regulation and function of the mammalian tricarboxylic acid cycle (2023) · cites this paper as [121]
Myogenic differentiation is coupled with increased pyruvate oxidation and OXPHOS, and this metabolic shift is likely driven, in part, by the significant energy demands of skeletal muscle.
“Myogenic differentiation is also coupled with increased pyruvate oxidation and OXPHOS, and this metabolic shift is likely driven, in part, by the significant energy demands of skeletal muscle (121, 204, 209).”
From Regulation and function of the mammalian tricarboxylic acid cycle (2023) · cites this paper as [121]
Naïve ESCs primarily oxidize citrate in the traditional TCA cycle, and loss of ACO2 compromises acquisition of naïve pluripotency.
“For example, we recently showed that naïve ESCs primarily oxidize citrate in the traditional TCA cycle, and, accordingly, loss of ACO2 compromises acquisition of naïve pluripotency (121).”
From Regulation and function of the mammalian tricarboxylic acid cycle (2023) · cites this paper as [121]
Blocking the citrate-malate shuttle by disrupting ACL causes significant defects in TCA cycle metabolite homeostasis and prevents ESCs from exiting from the naïve pluripotent state.
“Consequently, blocking the citrate–malate shuttle by disrupting ACL causes significant defects in TCA cycle metabolite homeostasis and prevents ESCs from exiting from the naïve pluripotent state (121).”
From Regulation and function of the mammalian tricarboxylic acid cycle (2023) · cites this paper as [121]
Cells undergoing exit from the naïve pluripotent state shift toward cytosolic TCA cycle metabolism via the citrate-malate shuttle.
“Conversely, cells undergoing exit from the naïve pluripotent state shift toward cytosolic TCA cycle metabolism via the citrate–malate shuttle.”
From Regulation and function of the mammalian tricarboxylic acid cycle (2023) · cites this paper as [121]
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0686-2 · Cited by 38,430 · see citing works
fastp: an ultra-fast all-in-one FASTQ preprocessor
(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219 · see citing works
Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133 · see citing works
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2019) · Apollo - University of Cambridge Repository · doi:10.17863/cam.64134 · Cited by 10,460 · see citing works
The Gene Ontology Resource: 20 years and still GOing strong
The Gene Ontology Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1055 · Cited by 4,747 · see citing works
Next-generation characterization of the Cancer Cell Line Encyclopedia
Ghandi, M., Huang, F. W., Jané-Valbuena, J., Kryukov, G. V., Lo, C. C., McDonald, E. R., Barretina, J., Gelfand, E. T., Bielski, C. M., Li, H., et al. (2019) · Nature · doi:10.1038/s41586-019-1186-3 · Cited by 3,394 · see citing works
Defining a Cancer Dependency Map
Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., Gill, S., Harrington, W. F., Pantel, S., Krill-Burger, J. M., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.010 · Cited by 3,276 · see citing works
Fundamentals of Cancer Metabolism
DeBerardinis, R. J., & Chandel, N. S. (2016) · Science Advances · doi:10.1126/sciadv.1600200 · Cited by 3,013 · see citing works
Meyers, R. M., Bryan, J. G., McFarland, J. M., Weir, B. A., Sizemore, A. E., Xu, H., Dharia, N. V., Montgomery, P. G., Cowley, G. S., Pantel, S., et al. (2017) · Nature Genetics · doi:10.1038/ng.3984 · Cited by 1,952 · see citing works
Williamson, D., Lund, P., & Krebs, H. (1967) · Biochemical Journal · doi:10.1042/bj1030514 · Cited by 1,871 · see citing works
