Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells.

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  1. 1.

    On respiratory impairment in cancer cells. Science 124, 269–270 (1956).

  2. 2.

    et al. An essential role of the mitochondrial electron transport chain in cell proliferation is to enable aspartate synthesis. Cell 162, 540–551 (2015).

  3. 3.

    et al. Supporting aspartate biosynthesis is an essential function of respiration in proliferating cells. Cell 162, 552–563 (2015).

  4. 4.

    Mitochondrion as a multifunctional organelle. Nature 230, 504–506 (1971).

  5. 5.

    et al. TCA cycle and mitochondrial membrane potential are necessary for diverse biological functions. Mol. Cell 61, 199–209 (2016).

  6. 6.

    et al. The distinct metabolic profile of hematopoietic stem cells reflects their location in a hypoxic niche. Cell Stem Cell 7, 380–390 (2010).

  7. 7.

    & Metabolic requirements for the maintenance of self-renewing stem cells. Nat. Rev. Mol. Cell Biol. 15, 243–256 (2014).

  8. 8.

    et al. Metabolic trajectory of cellular differentiation in small intestine by Phasor Fluorescence Lifetime Microscopy of NADH. Sci. Rep. 2, 568 (2012).

  9. 9.

    et al. A bioassay to measure energy metabolism in mouse colonic crypts, organoids, and sorted stem cells. Am. J. Physiol. Gastrointest. Liver Physiol. 309, G1–G9 (2015).

  10. 10.

    et al. Interplay between metabolic identities in the intestinal crypt supports stem cell function. Nature 543, 424–427 (2017).

  11. 11.

    et al. Mitochondrial function controls intestinal epithelial stemness and proliferation. Nat. Commun. 7, 13171 (2016).

  12. 12.

    et al. A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans. Science 337, 96–100 (2012).

  13. 13.

    et al. Identification and functional expression of the mitochondrial pyruvate carrier. Science 337, 93–96 (2012).

  14. 14.

    et al. A role for the mitochondrial pyruvate carrier as a repressor of the Warburg effect and colon cancer cell growth. Mol. Cell 56, 400–413 (2014).

  15. 15.

    et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009).

  16. 16.

    & Primary mouse small intestinal epithelial cell cultures. Methods Mol. Biol. 945, 319–328 (2013).

  17. 17.

    et al. Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol. 28, 1248–1250 (2010).

  18. 18.

    , & Charting the human proteome: understanding disease using a tissue-based atlas. Science 347, 1274–1274 (2015).

  19. 19.

    & Intestinal stem cell function in Drosophila and mice. Curr. Opin. Genet. Dev. 22, 354–360 (2012).

  20. 20.

    & Gastrointestinal stem cells in health and disease: from flies to humans. Dis. Model Mech. 9, 487–499 (2016).

  21. 21.

    et al. Regional cell-specific transcriptome mapping reveals regulatory complexity in the adult Drosophila midgut. Cell Rep. 12, 346–358 (2015).

  22. 22.

    et al. Morphological and molecular characterization of adult midgut compartmentalization in Drosophila. Cell Rep. 3, 1725–1738 (2013).

  23. 23.

    & A protocol for mosaic analysis with a repressible cell marker (MARCM) in Drosophila. Nat. Protoc. 1, 2583–2589 (2006).

  24. 24.

    & Evidence that stem cells reside in the adult Drosophila midgut epithelium. Nature 439, 475–479 (2006).

  25. 25.

    & The adult Drosophila posterior midgut is maintained by pluripotent stem cells. Nature 439, 470–474 (2006).

  26. 26.

    et al. Drosophila larvae synthesize the putative oncometabolite L-2-hydroxyglutarate during normal developmental growth. Proc. Natl Acad. Sci. USA 114, 1353–1358 (2017).

  27. 27.

    Whole-mount immunostaining of the adult Drosophila gastrointestinal tract. Methods 68, 273–279 (2014).

  28. 28.

    et al. Mitochondrial pyruvate carrier 2 hypomorphism in mice leads to defects in glucose-stimulated insulin secretion. Cell Rep. 7, 2042–2053 (2014).

  29. 29.

    et al. Regulation of substrate utilization by the mitochondrial pyruvate carrier. Mol. Cell 56, 425–435 (2014).

  30. 30.

    , & Regulation of mitochondrial pyruvate uptake by alternative pyruvate carrier complexes. EMBO J. 34, 911–924 (2015).

  31. 31.

    et al. Glutamine oxidation maintains the TCA cycle and cell survival during impaired mitochondrial pyruvate transport. Mol. Cell 56, 414–424 (2014).

