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Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22

Nature volume 647, pages 706–715 (2025) Cite this article

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Abstract

A fundamental question in physiology is understanding how tissues adapt and alter their cellular composition in response to dietary cues1,2,3,4,5,6,7,8. The mammalian small intestine is maintained by rapidly renewing LGR5+ intestinal stem cells (ISCs) that respond to macronutrient changes such as fasting regimens and obesogenic diets, yet how specific amino acids control ISC function during homeostasis and injury remains unclear. Here we demonstrate that dietary cysteine, a semi-essential amino acid, enhances ISC-mediated intestinal regeneration following injury. Cysteine contributes to coenzyme A (CoA) biosynthesis in intestinal epithelial cells, which promotes expansion of intraepithelial CD8αβ+ T cells and their production of interleukin-22 (IL-22). This enhanced IL-22 signalling directly augments ISC reparative capacity after injury. The mechanistic involvement of the pathway in driving the effects of cysteine is demonstrated by several findings: CoA supplementation recapitulates cysteine effects, epithelial-specific loss of the cystine transporter SLC7A11 blocks the response, and mice with CD8αβ+ T cells lacking IL-22 or a depletion of CD8αβ+ T cells fail to show enhanced regeneration despite cysteine treatment. These findings highlight how coupled cysteine metabolism between ISCs and CD8+ T cells augments intestinal stemness, providing a dietary approach that exploits ISC and immune cell crosstalk for ameliorating intestinal damage.

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Fig. 1: Cysteine boosts ISC-mediated regeneration.
The alternative text for this image may have been generated using AI.
Fig. 2: Cysteine expands crypt-associated CD8αβ T cells and their ISC-enhancing ability.
The alternative text for this image may have been generated using AI.
Fig. 3: CD8αβ+ T cell-derived IL-22 mediates the pro-regenerative effects of cysteine.
The alternative text for this image may have been generated using AI.
Fig. 4: Cysteine-derived CoA in the crypt epithelium enhances IL-22 production in CD8αβ+ T cells.
The alternative text for this image may have been generated using AI.
Fig. 5: Epithelial cysteine mediates CoA-induced IL-22 in CD8αβ T cells to promote post-injury repair.
The alternative text for this image may have been generated using AI.

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Data availability

The single-cell RNA sequencing dataset generated in this study is available at the Gene Expression Omnibus repository (GSE279543). The metabolomics data generated and used for this project are available at Metabolomics Workbench (project ID: PR002592; https://doi.org/10.21228/M8M54Q)65. Any additional information required to reanalyse the data reported in this paper is available on request. Source data are provided with this paper.

References

  1. Yilmaz, Ö. H. et al. mTORC1 in the Paneth cell niche couples intestinal stem-cell function to calorie intake. Nature 486, 490–495 (2012).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  2. Imada, S. et al. Short-term post-fast refeeding enhances intestinal stemness via polyamines. Nature 633, 895–904 (2024).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  4. Schell, J. C. et al. Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism. Nat. Cell Biol. 19, 1027–1036 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Mihaylova, M. M. et al. Fasting activates fatty acid oxidation to enhance intestinal stem cell function during homeostasis and aging. Cell Stem Cell 22, 769–778 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Wang, B. et al. Phospholipid remodeling and cholesterol availability regulate intestinal stemness and tumorigenesis. Cell Stem Cell 22, 206–220 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Cheng, C. W. et al. Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet. Cell 178, 1115–1131 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Mana, M. D. et al. High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity. Cell Rep. 35, 109212 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Gehart, H. & Clevers, H. Tales from the crypt: new insights into intestinal stem cells. Nat. Rev. Gastroenterol. Hepatol. 16, 19–34 (2019).

