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  • Review Article
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Mitochondrial function — gatekeeper of intestinal epithelial cell homeostasis

Abstract

The intestinal epithelium is a multicellular interface in close proximity to a dense microbial milieu that is completely renewed every 3–5 days. Pluripotent stem cells reside at the crypt, giving rise to transient amplifying cells that go through continuous steps of proliferation, differentiation and finally anoikis (a form of programmed cell death) while migrating upwards to the villus tip. During these cellular transitions, intestinal epithelial cells (IECs) possess distinct metabolic identities reflected by changes in mitochondrial activity. Mitochondrial function emerges as a key player in cell fate decisions and in coordinating cellular metabolism, immunity, stress responses and apoptosis. Mediators of mitochondrial signalling include molecules such as ATP and reactive oxygen species and interrelate with pathways such as the mitochondrial unfolded protein response (MT-UPR) and AMP kinase signalling, in turn affecting cell cycle progression and stemness. Alterations in mitochondrial function and MT-UPR activation are integral aspects of pathologies, including IBD and cancer. Mitochondrial signalling and concomitant changes in metabolism contribute to intestinal homeostasis and regulate IEC dedifferentiation–differentiation programmes in the context of diseases, suggesting that mitochondrial function as a cellular checkpoint critically contributes to disease outcome. This Review highlights mitochondrial function and MT-UPR signalling in epithelial cell stemness, differentiation and lineage commitment and illustrates mitochondrial function in intestinal diseases.

Key points

  • The intestinal epithelium is a constantly renewing monolayer of cells undergoing continuous steps of proliferation, differentiation and finally cell death, representing an excellent model system to study stem cell regulation.

  • Intestinal epithelial cells (IECs) are key players in intestinal diseases such as IBD and colorectal cancer (CRC), constituting a dynamic interface between microbiota and host.

  • Mitochondrial function and metabolism determine and regulate IEC properties, such as differentiation status and proliferation.

  • Mitochondrial unfolded protein response (MT-UPR) coordinates mitochondrial function, metabolism and cellular phenotype and is activated in various diseases, including IBD and CRC.

  • MT-UPR might act as a sensor of the luminal and host environment, orchestrating epithelial tissue responses.

  • Determining the proliferative and regenerative capacity of IECs, the MT-UPR constitutes an attractive target for future therapeutic approaches for intestinal diseases.

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Fig. 1: Overview of different branches of mammalian MT-UPR signalling.
Fig. 2: Mitochondrial function of IEC along the crypt–villus axis.
Fig. 3: Interrelated aspects of IEC properties, mitochondrial function and intestinal disease mechanisms.

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References

  1. Gribble, F. M. & Reimann, F. Signalling in the gut endocrine axis. Physiol. Behav. 176, 183–188 (2017).

    Article  PubMed  CAS  Google Scholar 

  2. Peterson, L. W. & Artis, D. Intestinal epithelial cells: regulators of barrier function and immune homeostasis. Nat. Rev. Immunol. 14, 141–153 (2014).

    Article  PubMed  CAS  Google Scholar 

  3. Rath, E. & Haller, D. Inflammation and cellular stress: a mechanistic link between immune-mediated and metabolically driven pathologies. Eur. J. Nutr. 50, 219–233 (2011).

    Article  PubMed  CAS  Google Scholar 

  4. Barker, N. Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration. Nat. Rev. Mol. Cell Biol. 15, 19–33 (2014).

    Article  PubMed  CAS  Google Scholar 

  5. Potten, C. S. A comprehensive study of the radiobiological response of the murine (BDF1) small intestine. Int. J. Radiat. Biol. 58, 925–973 (1990).

    Article  PubMed  CAS  Google Scholar 

  6. Leushacke, M. & Barker, N. Ex vivo culture of the intestinal epithelium: strategies and applications. Gut 63, 1345–1354 (2014).

    Article  PubMed  CAS  Google Scholar 

  7. Bellafante, E. et al. PGC-1beta promotes enterocyte lifespan and tumorigenesis in the intestine. Proc. Natl Acad. Sci. USA 111, E4523–E4531 (2014).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  8. D’Errico, I. et al. Peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC1alpha) is a metabolic regulator of intestinal epithelial cell fate. Proc. Natl Acad. Sci. USA 108, 6603–6608 (2011). This paper identified PGC1α as driver of mitochondrial biogenesis and respiration in IECs and the balance of ROS accumulation and antioxidant enzyme activities as metabolic regulator of IEC fate.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  9. Rodriguez-Colman, M. J. et al. Interplay between metabolic identities in the intestinal crypt supports stem cell function. Nature 543, 424–427 (2017). This research shows that Lgr5 + CBCs and Paneth cells display different metabolic programmes, with Paneth cells supporting intestinal stem cell function by providing lactate to sustain the enhanced mitochondrial oxidative phosphorylation in the Lgr5 + CBCs.

    Article  PubMed  CAS  Google Scholar 

  10. Sethi, J. K. & Vidal-Puig, A. Wnt signalling and the control of cellular metabolism. Biochem. J. 427, 1–17 (2010).

    Article  PubMed  CAS  Google Scholar 

  11. Berger, E. et al. Mitochondrial function controls intestinal epithelial stemness and proliferation. Nat. Commun. 7, 13171 (2016). This paper demonstrates that mitochondrial function has a critical role in maintaining intestinal stemness and homeostasis and links mitochondrial unfolded protein response to mitochondrial dysfunction.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Heijmans, J. et al. ER stress causes rapid loss of intestinal epithelial stemness through activation of the unfolded protein response. Cell Rep. 3, 1128–1139 (2013).

    Article  PubMed  CAS  Google Scholar 

  13. Ohashi, W. et al. Zinc transporter SLC39A7/ZIP7 promotes intestinal epithelial self-renewal by resolving ER stress. PLoS Genet. 12, e1006349 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Rath, E. & Haller, D. Mitochondria at the interface between danger signaling and metabolism: role of unfolded protein responses in chronic inflammation. Inflamm. Bowel Dis. 18, 1364–1377 (2012).

    Article  PubMed  Google Scholar 

  15. Ryan, M. T. & Hoogenraad, N. J. Mitochondrial-nuclear communications. Annu. Rev. Biochem. 76, 701–722 (2007).

    Article  PubMed  CAS  Google Scholar 

  16. Cabibi, D. et al. CD1A-positive cells and HSP60 (HSPD1) levels in keratoacanthoma and squamous cell carcinoma. Cell Stress Chaperones 21, 131–137 (2016).

    Article  PubMed  CAS  Google Scholar 

  17. Tong, W. W., Tong, G. H., Kong, H. & Liu, Y. The tumor promoting roles of HSP60 and HIF2alpha in gastric cancer cells. Tumour Biol. 37, 9849–9854 (2016).

    Article  PubMed  CAS  Google Scholar 

  18. Rappa, F. et al. Quantitative patterns of Hsps in tubular adenoma compared with normal and tumor tissues reveal the value of Hsp10 and Hsp60 in early diagnosis of large bowel cancer. Cell Stress Chaperones 21, 927–933 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Hwang, Y. J. et al. Expression of heat shock protein 60 kDa is upregulated in cervical cancer. Yonsei Med. J. 50, 399–406 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Castilla, C. et al. Immunohistochemical expression of Hsp60 correlates with tumor progression and hormone resistance in prostate cancer. Urology 76, 1017.e1–1017.e6 (2010).

    Article  Google Scholar 

  21. Hamrita, B. et al. Identification of tumor antigens that elicit a humoral immune response in breast cancer patients’ sera by serological proteome analysis (SERPA). Clin. Chim. Acta 393, 95–102 (2008).