Birsoy, K., Wang, T., Chen, W. W., Freinkman, E., Abu-Remaileh, M., & Sabatini, D. M. (2015) · Cell · doi:10.1016/j.cell.2015.07.016 · Cited by 1,388 · see citing works
Supporting aspartate biosynthesis is an essential function of respiration in proliferating cells
Sullivan, L. B., Gui, D. Y., Hosios, A. M., Bush, L. N., Freinkman, E., & Vander Heiden, M. G. (2015) · Cell · doi:10.1016/j.cell.2015.07.017 · Cited by 1,173 · see citing works
Self-citationATP citrate lyase inhibition can suppress tumor cell growth
Hatzivassiliou, G., Zhao, F., Bauer, D. E., Andreadis, C., Shaw, A. N., Dhanak, D., Hingorani, S. R., Tuveson, D. A., & Thompson, C. B. (2005) · Cancer Cell · doi:10.1016/j.ccr.2005.09.008 · Cited by 1,086 · see citing works
Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells
Carey, B. W., Finley, L. W. S., Cross, J. R., Allis, C. D., & Thompson, C. B. (2015) · Nature · doi:10.1038/nature13981 · Cited by 1,007 · see citing works
Self-citationEnvironment impacts the metabolic dependencies of Ras-driven non-small cell lung cancer
Davidson, S. M., Papagiannakopoulos, T., Olenchock, B. A., Heyman, J. E., Keibler, M. A., Luengo, A., Bauer, M. R., Jha, A. K., O’Brien, J. P., Pierce, K. A., et al. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.01.007 · Cited by 737 · see citing works
Self-citationAn Optimized microRNA Backbone for Effective Single-Copy RNAi
Fellmann, C., Hoffmann, T., Sridhar, V., Hopfgartner, B., Muhar, M., Roth, M., Lai, D. Y., Barbosa, I. A. M., Kwon, J. S., Guan, Y., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.11.020 · Cited by 705 · see citing works
Moussaieff, A., Rouleau, M., Kitsberg, D., Cohen, M., Levy, G., Barasch, D., Nemirovski, A., Shen-Orr, S., Laevsky, I., Amit, M., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.02.002 · Cited by 666 · see citing works
Mechanisms and Implications of Metabolic Heterogeneity in Cancer
Kim, J., & DeBerardinis, R. J. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.08.013 · Cited by 606 · see citing works
Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells
Lewis, C. A., Parker, S. J., Fiske, B. P., McCloskey, D., Gui, D. Y., Green, C. R., Vokes, N. I., Feist, A. M., Vander Heiden, M. G., & Metallo, C. M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.008 · Cited by 562 · see citing works
Increased demand for NAD(+) relative to ATP drives aerobic glycolysis
Luengo, A., Li, Z., Gui, D. Y., Sullivan, L. B., Zagorulya, M., Do, B. T., Ferreira, R., Naamati, A., Ali, A., Lewis, C. A., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.012 · Cited by 547 · see citing works
Self-citationMarin-Valencia, I., Yang, C., Mashimo, T., Cho, S., Baek, H., Yang, X.-L., Rajagopalan, K. N., Maddie, M., Vemireddy, V., Zhao, Z., et al. (2012) · Cell Metabolism · doi:10.1016/j.cmet.2012.05.001 · Cited by 529 · see citing works
Wray, J. P., Kalkan, T., Gómez‐López, S., Eckardt, D., Cook, A. S., Kemler, R., & Smith, A. G. (2011) · Nature Cell Biology · doi:10.1038/ncb2267 · Cited by 525 · see citing works
The pharmacology of dichloroacetate
Stacpoole, P. W. (1989) · Metabolism · doi:10.1016/0026-0495(89)90051-6 · Cited by 485 · see citing works
Inducible in vivo genome editing with CRISPR-Cas9
Dow, L. E., Fisher, J., O’Rourke, K. P., Muley, A., Kastenhuber, E. R., Livshits, G., Tschaharganeh, D. F., Socci, N. D., & Lowe, S. W. (2015) · Nature Biotechnology · doi:10.1038/nbt.3155 · Cited by 482 · see citing works
ATP-citrate lyase controls a glucose-to-acetate metabolic switch
Zhao, S., Torres, A., Henry, R. A., Trefely, S., Wallace, M., Lee, J. V., Carrer, A., Sengupta, A., Campbell, S. L., Kuo, Y.-M., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.09.069 · Cited by 394 · see citing works