    Article  PubMed  Google Scholar 

  10. Biton, M. et al. T helper cell cytokines modulate intestinal stem cell renewal and differentiation. Cell 175, 1307–1320 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Jiang, H. et al. Cytokine/Jak/Stat signaling mediates regeneration and homeostasis in the Drosophila midgut. Cell 137, 1343–1355 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  12. McCarthy, N. et al. Distinct mesenchymal cell populations generate the essential intestinal BMP signaling gradient. Cell Stem Cell 26, 391–402 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Goto, N. et al. Lymphatics and fibroblasts support intestinal stem cells in homeostasis and injury. Cell Stem Cell 29, 1246–1261 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hou, Q., Huang, J., Ayansola, H., Masatoshi, H. & Zhang, B. Intestinal stem cells and immune cell relationships: potential therapeutic targets for inflammatory bowel diseases. Front. Immunol. 11, 623691 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  15. Valeri, M. & Raffatellu, M. Cytokines IL-17 and IL-22 in the host response to infection. Pathog. Dis. 74, ftw111 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Schreurs, R. et al. Intestinal CD8+ T cell responses are abundantly induced early in human development but show impaired cytotoxic effector capacities. Mucosal Immunol. 14, 605–614 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Lutter, L., Hoytema van Konijnenburg, D. P., Brand, E. C., Oldenburg, B. & van Wijk, F. The elusive case of human intraepithelial T cells in gut homeostasis and inflammation. Nat. Rev. Gastroenterol. Hepatol. 15, 637–649 (2018).

    Article  CAS  PubMed  Google Scholar 

  18. Sullivan, Z. A. et al. γδ T cells regulate the intestinal response to nutrient sensing. Science 371, eaba8310 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hanash, A. M. et al. Interleukin-22 protects intestinal stem cells from immune-mediated tissue damage and regulates sensitivity to graft versus host disease. Immunity 37, 339–350 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Lindemans, C. A. et al. Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration. Nature 528, 560–564 (2015).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Gronke, K. et al. Interleukin-22 protects intestinal stem cells against genotoxic stress. Nature 566, 249–253 (2019).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zenewicz, L. A. et al. Innate and adaptive interleukin-22 protects mice from inflammatory bowel disease. Immunity 29, 947–957 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Aparicio-Domingo, P. et al. Type 3 innate lymphoid cells maintain intestinal epithelial stem cells after tissue damage. J. Exp. Med. 212, 1783–1791 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Keir, M. E., Yi, T., Lu, T. T. & Ghilardi, N. The role of IL-22 in intestinal health and disease. J. Exp. Med. 217, e20192195 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  25. Muñoz, J. et al. The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+ 4’ cell markers. EMBO J. 31, 3079–3091 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333–339 (2017).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  27. Gebert, N. et al. Region-specific proteome changes of the intestinal epithelium during aging and dietary restriction. Cell Rep. 31, 107565 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Hou, Q. et al. Exogenous l-arginine increases intestinal stem cell function through CD90+ stromal cells producing mTORC1-induced Wnt2b. Commun. Biol. 3, 611 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Bannai, S. Exchange of cystine and glutamate across plasma membrane of human fibroblasts. J. Biol. Chem. 261, 2256–2263 (1986).

    Article  CAS  PubMed  Google Scholar 

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

    Article  ADS  CAS  PubMed  Google Scholar 

  31. Huch, M. et al. In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration. Nature 494, 247–250 (2013).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  32. Zhang, L. et al. Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature 564, 268–272 (2018).

    Article  ADS  CAS  PubMed  Google Scholar 

  33. Oliveira, G. et al. Landscape of helper and regulatory antitumour CD4+ T cells in melanoma. Nature 605, 532–538 (2022).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hao, Z. & Rajewsky, K. Homeostasis of peripheral B cells in the absence of B cell influx from the bone marrow. J. Exp. Med. 194, 1151–1164 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Taub, D. D. et al. Recombinant human interferon-inducible protein 10 is a chemoattractant for human monocytes and T lymphocytes and promotes T cell adhesion to endothelial cells. J. Exp. Med. 177, 1809–1814 (1993).