    Article  PubMed  CAS  Google Scholar 

  22. Piselli, P. et al. Different expression of CD44, ICAM-1, and HSP60 on primary tumor and metastases of a human pancreatic carcinoma growing in scid mice. Anticancer Res. 20, 825–831 (2000).

    PubMed  CAS  Google Scholar 

  23. De Cecco, L. et al. Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2. Oncogene 23, 8171–8183 (2004).

    Article  PubMed  CAS  Google Scholar 

  24. Rath, E. et al. Induction of dsRNA-activated protein kinase links mitochondrial unfolded protein response to the pathogenesis of intestinal inflammation. Gut 61, 1269–1278 (2012). This study identifies dsRNA-activated protein kinase as mediator of the MT-UPR and demonstrates MT-UPR activation in intestinal epithelial cells from patients with IBD and from mouse models of intestinal inflammation.

    Article  PubMed  CAS  Google Scholar 

  25. Scorrano, L. Keeping mitochondria in shape: a matter of life and death. Eur. J. Clin. Invest. 43, 886–893 (2013).

    Article  PubMed  CAS  Google Scholar 

  26. Brookes, P. S. et al. Control of mitochondrial respiration by NO*, effects of low oxygen and respiratory state. J. Biol. Chem. 278, 31603–31609 (2003).

    Article  PubMed  CAS  Google Scholar 

  27. Zong, H. et al. AMP kinase is required for mitochondrial biogenesis in skeletal muscle in response to chronic energy deprivation. Proc. Natl Acad. Sci. USA 99, 15983–15987 (2002).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  28. Kelly, D. P. & Scarpulla, R. C. Transcriptional regulatory circuits controlling mitochondrial biogenesis and function. Genes Dev. 18, 357–368 (2004).

    Article  PubMed  CAS  Google Scholar 

  29. Schell, J. C. et al. Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism. Nat. Cell Biol. 19, 1027–1036 (2017). This study shows that mitochondrial pyruvate metabolism is important for ISC maintenance and that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain ISC proliferation.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  30. Bukau, B., Weissman, J. & Horwich, A. Molecular chaperones and protein quality control. Cell 125, 443–451 (2006).

    Article  PubMed  CAS  Google Scholar 

  31. Ron, D. & Walter, P. Signal integration in the endoplasmic reticulum unfolded protein response. Nat. Rev. Mol. Cell Biol. 8, 519–529 (2007).

    Article  PubMed  CAS  Google Scholar 

  32. Aldridge, J. E., Horibe, T. & Hoogenraad, N. J. Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements. PLoS ONE 2, e874 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Zhao, Q. et al. A mitochondrial specific stress response in mammalian cells. EMBO J. 21, 4411–4419 (2002). This paper was the first description and characterization of the mitochondrial unfolded protein stress response in mammalian cells.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Martinus, R. D. et al. Selective induction of mitochondrial chaperones in response to loss of the mitochondrial genome. Eur. J. Biochem. 240, 98–103 (1996).

    Article  PubMed  CAS  Google Scholar 

  35. Nargund, A. M., Fiorese, C. J., Pellegrino, M. W., Deng, P. & Haynes, C. M. Mitochondrial and nuclear accumulation of the transcription factor ATFS-1 promotes OXPHOS recovery during the UPR(mt). Mol. Cell 58, 123–133 (2015). This study identifies the transcription factor ATFS-1 as important factor for the recovery of the OXPHOS machinery under MT-UPR conditions, next to regulating genes involved in proteostasis in C. elegans.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. He, C., Hart, P. C., Germain, D. & Bonini, M. G. SOD2 and the mitochondrial UPR: partners regulating cellular phenotypic transitions. Trends Biochem. Sci. 41, 568–577 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Horibe, T. & Hoogenraad, N. J. The chop gene contains an element for the positive regulation of the mitochondrial unfolded protein response. PLoS ONE 2, e835 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  38. Pellegrino, M. W., Nargund, A. M. & Haynes, C. M. Signaling the mitochondrial unfolded protein response. Biochim. Biophys. Acta 1833, 410–416 (2013).

    Article  PubMed  CAS  Google Scholar 

  39. Yano, M. ABCB10 depletion reduces unfolded protein response in mitochondria. Biochem. Biophys. Res. Commun. 486, 465–469 (2017).

    Article  PubMed  CAS  Google Scholar 

  40. Jovaisaite, V., Mouchiroud, L. & Auwerx, J. The mitochondrial unfolded protein response, a conserved stress response pathway with implications in health and disease. J. Exp. Biol. 217, 137–143 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Ishikawa, F. et al. Gene expression profiling identifies a role for CHOP during inhibition of the mitochondrial respiratory chain. J. Biochem. 146, 123–132 (2009).

    Article  PubMed  CAS  Google Scholar 

  42. Quiros, P. M. et al. Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals. J. Cell Biol. 216, 2027–2045 (2017). This study identifies activating transcription factor 4 as the main regulator of the mammalian response towards mitochondrial stress.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Fiorese, C. J. et al. The transcription factor ATF5 mediates a mammalian mitochondrial UPR. Curr. Biol. 26, 2037–2043 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Baker, B. M., Nargund, A. M., Sun, T. & Haynes, C. M. Protective coupling of mitochondrial function and protein synthesis via the eIF2alpha kinase GCN-2. PLoS Genet. 8, e1002760 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  45. Hood, D. A., Irrcher, I., Ljubicic, V. & Joseph, A. M. Coordination of metabolic plasticity in skeletal muscle. J. Exp. Biol. 209, 2265–2275 (2006).

    Article  PubMed  CAS  Google Scholar 

  46. Lin, Y. F. & Haynes, C. M. Metabolism and the UPR(mt). Mol. Cell 61, 677–682 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  47. Kim, H. E. et al. Lipid biosynthesis coordinates a mitochondrial-to-cytosolic stress response. Cell 166, 1539–1552.e16 (2016). This paper demonstrates a conserved mechanism linking mitochondrial protein homeostasis and the cytosolic folding environment through changes in lipid homeostasis.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Zhang, Y. et al. SIRT3 and SIRT5 regulate the enzyme activity and cardiolipin binding of very long-chain acyl-CoA dehydrogenase. PLoS ONE 10, e0122297 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Berendzen, K. M. et al. Neuroendocrine coordination of mitochondrial stress signaling and proteostasis. Cell 166, 1553–1563.e10 (2016). This research shows that neuronal mitochondrial stress induces a cell-non-autonomous MT-UPR, eliciting a global induction of MT-UPR-specific changes, thereby affecting whole-animal physiology.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Durieux, J., Wolff, S. & Dillin, A. The cell-non-autonomous nature of electron transport chain-mediated longevity. Cell 144, 79–91 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  51. Murphy, M. P. How mitochondria produce reactive oxygen species. Biochem. J. 417, 1–13 (2009).

    Article  PubMed  CAS  Google Scholar 

  52. Muller, F. L., Liu, Y. & Van Remmen, H. Complex III releases superoxide to both sides of the inner mitochondrial membrane. J. Biol. Chem. 279, 49064–49073 (2004).

    Article  PubMed  CAS  Google Scholar 

  53. Lustgarten, M. S. et al. Complex I generated, mitochondrial matrix-directed superoxide is released from the mitochondria through voltage dependent anion channels. Biochem. Biophys. Res. Commun. 422, 515–521 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  54. Tatsuta, T., Scharwey, M. & Langer, T. Mitochondrial lipid trafficking. Trends Cell Biol. 24, 44–52 (2014).