  32. 32.

    et al. Niche-independent high-purity cultures of Lgr5 + intestinal stem cells and their progeny. Nat. Methods 11, 106–112 (2014).

  33. 33.

    et al. Pyruvate uptake is inhibited by valproic acid and metabolites in mitochondrial membranes. FEBS Lett. 582, 3359–3366 (2008).

  34. 34.

    , , & Inhibition by valproic acid of pyruvate uptake by brain mitochondria. Biochem. Pharmacol. 31, 1633–1636 (1982).

  35. 35.

    Nutrient-induced intestinal adaption and its effect in obesity. Physiol. Behav. 136, 74–78 (2014).

  36. 36.

    et al. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature 531, 53–58 (2016).

  37. 37.

    et al. Transcriptional and functional profiling of human embryonic stem cell-derived cardiomyocytes. PLoS ONE 3, e3474 (2008).

  38. 38.

    et al. Identification of microRNAs expressed highly in pancreatic islet-like cell clusters differentiated from human embryonic stem cells. Cell Biol. Int. 35, 29–37 (2011).

  39. 39.

    et al. Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2. Development 137, 395–403 (2010).

  40. 40.

    et al. The PAF complex synergizes with MLL fusion proteins at HOX loci to promote leukemogenesis. Cancer Cell 17, 609–621 (2010).

  41. 41.

    et al. Transcriptional regulatory network analysis of developing human erythroid progenitors reveals patterns of coregulation and potential transcriptional regulators. Physiol. Genomics 28, 114–128 (2006).

  42. 42.

    et al. Glycome diagnosis of human induced pluripotent stem cells using lectin microarray. J. Biol. Chem. 286, 20345–20353 (2011).

  43. 43.

    et al. DNA methylation dynamics in human induced pluripotent stem cells over time. PLoS Genet. 7, e1002085 (2011).

  44. 44.

    et al. Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells. BMC Syst. Biol. 5 (Suppl. 1), S17 (2011).

  45. 45.

    et al. The gene expression profiles of induced pluripotent stem cells from individuals with childhood cerebral adrenoleukodystrophy are consistent with proposed mechanisms of pathogenesis. Stem Cell Res. Ther. 3, 39 (2012).

  46. 46.

    et al. Lactate dehydrogenase activity drives hair follicle stem cell activation. Nat. Cell Biol. (2017).

  47. 47.

    et al. Inhibition of fatty acid oxidation as a therapy for MYC-overexpressing triple-negative breast cancer. Nat. Med. 22, 427–432 (2016).

  48. 48.

    & Metabolic pathways promoting cancer cell survival and growth. Nat. Cell Biol. 17, 351–359 (2015).

  49. 49.

    et al. c-Myc programs fatty acid metabolism and dictates acetyl-CoA abundance and fate. J. Biol. Chem. 289, 25382–25392 (2014).

  50. 50.

    et al. Wnt signaling directs a metabolic program of glycolysis and angiogenesis in colon cancer. EMBO J. 33, 1454–1473 (2014).

  51. 51.

    et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100 (2012).

  52. 52.

    et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 41, D171–D176 (2013).

  53. 53.

    et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 22, 1798–1812 (2012).

  54. 54.

    et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42, D764–D770 (2014).

  55. 55.

    , , , & The role of histone acetylation in regulating early gene expression patterns during early embryonic stem cell differentiation. J. Biol. Chem. 282, 6696–6706 (2007).

  56. 56.

    , , & Epigenetics in intestinal epithelial cell renewal. J. Cell. Physiol. 231, 2361–2367 (2016).

  57. 57.

    , , , & Chromatin remodeling during mouse and human embryonic stem cell differentiation. Dev. Dyn. 237, 1389–1398 (2008).

  58. 58.

    et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003–1007 (2007).

  59. 59.

    et al. Hepatic mitochondrial pyruvate carrier 1 is required for efficient regulation of gluconeogenesis and whole-body glucose homeostasis. Cell Metab. 22, 669–681 (2015).

  60. 60.

    & The ‘Swiss roll’: a simple technique for histological studies of the rodent intestine. Lab. Anim. 15, 57–59 (1981).

  61. 61.

    , , & Expression of multiple transgenes from a single construct using viral 2A peptides in Drosophila. PLoS ONE 9, e100637 (2014).

  62. 62.

    et al. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 469, 415–418 (2011).

  63. 63.

    et al. Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche. Nat. Med. 15, 701–706 (2009).

  64. 64.

    et al. Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2. Nat. Commun. 5, 5728 (2014).

  65. 65.