    Article  CAS  PubMed  Google Scholar 

  36. Klein, R. S. et al. Neuronal CXCL10 directs CD8+ T-cell recruitment and control of West Nile virus encephalitis. J. Virol. 79, 11457–11466 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Sabat, R., Ouyang, W. & Wolk, K. Therapeutic opportunities of the IL-22–IL-22R1 system. Nat. Rev. Drug Discov. 13, 21–38 (2014).

    Article  CAS  PubMed  Google Scholar 

  38. Rankin, L. C. et al. Complementarity and redundancy of IL-22-producing innate lymphoid cells. Nat. Immunol. 17, 179–186 (2016).

    Article  CAS  PubMed  Google Scholar 

  39. Corrêa, R. O. et al. Inulin diet uncovers complex diet–microbiota–immune cell interactions remodeling the gut epithelium. Microbiome 11, 90 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Liu, X. et al. Cystine transporter regulation of pentose phosphate pathway dependency and disulfide stress exposes a targetable metabolic vulnerability in cancer. Nat. Cell Biol. 22, 476–486 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Paul, M. S. et al. Coenzyme A fuels T cell anti-tumor immunity. Cell Metab. 33, 2415–2427 (2021).

    Article  Google Scholar 

  42. Dibble, C. C. et al. PI3K drives the de novo synthesis of coenzyme A from vitamin B5. Nature 608, 192–198 (2022).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  43. Barritt, S. A., DuBois-Coyne, S. E. & Dibble, C. C. Coenzyme A biosynthesis: mechanisms of regulation, function and disease. Nat. Metab. 6, 1008–1023 (2024).

    Article  CAS  PubMed  Google Scholar 

  44. Sibon, O. C. M. & Strauss, E. Coenzyme A: to make it or uptake it? Nat. Rev. Mol. Cell Biol. 17, 605–606 (2016).

    Article  CAS  PubMed  Google Scholar 

  45. Siudeja, K. et al. Impaired coenzyme A metabolism affects histone and tubulin acetylation in Drosophila and human cell models of pantothenate kinase associated neurodegeneration. EMBO Mol. Med. 3, 755–766 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Srinivasan, B. et al. Extracellular 4′-phosphopantetheine is a source for intracellular coenzyme A synthesis. Nat. Chem. Biol. 11, 784–792 (2015).

    Article  CAS  PubMed  Google Scholar 

  47. Tu, W. B., Christofk, H. R. & Plath, K. Nutrient regulation of development and cell fate decisions. Development 150, dev199961 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  49. Shyh-Chang, N. et al. Influence of threonine metabolism on S-adenosylmethionine and histone methylation. Science 339, 222–226 (2013).

    Article  ADS  PubMed  Google Scholar 

  50. Shiraki, N. et al. Methionine metabolism regulates maintenance and differentiation of human pluripotent stem cells. Cell Metab. 19, 780–794 (2014).

    Article  CAS  PubMed  Google Scholar 

  51. Taya, Y. et al. Depleting dietary valine permits nonmyeloablative mouse hematopoietic stem cell transplantation. Science 354, 1152–1155 (2016).

    Article  ADS  CAS  PubMed  Google Scholar 

  52. Jones, C. L. et al. Cysteine depletion targets leukemia stem cells through inhibition of electron transport complex II. Blood 134, 389–394 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Farrelly, L. A. et al. Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3. Nature 567, 535–539 (2019).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  54. Qi, L. et al. Aspartate availability limits hematopoietic stem cell function during hematopoietic regeneration. Cell Stem Cell 28, 1982–1999 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Bao, L. et al. Amino acid transporter SLC7A5 regulates cell proliferation and secretary cell differentiation and distribution in the mouse intestine. Int. J. Biol. Sci. 20, 2187–2201 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Hughes, C. E. et al. Cysteine toxicity drives age-related mitochondrial decline by altering iron homeostasis. Cell 180, 296–310 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Jouandin, P. et al. Lysosomal cystine mobilization shapes the response of TORC1 and tissue growth to fasting. Science 375, eabc4203 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Song, T. et al. Dietary cysteine drives body fat loss via FMRFamide signaling in Drosophila and mouse. Cell Res. 33, 434–447 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Ishii, I. et al. Cystathionine γ-lyase-deficient mice require dietary cysteine to protect against acute lethal myopathy and oxidative injury. J. Biol. Chem. 285, 26358–26368 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Mani, S., Yang, G. & Wang, R. A critical life-supporting role for cystathionine γ-lyase in the absence of dietary cysteine supply. Free Radical Biol. Med. 50, 1280–1287 (2011).