    Article  PubMed  CAS  Google Scholar 

  55. Cadenas, E. & Davies, K. J. Mitochondrial free radical generation, oxidative stress, and aging. Free Radic. Biol. Med. 29, 222–230 (2000).

    Article  PubMed  CAS  Google Scholar 

  56. Riemer, J., Schwarzlander, M., Conrad, M. & Herrmann, J. M. Thiol switches in mitochondria: operation and physiological relevance. Biol. Chem. 396, 465–482 (2015).

    Article  PubMed  CAS  Google Scholar 

  57. Smeitink, J. A., Zeviani, M., Turnbull, D. M. & Jacobs, H. T. Mitochondrial medicine: a metabolic perspective on the pathology of oxidative phosphorylation disorders. Cell Metab. 3, 9–13 (2006).

    Article  PubMed  CAS  Google Scholar 

  58. Chandel, N. S. et al. Mitochondrial reactive oxygen species trigger hypoxia-induced transcription. Proc. Natl Acad. Sci. USA 95, 11715–11720 (1998).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  59. Bell, E. L. et al. The Qo site of the mitochondrial complex III is required for the transduction of hypoxic signaling via reactive oxygen species production. J. Cell Biol. 177, 1029–1036 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  60. Raimundo, N. et al. Mitochondrial stress engages E2F1 apoptotic signaling to cause deafness. Cell 148, 716–726 (2012). This study demonstrates that mitochondrial stress and dysfunction engage specific cellular signalling cascades in the context of a human pathology caused by a mitochondrial DNA mutation.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  61. Formentini, L., Sanchez-Arago, M., Sanchez-Cenizo, L. & Cuezva, J. M. The mitochondrial ATPase inhibitory factor 1 triggers a ROS-mediated retrograde prosurvival and proliferative response. Mol. Cell 45, 731–742 (2012).

    Article  PubMed  CAS  Google Scholar 

  62. Raimundo, N. Mitochondrial pathology: stress signals from the energy factory. Trends Mol. Med. 20, 282–292 (2014).

    Article  PubMed  CAS  Google Scholar 

  63. Hamanaka, R. B. et al. Mitochondrial reactive oxygen species promote epidermal differentiation and hair follicle development. Sci. Signal. 6, ra8 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  64. West, A. P. et al. TLR signalling augments macrophage bactericidal activity through mitochondrial ROS. Nature 472, 476–480 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  65. Schroeder, E. A., Raimundo, N. & Shadel, G. S. Epigenetic silencing mediates mitochondria stress-induced longevity. Cell Metab. 17, 954–964 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Zarse, K. et al. Impaired insulin/IGF1 signaling extends life span by promoting mitochondrial L-proline catabolism to induce a transient ROS signal. Cell Metab. 15, 451–465 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Senapedis, W. T., Kennedy, C. J., Boyle, P. M. & Silver, P. A. Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. Mol. Biol. Cell 22, 1791–1805 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  68. Lim, J. H., Lee, H. J., Ho Jung, M. & Song, J. Coupling mitochondrial dysfunction to endoplasmic reticulum stress response: a molecular mechanism leading to hepatic insulin resistance. Cell Signal. 21, 169–177 (2009).

    Article  PubMed  CAS  Google Scholar 

  69. Fukushima, K. & Fiocchi, C. Paradoxical decrease of mitochondrial DNA deletions in epithelial cells of active ulcerative colitis patients. Am. J. Physiol. Gastrointest. Liver Physiol. 286, G804–G813 (2004).

    Article  PubMed  CAS  Google Scholar 

  70. Haga, N. et al. Mitochondria regulate the unfolded protein response leading to cancer cell survival under glucose deprivation conditions. Cancer Sci. (2010).

  71. Barker, N., van Oudenaarden, A. & Clevers, H. Identifying the stem cell of the intestinal crypt: strategies and pitfalls. Cell Stem Cell 11, 452–460 (2012).

    Article  PubMed  CAS  Google Scholar 

  72. Tan, S. & Barker, N. Epithelial stem cells and intestinal cancer. Semin. Cancer Biol. 32, 40–53 (2015).

    Article  PubMed  CAS  Google Scholar 

  73. Barriga, F. M. et al. Mex3a Marks a Slowly Dividing Subpopulation of Lgr5+ Intestinal Stem Cells. Cell Stem Cell 20, 801–816.e7 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  74. Roth, S. et al. Paneth cells in intestinal homeostasis and tissue injury. PLoS ONE 7, e38965 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  75. Nakanishi, Y. et al. Dclk1 distinguishes between tumor and normal stem cells in the intestine. Nat. Genet. 45, 98–103 (2013).

    Article  PubMed  CAS  Google Scholar 

  76. Tsubouchi, S. & Leblond, C. P. Migration and turnover of entero-endocrine and caveolated cells in the epithelium of the descending colon, as shown by radioautography after continuous infusion of 3H-thymidine into mice. Am. J. Anat. 156, 431–451 (1979).

    Article  PubMed  CAS  Google Scholar 

  77. Folmes, C. D., Dzeja, P. P., Nelson, T. J. & Terzic, A. Metabolic plasticity in stem cell homeostasis and differentiation. Cell Stem Cell 11, 596–606 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Zhang, J., Nuebel, E., Daley, G. Q., Koehler, C. M. & Teitell, M. A. Metabolic regulation in pluripotent stem cells during reprogramming and self-renewal. Cell Stem Cell 11, 589–595 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  79. Xu, X. et al. Mitochondrial regulation in pluripotent stem cells. Cell Metab. 18, 325–332 (2013).

    Article  PubMed  CAS  Google Scholar 

  80. Cho, Y. M. et al. Dynamic changes in mitochondrial biogenesis and antioxidant enzymes during the spontaneous differentiation of human embryonic stem cells. Biochem. Biophys. Res. Commun. 348, 1472–1478 (2006). This study shows that differentiation of human embryonic stem cells is accompanied by dynamic changes in mitochondrial mass, ATP and ROS production, as well as antioxidant enzyme expressions.

    Article  PubMed  CAS  Google Scholar 

  81. Hom, J. R. et al. The permeability transition pore controls cardiac mitochondrial maturation and myocyte differentiation. Dev. Cell 21, 469–478 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  82. Tormos, K. V. et al. Mitochondrial complex III ROS regulate adipocyte differentiation. Cell Metab. 14, 537–544 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  83. Kasahara, A. et al. Mitochondrial fusion directs cardiomyocyte differentiation via calcineurin and Notch signaling. Science 342, 734–737 (2013).

    Article  PubMed  CAS  Google Scholar 

  84. Yuan, D. et al. Kupffer cell-derived tnf triggers cholangiocellular tumorigenesis through JNK due to chronic mitochondrial dysfunction and ROS. Cancer Cell 31, 771–789.e6 (2017).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  85. Waldschmitt, N. et al. C/EBP homologous protein inhibits tissue repair in response to gut injury and is inversely regulated with chronic inflammation. Mucosal Immunol. 7, 1452–1466 (2014).

    Article  PubMed  CAS  Google Scholar 

  86. Chandel, N. S., Jasper, H., Ho, T. T. & Passegue, E. Metabolic regulation of stem cell function in tissue homeostasis and organismal ageing. Nat. Cell Biol. 18, 823–832 (2016).

    Article  PubMed  CAS  Google Scholar 

  87. Mohrin, M. et al. Stem cell aging. A mitochondrial UPR-mediated metabolic checkpoint regulates hematopoietic stem cell aging. Science 347, 1374–1377 (2015). This research identifies a regulatory branch of the mitochondrial unfolded protein response, which is coupled to cellular energy metabolism and proliferation, and determines hematopoietic stem cell quiescence and regenerative capacity.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  88. Kobayashi, M. et al. The antioxidant defense system Keap1-Nrf2 comprises a multiple sensing mechanism for responding to a wide range of chemical compounds. Mol. Cell. Biol. 29, 493–502 (2009).