Srebp-controlled glucose metabolism is essential for NK cell functional responses
Assmann, N., O'Brien, K. L., Donnelly, R. P., Dyck, L., Zaiatz-Bittencourt, V., Loftus, R. M., Heinrich, P., Oefner, P. J., Lynch, L., Gardiner, C. M., et al. (2017) · Nature Immunology · doi:10.1038/ni.3838 · Cited by 375 · see citing works
Dempster, J. M., Rossen, J., Kazachkova, M., Pan, J., Kugener, G., Root, D., & Tsherniak, A. (2019) · bioRxiv · doi:10.1101/720243 · Cited by 348 · see citing works
Aspartate is an endogenous metabolic limitation for tumour growth
Sullivan, L. B., Luengo, A., Danai, L. V., Bush, L. N., Diehl, F. F., Hosios, A. M., Lau, A. N., Elmiligy, S., Malstrom, S. E., Lewis, C. A., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0125-0 · Cited by 339 · see citing works
Self-citationRepression of Nanog Gene Transcription by Tcf3 Limits Embryonic Stem Cell Self-Renewal
Pereira, L., Yi, F., & Merrill, B. J. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.00368-06 · Cited by 316 · see citing works
α-Ketoglutarate links p53 to cell fate during tumour suppression
Morris, J. P., Yashinskie, J. J., Koche, R., Chandwani, R., Tian, S., Chen, C.-C., Baslan, T., Marinkovic, Z. S., Sánchez-Rivera, F. J., Leach, S. D., et al. (2019) · Nature · doi:10.1038/s41586-019-1577-5 · Cited by 296 · see citing works
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Kalkan, T., Olova, N. N., Roode, M., Mulas, C., Lee, H. J., Nett, I., Marks, H., Walker, R. V., Stunnenberg, H. G., Lilley, K. S., et al. (2017) · Development · doi:10.1242/dev.142711 · Cited by 281 · see citing works
The oxidation of pyruvate in pigeon breast muscle
Krebs, H. A., & Eggleston, L. V. (1940) · Biochemical Journal · doi:10.1042/bj0340442 · Cited by 256 · see citing works
Borst, P. (2020) · IUBMB Life · doi:10.1002/iub.2367 · Cited by 252 · see citing works
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Chen, P.-H., Cai, L., Huffman, K. E., Yang, C., Kim, J., Faubert, B., Boroughs, L. K., Ko, B., Sudderth, J., McMillan, E. A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.028 · Cited by 206 · see citing works
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes
Wainberg, M., Kamber, R. A., Balsubramani, A., Meyers, R. M., Sinnott-Armstrong, N., Hornburg, D., Jiang, L., Chan, J., Jian, R., Gu, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00840-z · Cited by 204 · see citing works
A genome-wide almanac of co-essential modules assigns function to uncharacterized genes
Wainberg, M., Kamber, R. A., Balsubramani, A., Meyers, R. M., Sinnott-Armstrong, N., Hornburg, D., Jiang, L., Chan, J., Jian, R., Gu, M., et al. (2019) · doi:10.1101/827071 · Cited by 204 · see citing works
IsoCor: isotope correction for high-resolution MS labeling experiments
Millard, P., Delépine, B., Guionnet, M., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz209 · Cited by 197 · see citing works
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Zhu, X. G., Chudnovskiy, A., Baudrier, L., Prizer, B., Liu, Y., Ostendorf, B. N., Yamaguchi, N., Arab, A., Tavora, B., Timson, R., et al. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2020.10.017 · Cited by 130 · see citing works
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Alves, T. C., Pongratz, R. L., Zhao, X., Yarborough, O. H., Sereda, S., Shirihai, O. S., Cline, G. W., Mason, G. F., & Kibbey, R. G. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.08.021 · Cited by 129 · see citing works
Muir, A., Danai, L. V., & Heiden, M. G. V. (2018) · Disease Models & Mechanisms · doi:10.1242/dmm.035758 · Cited by 121 · see citing works