    Article  CAS  Google Scholar 

  61. Varghese, A. et al. Unravelling cysteine-deficiency-associated rapid weight loss. Nature 643, 776–784 (2025).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  62. Lee, A. H. et al. Cysteine depletion triggers adipose tissue thermogenesis and weight loss. Nat. Metab. 7, 1204–1222 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Marí, M. et al. Mitochondrial glutathione: recent insights and role in disease. Antioxidants 9, 909 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  64. Singh, P. et al. Taurine deficiency as a driver of aging. Science 380, eabn9257 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Chi, F. Summary of project PR002592. Metabolomics Workbench https://doi.org/10.21228/M8M54Q (2025).

Download references

Acknowledgements

We thank the Swanson Biotechnology Center at the Koch Institute, including the Flow Cytometry, Histology, and ES Cell and Transgenics core facilities; the Department of Comparative Medicine for mouse husbandry support; S. Holder and members of the Hope Babette Tang (1983) Histology Facility for substantial histological support; all the members of the Yilmaz laboratory for discussions; K. Kelley for laboratory management; and L. Galoyan for administrative assistance. Ö.H.Y. is supported by the US National Institutes of Health (R01CA245314, R01CA211184, R01CA257523, R01DK133919, R01DK140310, P30CA014051, R01DK126545 and U01CA250554), a Pew-Stewart Trust scholar award, the Kathy and Curt Marble cancer research award, a Koch Institute–Dana-Farber/Harvard Cancer Center Bridge project grant and AFAR; and receives support from the MIT Stem Cell Initiative. This work was supported in part by the Koch Institute Support (core) grant (NCI P30-CA14051). F.C. is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRG-2463-22). Q.Z. is supported by a Cancer Research Institute Postdoctoral Fellowship (CRI4478). J.E.S.S. is supported by the National Institutes of Health F32 and P30 Fellowships (F32DK128872 and P30DK040561). S.S. is supported by the Crohn’s and Colitis Foundation Award (CCFA-623914) and the American Heart Association Award (19POST34380588). S.B. is supported by a National Institutes of Health T32 Fellowship (T32HL007118). Y.M.S. is supported by the National Institutes of Health (R01CA245546). M.G.V.H. is supported by the MIT Center for Precision Cancer Medicine, the Ludwig Center at MIT and the National Institutes of Health (R35CA242379 and P30CA014051). J.A. is supported by R01DK132544, the Smith Family Awards Program for Excellence in Biomedical Research, the Ludwig Center at Harvard, the Ira Schneider Foundation, the Claudia Adams Barr Program in Innovative Basic Cancer Research Program, and the Innovation research Funds at the DFCI.

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Authors and Affiliations

  1. Department of Biology, The David H. Koch Institute for Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA

    Fangtao Chi, Qiming Zhang, Jessica E. S. Shay, Shixun Han, Yin Yuan, Zhenning Yang, Heaji Shin, Samuel Block, Matthew G. Vander Heiden & Ömer H. Yilmaz

  2. UCLA Metabolomics Center, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA

    Johanna Ten Hoeve

  3. Molecular and Integrative Physiology Department, University of Michigan, Ann Arbor, MI, USA

    Sumeet Solanki & Yatrik M. Shah

  4. Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA

    Sumeet Solanki & Yatrik M. Shah

  5. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Matthew G. Vander Heiden & Ömer H. Yilmaz