    Article  PubMed  CAS  Google Scholar 

  89. Li, Q. & Engelhardt, J. F. Interleukin-1beta induction of NFkappaB is partially regulated by H2O2-mediated activation of NFkappaB-inducing kinase. J. Biol. Chem. 281, 1495–1505 M511153200 (2006).

    Article  PubMed  CAS  Google Scholar 

  90. Rera, M. et al. Modulation of longevity and tissue homeostasis by the Drosophila PGC-1 homolog. Cell Metab. 14, 623–634 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  91. Laplante, M. & Sabatini, D. M. mTOR signaling in growth control and disease. Cell 149, 274–293 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  92. Jasper, H. & Jones, D. L. Metabolic regulation of stem cell behavior and implications for aging. Cell Metab. 12, 561–565 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  93. Sampson, L. L., Davis, A. K., Grogg, M. W. & Zheng, Y. mTOR disruption causes intestinal epithelial cell defects and intestinal atrophy postinjury in mice. FASEB J. 30, 1263–1275 (2016).

    Article  PubMed  CAS  Google Scholar 

  94. Chen, T. et al. Rapamycin and other longevity-promoting compounds enhance the generation of mouse induced pluripotent stem cells. Aging Cell 10, 908–911 (2011).

    Article  PubMed  CAS  Google Scholar 

  95. Chen, C. et al. TSC-mTOR maintains quiescence and function of hematopoietic stem cells by repressing mitochondrial biogenesis and reactive oxygen species. J. Exp. Med. 205, 2397–2408 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  96. Yilmaz, O. H. et al. mTORC1 in the Paneth cell niche couples intestinal stem-cell function to calorie intake. Nature 486, 490–495 (2012). This paper demonstrates that caloric restriction augments intestinal stem cell function via mTOR-signalling in Paneth cells to couple this process to organismal physiology.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Kaiko, G. E. et al. The colonic crypt protects stem cells from microbiota-derived metabolites. Cell 165, 1708–1720 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  98. Donohoe, D. R. et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab. 13, 517–526 (2011). This study shows that the microbiome via butyrate production ensures energy homeostasis in colonocytes, and that colonocytes from germ-free mice exhibit decreased oxidative phosphorylation, decreased expression of enzymes in the intermediary metabolism, and decreased ATP levels.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  100. Jeynes, B. J. & Altmann, G. G. A region of mitochondrial division in the epithelium of the small intestine of the rat. Anat. Rec. 182, 289–296 (1975).

    Article  PubMed  CAS  Google Scholar 

  101. Lin, J. E. et al. The hormone receptor GUCY2C suppresses intestinal tumor formation by inhibiting AKT signaling. Gastroenterology 138, 241–254 (2010).

    Article  PubMed  CAS  Google Scholar 

  102. Cristofaro, M. et al. Adenomatous polyposis coli (APC)-induced apoptosis of HT29 colorectal cancer cells depends on mitochondrial oxidative metabolism. Biochim. Biophys. Acta 1852, 1719–1728 (2015).

    Article  PubMed  CAS  Google Scholar 

  103. Wu, Z. et al. Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1. Cell 98, 115–124 (1999).

    Article  PubMed  CAS  Google Scholar 

  104. Lin, J. et al. Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres. Nature 418, 797–801 (2002).

    Article  PubMed  CAS  Google Scholar 

  105. Kumar, N. et al. A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis. Development 143, 3711–3722 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  106. Blattler, S. M. et al. Defective mitochondrial morphology and bioenergetic function in mice lacking the transcription factor Yin Yang 1 in skeletal muscle. Mol. Cell. Biol. 32, 3333–3346 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  107. Cunningham, J. T. et al. mTOR controls mitochondrial oxidative function through a YY1-PGC-1alpha transcriptional complex. Nature 450, 736–740 (2007).

    Article  PubMed  CAS  Google Scholar 

  108. Kluck, R. M., Bossy-Wetzel, E., Green, D. R. & Newmeyer, D. D. The release of cytochrome c from mitochondria: a primary site for Bcl-2 regulation of apoptosis. Science 275, 1132–1136 (1997).

    Article  PubMed  CAS  Google Scholar 

  109. Turan, A. & Mahmood, A. The profile of antioxidant systems and lipid peroxidation across the crypt-villus axis in rat intestine. Dig. Dis. Sci. 52, 1840–1844 (2007).

    Article  PubMed  CAS  Google Scholar 

  110. D’Errico, I. et al. Bax is necessary for PGC1alpha pro-apoptotic effect in colorectal cancer cells. Cell Cycle 10, 2937–2945 (2011).

    Article  PubMed  CAS  Google Scholar 

  111. Boohaker, R. J., Zhang, G., Carlson, A. L., Nemec, K. N. & Khaled, A. R. BAX supports the mitochondrial network, promoting bioenergetics in nonapoptotic cells. Am. J. Physiol. Cell Physiol. 300, C1466–1478 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  112. McCarthy, N. Metabolism: a TIGAR tale. Nat. Rev. Cancer 13, 522 (2013).

    Article  PubMed  CAS  Google Scholar 

  113. Cheung, E. C. et al. TIGAR is required for efficient intestinal regeneration and tumorigenesis. Dev. Cell 25, 463–477 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  114. Cheung, E. C. et al. Opposing effects of TIGAR- and RAC1-derived ROS on Wnt-driven proliferation in the mouse intestine. Genes Dev. 30, 52–63 (2016). This paper shows that two key targets in the Wnt pathway function to integrate pro-proliferative and anti-proliferative effects of ROS, modulating cell proliferation.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  115. O’Hara, A. M. & Shanahan, F. The gut flora as a forgotten organ. EMBO Rep. 7, 688–693 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  116. Macpherson, A. J. & McCoy, K. D. Standardised animal models of host microbial mutualism. Mucosal Immunol. 8, 476–486 (2015).

    Article  PubMed  CAS  Google Scholar 

  117. Chu, H. & Mazmanian, S. K. Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat. Immunol. 14, 668–675 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  118. Haller, D., Russo, M. P., Sartor, R. B. & Jobin, C. IKK beta and phosphatidylinositol 3-kinase/Akt participate in non-pathogenic Gram-negative enteric bacteria-induced RelA phosphorylation and NF-kappa B activation in both primary and intestinal epithelial cell lines. J. Biol. Chem. 277, 38168–38178 (2002).

    Article  PubMed  CAS  Google Scholar 

  119. Haller, D. et al. Transforming growth factor-beta 1 inhibits non-pathogenic Gram negative bacteria-induced NF-kappa B recruitment to the interleukin-6 gene promoter in intestinal epithelial cells through modulation of histone acetylation. J. Biol. Chem. 278, 23851–23860 (2003).

    Article  PubMed  CAS  Google Scholar 

  120. Nenci, A. et al. Epithelial NEMO links innate immunity to chronic intestinal inflammation. Nature 446, 557–561 (2007).

    Article  PubMed  CAS  Google Scholar 

  121. Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S. & Medzhitov, R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118, 229–241 (2004).

    Article  PubMed  CAS  Google Scholar 

  122. Rakoff-Nahoum, S. & Medzhitov, R. Regulation of spontaneous intestinal tumorigenesis through the adaptor protein MyD88. Science 317, 124–127 (2007). This study identifies bacterial sensing and innate immune signalling as important contributors to spontaneous and carcinogen-induced intestinal tumour development.