MyoD Regulates Skeletal Muscle Oxidative Metabolism Cooperatively with Alternative NF-κB
Shintaku, J., Peterson, J. M., Talbert, E. E., Gu, J.-M., Ladner, K. J., Williams, D. R., Mousavi, K., Wang, R., Sartorelli, V., & D, D. C. G. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.09.010 · Cited by 104 · see citing works
Glutamine independence is a selectable feature of pluripotent stem cells
Vardhana, S. A., Arnold, P. K., Rosen, B. P., Chen, Y., Carey, B. W., Huangfu, D., Carmona‐Fontaine, C., Thompson, C. B., & Finley, L. W. S. (2019) · Nature Metabolism · doi:10.1038/s42255-019-0082-3 · Cited by 67 · see citing works
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Kalkan, T., Olova, N. N., Roode, M., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/092510 · Cited by 41 · see citing works
Intracellular Ca2+ Homeostasis and Nuclear Export Mediate Exit from Naive Pluripotency
MacDougall, M. S., Clarke, R., & Merrill, B. J. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.04.015 · Cited by 39 · see citing works
Metabolic Diversity in Human Non-Small Cell Lung Cancer CellsPreprint
Chen, P.-H., Cai, L., Huffman, K. E., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/561688 · Cited by 18 · see citing works
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Regulation and function of the mammalian tricarboxylic acid cycle
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“Myogenic differentiation is also coupled with increased pyruvate oxidation and OXPHOS, and this metabolic shift is likely driven, in part, by the significant energy demands of skeletal muscle (121, 204, 209).”
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Morrow, M. R., Batchuluun, B., Wu, J., Ahmadi, E., Leroux, J. M., Mohammadi-Shemirani, P., Desjardins, E. M., Wang, Z., Tsakiridis, E. E., Lavoie, D. C. T., et al. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.05.004 · Cited by 199 · see citing works
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Luda, K. M., Longo, J., Kitchen-Goosen, S. M., Duimstra, L. R., Ma, E. H., Watson, M. J., Oswald, B. M., Fu, Z., Madaj, Z., Kupai, A., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.07.002 · Cited by 140 · see citing works
- Authors
- Arnold, P. K., Jackson, B. T., Paras, K. I., Brunner, J. S., Hart, M. L., Newsom, O. J., Alibeckoff, S. P., Endress, J., Drill, E., Sullivan, L. B., & Finley, L. W. S.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Fred Hutch Cancer Center (US)
- Corresponding author
- Finley, Lydia W. S.
- ORCID
- Venue
- Nature
- Published
- 2022-03-09
- Volume
- 603
- Issue
- 7901
- Pages
- 477-481
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC8934290
- OpenAlex
- W4220700063
- Cited by
- 304
- References
- 50
- Citations by year
- 2026: 50 · 2025: 87 · 2024: 77 · 2023: 66 · 2022: 24
- FWCI
- 27.18
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Cancer Institute (R00CA218679, P30CA008748, R37CA252305, P30CA015704)
- National Institute of General Medical Sciences (T32GM007739)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (F31HD098824, F30HD107943)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer, Hypoxia, and Metabolism
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Keywords
- ATP citrate lyase, aconitase 2, cell fate transitions, pluripotency exit, embryonic stem cells, myoblasts, mitochondrial metabolism
- MeSH terms
- Animals, ATP Citrate (pro-S)-Lyase, Cell Differentiation, Citric Acid Cycle, Mammals, Mitochondria, Citric Acid, Pluripotent Stem Cells, Mice, Embryonic Stem Cells
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