  6. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA

    Matthew G. Vander Heiden

  7. Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA

    Judith Agudo

  8. Department of Immunology, Harvard Medical School, Boston, MA, USA

    Judith Agudo

  9. Ludwig Center at Harvard, Boston, MA, USA

    Judith Agudo

  10. Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA

    Judith Agudo

  11. Department of Pathology, Beth Israel Deaconess Medical Center, Massachusetts General Hospital Boston and Harvard Medical School, Boston, MA, USA

    Ömer H. Yilmaz

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  1. Fangtao Chi
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Contributions

F.C. initiated the project; conceived, designed, performed and interpreted all the experiments; and wrote the manuscript with help from Ö.H.Y. Q.Z. analysed the single-cell RNA sequencing data and immune profiling. J.E.S.S., S.H., Y.Y., Z.Y. and H.S. performed the experiments and assisted with data collection. J.T.H., S.B. and M.G.V.H. assisted with the intestinal tissue metabolomic analysis. S.S. and Y.M.S. provided the research materials. J.A. assisted with immune cell experimental design and data interpretation. All authors assisted in interpreting the experiments, writing and editing the paper.

Corresponding author

Correspondence to Ömer H. Yilmaz.

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Competing interests

Ö.H.Y. holds equity and is a scientific advisory board member in Ava Lifesciences and AI Proteins; receives research support from Microbial Machines; and is a consultant for Nestle. M.G.V.H. is a scientific advisor for Agios Pharmaceuticals, iTeos Therapeutics, Faeth Therapeutics, Sage Therapeutics, Lime Therapeutics, Pretzel Therapeutics and Auron Therapeutics. The other authors declare no competing interests.

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Extended data figures and tables

Extended Data Fig. 1 Effect of individual amino acids on HMGCS2 expression and ISC function.

a, HMGCS2 IHC in small intestinal crypts from the mice treated with each of 20 proteinogenic amino acids in vivo. Scale bar, 20 µm. b, N-acetyl cysteine (NAC), Glutathione (GSH), and taurine are well-established metabolites associated with cysteine metabolism. HMGCS2 IHC in small intestinal crypts treated with NAC, GSH, and taurine by i.p. and oral gavage. Scale bar, 20 µm. c-d, Schematic of the short-term cysteine treatment by oral gavage (c), followed by in vitro crypt organoid formation assay (d). n = 4 biological replicates per group. Scale bar, 1 mm. Unpaired two-tailed Student’s t-tests (d). Data are mean ± s.d.

Source data

Extended Data Fig. 2 Cysteine-rich diet composition and mouse physiology.

a, Control and cysteine-rich diet (CysRD) composition. b, Mouse blood glucose (n = 13 per group) and ketone (n = 14 in control, n = 15 in CysRD) levels after 6 weeks of control and CysRD feeding. Mouse daily food uptake during the control and CysRD feeding (n = 15 per group). c-e, Relative body mass changes (c, n = 15 per group), terminal body mass (d, n = 15 per group) and visceral/subcutaneous white adipose tissue (visWAT and scWAT) weights (e, n = 5 per group) from mice fed with 6 weeks of control and CysRD. Unpaired two-tailed Student’s t-tests (b, c, d, e). Data (b, d) are mean ± s.d. Box and whiskers (e) are plotted min to the max value.

Source data

Extended Data Fig. 3 Effects of Cysteine-rich diet on ISC and progenitor cells.