    Article  PubMed  CAS  Google Scholar 

  123. Koh, A., De Vadder, F., Kovatcheva-Datchary, P. & Backhed, F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165, 1332–1345 (2016).

    Article  PubMed  CAS  Google Scholar 

  124. Wahlstrom, A., Sayin, S. I., Marschall, H. U. & Backhed, F. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab. 24, 41–50 (2016).

    Article  PubMed  CAS  Google Scholar 

  125. Lamas, B. et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat. Med. 22, 598–605 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  126. Li, Y. et al. Exogenous stimuli maintain intraepithelial lymphocytes via aryl hydrocarbon receptor activation. Cell 147, 629–640 (2011).

    Article  PubMed  CAS  Google Scholar 

  127. Bjeldanes, L. F., Kim, J. Y., Grose, K. R., Bartholomew, J. C. & Bradfield, C. A. Aromatic hydrocarbon responsiveness-receptor agonists generated from indole-3-carbinol in vitro and in vivo: comparisons with 2,3,7,8-tetrachlorodibenzo-p-dioxin. Proc. Natl Acad. Sci. USA 88, 9543–9547 (1991).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  128. Hwang, H. J. et al. Mitochondrial-targeted aryl hydrocarbon receptor and the impact of 2,3,7,8-tetrachlorodibenzo-p-dioxin on cellular respiration and the mitochondrial proteome. Toxicol. Appl. Pharmacol. 304, 121–132 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  129. Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).

    Article  PubMed  CAS  Google Scholar 

  130. O’Keefe, S. J. Diet, microorganisms and their metabolites, and colon cancer. Nat. Rev. Gastroenterol. Hepatol. 13, 691–706 (2016).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  131. Wichmann, A. et al. Microbial modulation of energy availability in the colon regulates intestinal transit. Cell Host Microbe 14, 582–590 (2013).

    Article  PubMed  CAS  Google Scholar 

  132. Greiner, T. U. & Backhed, F. Microbial regulation of GLP-1 and L-cell biology. Mol. Metab. 5, 753–758 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  133. Donohoe, D. R., Wali, A., Brylawski, B. P. & Bultman, S. J. Microbial regulation of glucose metabolism and cell-cycle progression in mammalian colonocytes. PLoS ONE 7, e46589 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  134. Kien, C. L. et al. Cecal infusion of butyrate increases intestinal cell proliferation in piglets. J. Nutr. 137, 916–922 (2007).

    Article  PubMed  CAS  Google Scholar 

  135. Guzman, J. R., Conlin, V. S. & Jobin, C. Diet, microbiome, and the intestinal epithelium: an essential triumvirate? Biomed. Res. Int. 2013, 425146 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  136. Zietek, T. & Rath, E. Inflammation meets metabolic disease: gut feeling mediated by GLP-1. Front. Immunol. 7, 154 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  137. Ni, J., Wu, G. D., Albenberg, L. & Tomov, V. T. Gut microbiota and IBD: causation or correlation? Nat. Rev. Gastroenterol. Hepatol. 14, 573–584 (2017).

    PubMed  PubMed Central  Google Scholar 

  138. Huda-Faujan, N. et al. The impact of the level of the intestinal short chain fatty acids in inflammatory bowel disease patients versus healthy subjects. Open Biochem. J. 4, 53–58 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  139. Sun, M., Wu, W., Liu, Z. & Cong, Y. Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases. J. Gastroenterol. 52, 1–8 (2017).

    Article  PubMed  CAS  Google Scholar 

  140. Fuentes, S. et al. Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J. 8, 1621–1633 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  141. Gribble, F. M. & Reimann, F. Enteroendocrine cells: chemosensors in the intestinal epithelium. Annu. Rev. Physiol. 78, 277–299 (2016).

    Article  PubMed  CAS  Google Scholar 

  142. Cipriani, S. et al. The bile acid receptor GPBAR-1 (TGR5) modulates integrity of intestinal barrier and immune response to experimental colitis. PLoS ONE 6, e25637 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  143. Neal, M. D. et al. Toll-like receptor 4 is expressed on intestinal stem cells and regulates their proliferation and apoptosis via the p53 up-regulated modulator of apoptosis. J. Biol. Chem. 287, 37296–37308 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  144. Santaolalla, R. et al. TLR4 activates the beta-catenin pathway to cause intestinal neoplasia. PLoS ONE 8, e63298 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  145. Nigro, G., Rossi, R., Commere, P. H., Jay, P. & Sansonetti, P. J. The cytosolic bacterial peptidoglycan sensor Nod2 affords stem cell protection and links microbes to gut epithelial regeneration. Cell Host Microbe 15, 792–798 (2014).

    Article  PubMed  CAS  Google Scholar 

  146. Kato, M. et al. The ROS-generating oxidase Nox1 is required for epithelial restitution following colitis. Exp. Anim. 65, 197–205 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  147. Datta, A. et al. Mouse lung development and NOX1 induction during hyperoxia are developmentally regulated and mitochondrial ROS dependent. Am. J. Physiol. Lung Cell. Mol. Physiol. 309, L369–377 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Chiarugi, P. et al. Reactive oxygen species as essential mediators of cell adhesion: the oxidative inhibition of a FAK tyrosine phosphatase is required for cell adhesion. J. Cell Biol. 161, 933–944 (2003).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  149. Ogier-Denis, E., Mkaddem, S. B. & Vandewalle, A. NOX enzymes and Toll-like receptor signaling. Semin. Immunopathol. 30, 291–300 (2008).

    Article  PubMed  CAS  Google Scholar 

  150. Jones, R. M., Mercante, J. W. & Neish, A. S. Reactive oxygen production induced by the gut microbiota: pharmacotherapeutic implications. Curr. Med. Chem. 19, 1519–1529 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  151. Lee, S. R. et al. Reversible inactivation of the tumor suppressor PTEN by H2O2. J. Biol. Chem. 277, 20336–20342 (2002).

    Article  PubMed  CAS  Google Scholar 

  152. Rhodes, J. M. & Campbell, B. J. Inflammation and colorectal cancer: IBD-associated and sporadic cancer compared. Trends Mol. Med. 8, 10–16 (2002).

    Article  PubMed  CAS  Google Scholar 

  153. Miyoshi, H. et al. Prostaglandin E2 promotes intestinal repair through an adaptive cellular response of the epithelium. EMBO J. 36, 5–24 (2017). This study characterizes formation of metabolically distinct wound-associated epithelial cells via the PGE2-Ptger4 pathway by adaptive cellular reprogramming of the intestinal epithelium following intestinal injury.

    Article  PubMed  CAS  Google Scholar 

  154. Marino Gammazza, A. et al. Doxorubicin anti-tumor mechanisms include Hsp60 post-translational modifications leading to the Hsp60/p53 complex dissociation and instauration of replicative senescence. Cancer Lett. 385, 75–86 (2017).

    Article  PubMed  CAS  Google Scholar 

  155. Tsai, Y. P. et al. Interaction between HSP60 and beta-catenin promotes metastasis. Carcinogenesis 30, 1049–1057 (2009).

    Article  PubMed  CAS  Google Scholar 

  156. Molodecky, N. A. et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology 142, 46–54.e2 (2012).

    Article  PubMed  Google Scholar 

  157. Ng, S. C. et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet 390, 2769–2778 (2018).

    Article  Google Scholar 

  158. de Souza, H. S. P., Fiocchi, C. & Iliopoulos, D. The IBD interactome: an integrated view of aetiology, pathogenesis and therapy. Nat. Rev. Gastroenterol. Hepatol. 14, 739–749 (2017).