    , , , & Lentiviral gene ontology (LeGO) vectors equipped with novel drug-selectable fluorescent proteins: new building blocks for cell marking and multi-gene analysis. Gene Ther. 17, 511–520 (2010).

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We thank B. Edgar (University of Utah, USA) for stocks and reagents, C. Micchelli (Washington University School of Medicine, USA) for providing the Notch RNAi line, K. Beebe for helpful advice and comments on the Drosophila intestinal studies, G. Lam for establishing the Drosophila MPC overexpression strain, O. Yilmaz and D. Sabatini for assistance and insight into intestinal stem cell metabolism, D. Tantin for critiques and comments, members of the Rutter laboratory for assistance and advice, J. O’Shea, R. Orbus and C. DeHeer for assistance with NanoString, W. Swiatek for mouse assistance, ARUP Institute for Clinical and Experimental Pathology, and S. R. Tripp and E. Hammond for histology; L. Nikolova at the University of Utah Electron Microscopy Core Laboratory performed electron microscopy; mass spectrometry analysis was performed at the Mass Spectrometry and Proteomics Core Facility at the University of Utah. Mass spectrometry equipment was obtained through NCRR Shared Instrumentation Grant no. 1 S10 RR020883-01, 1 S10 RR025532-01A1, NIH 1 S10OD021505-01 (J.E.C.) and the Diabetes and Metabolism Center at the University of Utah. This study was conducted with support from the Biorepository and Molecular Pathology Shared Resource supported by the Cancer Center Support Grant awarded to the Huntsman Cancer Institute by the National Cancer Institute of the National Institutes of Health. Nanostring transcript analysis utilized the Molecular Diagnostics Section of the Biorepository and Molecular Pathology Shared Resource and was supported by the National Cancer Institute of the National Institutes of Health under Award Number P30CA042014 (the content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH). J. Marvin at the University of Utah Flow Cytometry Facility carried out flow sorting (National Cancer Institute through Award Number 5P30CA042014-24, National Center for Research Resources of the National Institutes of Health under Award Number 1S10RR026802-01). Funding was also provided by HHMI (J.R.), Treadwell (J.R.) and RO1GM094232 (to J.R. and C.S.T.). J.C.S. was supported by an NIH Developmental Biology Training Grant (5T32 HD07491) and a University of Utah Graduate Research Fellowship. D.R.W. was supported by a University of Utah Graduate Research Fellowship.

Author information


  1. Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

    • John C. Schell
    • , Claire Bensard
    • , Peng Wei
    • , Jason Tanner
    • , Christian S. Earl
    • , Kristofor A. Olson
    • , Ren Miao
    • , T. Cameron Waller
    • , James E. Cox
    •  & Jared Rutter
  2. Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

    • Dona R. Wisidagama
    •  & Carl S. Thummel
  3. Department of Molecular Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

    • Helong Zhao
    • , Lise K. Sorensen
    •  & Dean Y. Li
  4. Eli and Edythe Broad Center for Regenerative Medicine, University of California Los Angeles, Los Angeles, California 90095, USA

    • Aimee Flores
    • , Heather R. Christofk
    •  & William E. Lowry
  5. Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA

    • Aimee Flores
    •  & William E. Lowry
  6. Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

    • Jeffrey Mohlman
    •  & Mary P. Bronner
  7. Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

    • Don Delker
    •  & Priyanka Kanth
  8. Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

    • Lei Jiang
    •  & Ralph J. DeBerardinis
  9. Department of Molecular and Cellular Endocrinology, Beckman Research Institute at City of Hope, Duarte, California 91010, USA

    • Lei Jiang
  10. Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, USA

    • Heather R. Christofk
  11. Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA

    • Jared Rutter


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Conceptualization, J.C.S., D.R.W., C.S.T. and J.R.; methodology, J.C.S., D.R.W., C.B., H.Z., P.W., J.T., A.F., J.M., L.K.S., C.S.E., K.A.O., D.D., P.K., M.P.B., D.Y.L., J.E.C., H.R.C., W.E.L., C.S.T. and J.R.; investigation, J.C.S., D.R.W., C.B., H.Z., P.W., J.T., A.F., J.M., L.K.S., C.S.E., R.M., D.D. and P.K.; formal analysis, J.C.S., D.R.W., C.B., P.W., T.C.W., R.M., L.J., R.J.D. and J.E.C.; writing—original draft, review and editing, J.C.S., D.R.W., C.S.T. and J.R.; funding acquisition, C.S.T. and J.R.; resources, D.Y.L., J.C., C.S.T. and J.R.; supervision, C.S.T. and J.R.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jared Rutter.

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