    Article  PubMed  Google Scholar 

  159. Gersemann, M., Stange, E. F. & Wehkamp, J. From intestinal stem cells to inflammatory bowel diseases. World J. Gastroenterol. 17, 3198–3203 (2011).

    PubMed  PubMed Central  Google Scholar 

  160. Roediger, W. E. The colonic epithelium in ulcerative colitis: an energy-deficiency disease? Lancet 2, 712–715 (1980).

    Article  PubMed  CAS  Google Scholar 

  161. Beltran, B. et al. Mitochondrial dysfunction, persistent oxidative damage, and catalase inhibition in immune cells of naive and treated Crohn’s disease. Inflamm. Bowel Dis. 16, 76–86 (2010).

    Article  PubMed  Google Scholar 

  162. Barrett, J. C. et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn’s disease. Nat. Genet. 40, 955–962 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  163. Yu, X. et al. Association of UCP2 -866 G/A polymorphism with chronic inflammatory diseases. Genes Immun. 10, 601–605 (2009).

    Article  PubMed  CAS  Google Scholar 

  164. Waller, S. et al. Evidence for association of OCTN genes and IBD5 with ulcerative colitis. Gut 55, 809–814 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  165. Rinaldo, P., Matern, D. & Bennett, M. J. Fatty acid oxidation disorders. Annu. Rev. Physiol. 64, 477–502 (2002).

    Article  PubMed  CAS  Google Scholar 

  166. Shekhawat, P. S. et al. Spontaneous development of intestinal and colonic atrophy and inflammation in the carnitine-deficient jvs (OCTN2(−/−)) mice. Mol. Genet. Metab. 92, 315–324 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  167. Roediger, W. E. & Nance, S. Metabolic induction of experimental ulcerative colitis by inhibition of fatty acid oxidation. Br. J. Exp. Pathol. 67, 773–782 (1986).

    PubMed  PubMed Central  CAS  Google Scholar 

  168. Santhanam, S., Venkatraman, A. & Ramakrishna, B. S. Impairment of mitochondrial acetoacetyl CoA thiolase activity in the colonic mucosa of patients with ulcerative colitis. Gut 56, 1543–1549 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  169. Treem, W. R., Ahsan, N., Shoup, M. & Hyams, J. S. Fecal short-chain fatty acids in children with inflammatory bowel disease. J. Pediatr. Gastroenterol. Nutr. 18, 159–164 (1994).

    Article  PubMed  CAS  Google Scholar 

  170. Ritzhaupt, A., Wood, I. S., Ellis, A., Hosie, K. B. & Shirazi-Beechey, S. P. Identification and characterization of a monocarboxylate transporter (MCT1) in pig and human colon: its potential to transport L-lactate as well as butyrate. J. Physiol. 513, 719–732 (1998).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  171. Thibault, R. et al. Down-regulation of the monocarboxylate transporter 1 is involved in butyrate deficiency during intestinal inflammation. Gastroenterology 133, 1916–1927 (2007).

    Article  PubMed  CAS  Google Scholar 

  172. Baur, P. et al. Metabolic phenotyping of the Crohn’s disease-like IBD etiopathology in the TNF(DeltaARE/WT) mouse model. J. Proteome Res. 10, 5523–5535 (2011).

    Article  PubMed  CAS  Google Scholar 

  173. Glover, L. E. & Colgan, S. P. Hypoxia and metabolic factors that influence inflammatory bowel disease pathogenesis. Gastroenterology 140, 1748–1755 (2011).

    Article  PubMed  CAS  Google Scholar 

  174. Colgan, S. P., Curtis, V. F. & Campbell, E. L. The inflammatory tissue microenvironment in IBD. Inflamm. Bowel Dis. 19, 2238–2244 (2013).

    Article  PubMed  Google Scholar 

  175. Colgan, S. P. & Taylor, C. T. Hypoxia: an alarm signal during intestinal inflammation. Nat. Rev. Gastroenterol. Hepatol. 7, 281–287 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  176. Campbell, E. L. et al. Transmigrating neutrophils shape the mucosal microenvironment through localized oxygen depletion to influence resolution of inflammation. Immunity 40, 66–77 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  177. Ledoux, S. et al. Hypoxia enhances Ecto-5′-Nucleotidase activity and cell surface expression in endothelial cells: role of membrane lipids. Circ. Res. 92, 848–855 (2003).

    Article  PubMed  CAS  Google Scholar 

  178. Taylor, C. T. & Cummins, E. P. The role of NF-kappaB in hypoxia-induced gene expression. Ann. NY Acad. Sci 1177, 178–184 (2009).

    Article  PubMed  CAS  Google Scholar 

  179. Giatromanolaki, A. et al. Hypoxia inducible factor 1alpha and 2alpha overexpression in inflammatory bowel disease. J. Clin. Pathol. 56, 209–213 (2003).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  180. Cummins, E. P. et al. The hydroxylase inhibitor dimethyloxalylglycine is protective in a murine model of colitis. Gastroenterology 134, 156–165 (2008).

    Article  PubMed  CAS  Google Scholar 

  181. Ogura, Y. et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 411, 603–606 (2001).

    Article  PubMed  CAS  Google Scholar 

  182. Franchimont, D. et al. Deficient host-bacteria interactions in inflammatory bowel disease? The toll-like receptor (TLR)-4 Asp299gly polymorphism is associated with Crohn’s disease and ulcerative colitis. Gut 53, 987–992 (2004).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  183. Hampe, J. et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat. Genet. 39, 207–211 (2007).

    Article  PubMed  CAS  Google Scholar 

  184. Parkes, M. et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn’s disease susceptibility. Nat. Genet. 39, 830–832 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  185. Travassos, L. H. et al. Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry. Nat. Immunol. 11, 55–62 (2010).

    Article  PubMed  CAS  Google Scholar 

  186. Adolph, T. E. et al. Paneth cells as a site of origin for intestinal inflammation. Nature 503, 272–276 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  187. Cadwell, K. et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456, 259–263 (2008). This study links the ATG16L1 Crohn’s disease risk allele to autophagy, Paneth cell granule abnormalities and degenerating mitochondria.

  188. Wehkamp, J. et al. Reduced Paneth cell alpha-defensins in ileal Crohn’s disease. Proc. Natl Acad. Sci. USA 102, 18129–18134 (2005).

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  189. Singh, S. B. et al. Human IRGM regulates autophagy and cell-autonomous immunity functions through mitochondria. Nat. Cell Biol. 12, 1154–1165 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  190. Chauhan, S., Mandell, M. A. & Deretic, V. IRGM governs the core autophagy machinery to conduct antimicrobial defense. Mol. Cell 58, 507–521 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  191. Pecqueur, C. et al. Uncoupling protein-2 controls proliferation by promoting fatty acid oxidation and limiting glycolysis-derived pyruvate utilization. FASEB J. 22, 9–18 (2008).

    Article  PubMed  CAS  Google Scholar 

  192. Emre, Y. et al. Mitochondria contribute to LPS-induced MAPK activation via uncoupling protein UCP2 in macrophages. Biochem. J. 402, 271–278 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  193. Seth, R. B., Sun, L., Ea, C. K. & Chen, Z. J. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3. Cell 122, 669–682 (2005).

    Article  PubMed  CAS  Google Scholar 

  194. Zhou, R., Yazdi, A. S., Menu, P. & Tschopp, J. A role for mitochondria in NLRP3 inflammasome activation. Nature 469, 221–225 (2011).

    Article  PubMed  CAS  Google Scholar 

  195. Schroder, K. & Tschopp, J. The inflammasomes. Cell 140, 821–832 (2010).

    Article  PubMed  CAS  Google Scholar 

  196. Villani, A. C. et al. Common variants in the NLRP3 region contribute to Crohn’s disease susceptibility. Nat. Genet. 41, 71–76 (2009).

    Article  PubMed  CAS  Google Scholar 

  197. Zhernakova, A. et al. Genetic analysis of innate immunity in Crohn’s disease and ulcerative colitis identifies two susceptibility loci harboring CARD9 and IL18RAP. Am. J. Hum. Genet. 82, 1202–1210 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  198. Lei-Leston, A. C., Murphy, A. G. & Maloy, K. J. Epithelial Cell Inflammasomes in Intestinal Immunity and Inflammation. Front. Immunol. 8, 1168 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  199. Ip, W. K. E., Hoshi, N., Shouval, D. S., Snapper, S. & Medzhitov, R. Anti-inflammatory effect of IL-10 mediated by metabolic reprogramming of macrophages. Science 356, 513–519 (2017). This research shows that the anti-inflammatory cytokine IL-10 controls immune responses by opposing the metabolic switch induced by inflammatory stimuli in macrophages, and promotes mitophagy to eliminate dysfunctional mitochondria.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  200. Kuhn, R., Lohler, J., Rennick, D., Rajewsky, K. & Muller, W. Interleukin-10-deficient mice develop chronic enterocolitis. Cell 75, 263–274 (1993).

    Article  PubMed  CAS  Google Scholar 

  201. Aithal, G. P. et al. Role of polymorphisms in the interleukin-10 gene in determining disease susceptibility and phenotype in inflamatory bowel disease. Dig. Dis. Sci 46, 1520–1525 (2001).

    Article  PubMed  CAS  Google Scholar 

  202. Glocker, E. O., Kotlarz, D., Klein, C., Shah, N. & Grimbacher, B. IL-10 and IL-10 receptor defects in humans. Ann. NY Acad. Sci. 1246, 102–107 (2011).

    Article  PubMed  CAS  Google Scholar 

  203. Mosser, D. M. & Zhang, X. Interleukin-10: new perspectives on an old cytokine. Immunol. Rev. 226, 205–218 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  204. Choi, C. R., Bakir, I. A., Hart, A. L. & Graham, T. A. Clonal evolution of colorectal cancer in IBD. Nat. Rev. Gastroenterol. Hepatol. 14, 218–229 (2017).

    Article  PubMed  Google Scholar 

  205. Schwitalla, S. et al. Intestinal tumorigenesis initiated by dedifferentiation and acquisition of stem-cell-like properties. Cell 152, 25–38 (2013). This study characterizes the contribution of NF-κB signalling in intestinal epithelial cells to Wnt activation, dedifferentiation of nonstem cells and generation of intestinal tumor-initiating cells.

    Article  PubMed  CAS  Google Scholar 

  206. Andersson-Rolf, A., Zilbauer, M., Koo, B. K. & Clevers, H. Stem cells in repair of gastrointestinal epithelia. Physiology 32, 278–289 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  207. Seno, H. et al. Efficient colonic mucosal wound repair requires Trem2 signaling. Proc. Natl Acad. Sci. USA 106, 256–261 (2009).

    Article  PubMed  Google Scholar 

  208. Dignass, A. U. Mechanisms and modulation of intestinal epithelial repair. Inflamm. Bowel Dis. 7, 68–77 (2001).

    Article  PubMed  CAS  Google Scholar 

  209. Miyoshi, H., Ajima, R., Luo, C. T., Yamaguchi, T. P. & Stappenbeck, T. S. Wnt5a potentiates TGF-beta signaling to promote colonic crypt regeneration after tissue injury. Science 338, 108–113 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  210. Kim, T. H. et al. Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity. Nature 506, 511–515 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  211. Mills, J. C. & Sansom, O. J. Reserve stem cells: Differentiated cells reprogram to fuel repair, metaplasia, and neoplasia in the adult gastrointestinal tract. Sci. Signal. 8, re8 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  212. Shao, J., Sheng, G. G., Mifflin, R. C., Powell, D. W. & Sheng, H. Roles of myofibroblasts in prostaglandin E2-stimulated intestinal epithelial proliferation and angiogenesis. Cancer Res. 66, 846–855 (2006).

    Article  PubMed  CAS  Google Scholar 

  213. Li, P. et al. Aspirin use after diagnosis but not prediagnosis improves established colorectal cancer survival: a meta-analysis. Gut 64, 1419–1425 (2015).

    Article  PubMed  CAS  Google Scholar 

  214. Oshima, M. et al. Suppression of intestinal polyposis in Apc delta716 knockout mice by inhibition of cyclooxygenase 2 (COX-2). Cell 87, 803–809 (1996).

    Article  PubMed  CAS  Google Scholar 

  215. Biancone, L., Tosti, C., De Nigris, F., Fantini, M. & Pallone, F. Selective cyclooxygenase-2 inhibitors and relapse of inflammatory bowel disease. Gastroenterology 125, 637–638 (2003).

    Article  PubMed  CAS  Google Scholar 

  216. Vander Heiden, M. G., Cantley, L. C. & Thompson, C. B. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 324, 1029–1033 (2009).

    Article  CAS  Google Scholar 

  217. Medema, J. P. & Vermeulen, L. Microenvironmental regulation of stem cells in intestinal homeostasis and cancer. Nature 474, 318–326 (2011).

    Article  PubMed  CAS  Google Scholar 

  218. Vermeulen, L., Sprick, M. R., Kemper, K., Stassi, G. & Medema, J. P. Cancer stem cells — old concepts, new insights. Cell Death Differ. 15, 947–958 (2008).

    Article  PubMed  CAS  Google Scholar 

  219. Vermeulen, L. et al. Wnt activity defines colon cancer stem cells and is regulated by the microenvironment. Nat. Cell Biol. 12, 468–476 (2010).

    Article  PubMed  CAS  Google Scholar 

  220. Barker, N. et al. Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 457, 608–611 (2009).

    Article  PubMed  CAS  Google Scholar 

  221. van Es, J. H. et al. Notch/gamma-secretase inhibition turns proliferative cells in intestinal crypts and adenomas into goblet cells. Nature 435, 959–963 (2005).

    Article  PubMed  CAS  Google Scholar 

  222. Todaro, M. et al. Colon cancer stem cells dictate tumor growth and resist cell death by production of interleukin-4. Cell Stem Cell 1, 389–402 (2007).

    Article  PubMed  CAS  Google Scholar 

  223. de Sousa, E. M., Vermeulen, L., Richel, D. & Medema, J. P. Targeting Wnt signaling in colon cancer stem cells. Clin. Cancer Res. 17, 647–653 (2011).

    Article  PubMed  CAS  Google Scholar 

  224. Todaro, M., Francipane, M. G., Medema, J. P. & Stassi, G. Colon cancer stem cells: promise of targeted therapy. Gastroenterology 138, 2151–2162 (2010).

    Article  PubMed  CAS  Google Scholar 

  225. Song, I. S. et al. FOXM1-induced PRX3 regulates stemness and survival of colon cancer cells via maintenance of mitochondrial function. Gastroenterology 149, 1006–1016.e9 (2015).

    Article  PubMed  CAS  Google Scholar 

  226. Siegelin, M. D. et al. Exploiting the mitochondrial unfolded protein response for cancer therapy in mice and human cells. J. Clin. Invest. 121, 1349–1360 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  227. Pace, A. et al. Hsp60, a novel target for antitumor therapy: structure-function features and prospective drugs design. Curr. Pharm. Des. 19, 2757–2764 (2013).

    Article  PubMed  CAS  Google Scholar 

  228. Hartl, M. The quest for targets executing MYC-dependent cell transformation. Front. Oncol. 6, 132 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  229. Tsai, Y. P., Teng, S. C. & Wu, K. J. Direct regulation of HSP60 expression by c-MYC induces transformation. FEBS Lett. 582, 4083–4088 (2008).

    Article  PubMed  CAS  Google Scholar 

  230. Yan, F. Q., Wang, J. Q., Tsai, Y. P. & Wu, K. J. HSP60 overexpression increases the protein levels of the p110alpha subunit of phosphoinositide 3-kinase and c-Myc. Clin. Exp. Pharmacol. Physiol. 42, 1092–1097 (2015).

    Article  PubMed  CAS  Google Scholar 

  231. Tang, H. et al. Down-regulation of HSP60 suppresses the proliferation of glioblastoma cells via the ROS/AMPK/mTOR pathway. Sci. Rep. 6, 28388 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  232. Lachat, J. J. & Goncalves, R. P. Influence of autonomic denervation upon the kinetics of the ileal epithelium of the rat. Cell Tissue Res. 192, 285–297 (1978).

    Article  PubMed  CAS  Google Scholar 

  233. Kaur, P. & Potten, C. S. Circadian variation in migration velocity in small intestinal epithelium. Cell Tissue Kinet. 19, 591–599 (1986).

    PubMed  CAS  Google Scholar 

  234. Williams, J. M. et al. Epithelial cell shedding and barrier function: a matter of life and death at the small intestinal villus tip. Vet. Pathol. 52, 445–455 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  235. Burrin, D. G. et al. Glucagon-like peptide 2 dose-dependently activates intestinal cell survival and proliferation in neonatal piglets. Endocrinology 146, 22–32 (2005).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  237. Shirkey, T. W. et al. Effects of commensal bacteria on intestinal morphology and expression of proinflammatory cytokines in the gnotobiotic pig. Exp. Biol. Med. 231, 1333–1345 (2006).

    Article  CAS  Google Scholar 

  238. Fallingborg, J. Intraluminal pH of the human gastrointestinal tract. Dan. Med. Bull. 46, 183–196 (1999).

    PubMed  CAS  Google Scholar 

  239. Taylor, C. T. & Colgan, S. P. Hypoxia and gastrointestinal disease. J. Mol. Med. 85, 1295–1300 (2007).

    Article  PubMed  Google Scholar 

  240. Bohlen, H. G. Intestinal tissue PO2 and microvascular responses during glucose exposure. Am. J. Physiol. 238, H164–H171 (1980).

    PubMed  CAS  Google Scholar 

  241. Arco, A. D. & Satrustegui, J. New mitochondrial carriers: an overview. Cell. Mol. Life Sci. 62, 2204–2227 (2005).

    Article  PubMed  CAS  Google Scholar 

  242. Lehmann, G., Udasin, R. G. & Ciechanover, A. On the linkage between the ubiquitin-proteasome system and the mitochondria. Biochem. Biophys. Res. Commun. 473, 80–86 (2016).

    Article  PubMed  CAS  Google Scholar 

  243. Frey, T. G. & Mannella, C. A. The internal structure of mitochondria. Trends Biochem. Sci. 25, 319–324 (2000).

    Article  PubMed  CAS  Google Scholar 

  244. Koehler, C. M., Beverly, K. N. & Leverich, E. P. Redox pathways of the mitochondrion. Antioxid. Redox Signal. 8, 813–822 (2006).

    Article  PubMed  CAS  Google Scholar 

  245. Amiri, M. & Hollenbeck, P. J. Mitochondrial biogenesis in the axons of vertebrate peripheral neurons. Dev. Neurobiol. 68, 1348–1361 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  246. Chen, H. et al. Mitofusins Mfn1 and Mfn2 coordinately regulate mitochondrial fusion and are essential for embryonic development. J. Cell Biol. 160, 189–200 (2003).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  247. Hayashi, T., Rizzuto, R., Hajnoczky, G. & Su, T. P. MAM: more than just a housekeeper. Trends Cell Biol. 19, 81–88 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  248. James, A. M., Collins, Y., Logan, A. & Murphy, M. P. Mitochondrial oxidative stress and the metabolic syndrome. Trends Endocrinol. Metab. 23, 429–434 (2012).

    Article  PubMed  CAS  Google Scholar 

  249. Kaelin, W. G. Jr & McKnight, S. L. Influence of metabolism on epigenetics and disease. Cell 153, 56–69 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  250. Raimundo, N., Baysal, B. E. & Shadel, G. S. Revisiting the TCA cycle: signaling to tumor formation. Trends Mol. Med. 17, 641–649 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  251. Selak, M. A. et al. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell 7, 77–85 (2005).

    Article  PubMed  CAS  Google Scholar 

  252. Raimundo, N., Vanharanta, S., Aaltonen, L. A., Hovatta, I. & Suomalainen, A. Downregulation of SRF-FOS-JUNB pathway in fumarate hydratase deficiency and in uterine leiomyomas. Oncogene 28, 1261–1273 (2009).

    Article  PubMed  CAS  Google Scholar 

  253. Adam, J. et al. Renal cyst formation in Fh1-deficient mice is independent of the Hif/Phd pathway: roles for fumarate in KEAP1 succination and Nrf2 signaling. Cancer Cell 20, 524–537 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  254. Zhang, Z. et al. Identification of lysine succinylation as a new post-translational modification. Nat. Chem. Biol. 7, 58–63 (2011).

    Article  PubMed  CAS  Google Scholar 

  255. Killela, P. J. et al. Mutations in IDH1, IDH2, and in the TERT promoter define clinically distinct subgroups of adult malignant gliomas. Oncotarget 5, 1515–1525 (2014).

    PubMed  PubMed Central  Google Scholar 

  256. Dang, L. et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 465, 966 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  257. Charitou, P. et al. FOXOs support the metabolic requirements of normal and tumor cells by promoting IDH1 expression. EMBO Rep. 16, 456–466 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  258. Figueroa, M. E. et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18, 553–567 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  259. Hall, J. A., Dominy, J. E., Lee, Y. & Puigserver, P. The sirtuin family’s role in aging and age-associated pathologies. J. Clin. Invest. 123, 973–979 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  260. Folmes, C. D. et al. Somatic oxidative bioenergetics transitions into pluripotency-dependent glycolysis to facilitate nuclear reprogramming. Cell Metab. 14, 264–271 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  261. Zhang, J. et al. UCP2 regulates energy metabolism and differentiation potential of human pluripotent stem cells. EMBO J. 30, 4860–4873 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  262. Wang, J. et al. Dependence of mouse embryonic stem cells on threonine catabolism. Science 325, 435–439 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  263. Ito, K. et al. A PML-PPAR-delta pathway for fatty acid oxidation regulates hematopoietic stem cell maintenance. Nat. Med. 18, 1350–1358 (2012).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  264. Shyh-Chang, N. & Ng, H. H. The metabolic programming of stem cells. Genes Dev. 31, 336–346 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  265. Arnould, T., Michel, S. & Renard, P. Mitochondria retrograde signaling and the UPR mt: where are we in mammals? Int. J. Mol. Sci. 16, 18224–18251 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  266. Quiros, P. M., Mottis, A. & Auwerx, J. Mitonuclear communication in homeostasis and stress. Nat. Rev. Mol. Cell Biol. 17, 213–226 (2016).

    Article  PubMed  CAS  Google Scholar 

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Rath, E., Moschetta, A. & Haller, D. Mitochondrial function — gatekeeper of intestinal epithelial cell homeostasis. Nat Rev Gastroenterol Hepatol 15, 497–516 (2018). https://doi.org/10.1038/s41575-018-0021-x

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