a, IHC detection for intestinal stem cell and progenitor cell proliferation (4-h BrdU pulse), crypts regeneration (OLFM4), and post-mitotic Paneth cell identity (Lysozyme, LYZ) from control- and CysRD-fed mice in homeostasis. Scale bar, 20 µm. b, Quantification of BrdU+ cells per crypt (n = 40), OLFM4+ crypt length (n = 14), and LYZ+ Paneth cells per crypt (n = 40) from 5 control and 5 CysRD diets treated mice under homeostasis condition. c, Villi length and crypt depth in the small intestine isolated from control- and CysRD-fed mice in homeostasis (n = 14 per group). d, Flow cytometry for Lgr5-GFP gating panel and quantification of ISCs (Lgr5-GFPhi) and progenitors (Lgr5-GFPlow) frequency from 6 weeks control- and CysRD-fed mice. n = 6 for each group. e, Representative crypt images of Hmgcs2, Lgr5 mRNAs (ISH) and proteins (IF) from control- and CysRD-fed mice intestine. Scale bar, 10 µm. f, Schematic (top) of the intestinal renewal assay including the timeline of dietary regimens, tamoxifen induction, and tissue collection in the Lgr5-IRES-CreERT2; Rosa26LSL-tdTomato lineage tracing reporter mice. Representative images (bottom) of IHC for tdTomato+ Lgr5+ ISC-derived progenies in the small intestine. Quantification (right) of day-3 RFP+ length (n = 100, 20 data points per mouse) from 5 control and 5 CysRD diets treated mice. Scale bar, 50 µm. g, Schematic (left) of the intestinal permeability assay including the timeline of dietary regimens, irradiation (XRT, 7.5 Gy x 2), and tissue collection in the WT/B6 mice. Quantification (right) of plasma FITC-dextran levels 4 h after oral gavage in unirradiated and irradiated cohorts (n = 5 per group). h-i, Immunoblots (h) and IHC (i) analyses of Cleaved Caspase-3 (CC3-Asp175) in small intestine crypts from control- and CysRD-fed mice, assessed both at baseline and 8 h after irradiation. Scale bar, 20 µm. Unpaired two-tailed Student’s t-tests (b, c, d, f, g, i). Data (b, c, d, f) are mean ± s.d. Box and whiskers (g, i) are plotted min to the max value.

Source data

Extended Data Fig. 4 Cysteine rich diet enriches crypt-associated effector CD8αβ+ T cell numbers.

a, UMAP plots demonstrating small intestinal intraepithelial immune cell clusters presented by individual samples. Dots represent individual cells, and colors represent different cell populations. b, UMAP plots showing the expression of canonical markers of major cell populations, including T cells (Nkg7 and Cd8b1), B cells (Cd79a), macrophages (Csf1r) and dendritic cells (Siglech). c, UMAP plots illustrating the subclusters of CD8αβ+ T cells grouped by individual samples. d, UMAP plots illustrating the expression of canonical markers of T cell subsets, including naïve (Ccr7 and Lef1) and effector/memory (Gzmk, Ccr9, and Cxcr6) populations. e, Bar graphs illustrating increased effector cells in the CD8αβ T cells (n = 2 per group). Data are mean ± s.d. f, Stacked bar graphs showing the numbers of clonotypes in CD8αβ T cell cluster in each sample. g, Representative crypt images (left) and quantification (right) of EPCAM (epithelial cells) and CD8αβ cells from control- and CysRD-fed mice before and 8 h after irradiation. Scale bar, 20 µm. Unpaired two-tailed Student’s t-tests (g). Box and whiskers (g) are plotted min to the max value.

Source data

Extended Data Fig. 5 Elevated proliferation of intraepithelial CD8αβ+ T cells drive their accumulation and mediate the CysRD-induced enhancement of ISCs.

a-b, Flow cytometry (a) and quantification (b) of BrdU+ intraepithelial CD8αβ+ T cells (n = 6 per group). c, Fraction of apoptotic intraepithelial CD8αβ+ T cells (n = 5 per group). d, Fraction of intraepithelial CD8αβ+ T cells in control and FTY720 treated cohorts (n = 5 per group). e, Schematic of the intestinal regeneration assay, including the timeline of CD8αβ T cells depletion, dietary regimen, irradiation (XRT, 7.5 Gy x 2), and tissue collection. f, Fraction of intraepithelial CD8αβ+ T cells after antibody-based depletion. g, Quantification of Lgr5+ (ISH) regenerating crypts, related to Fig. 2k. h-i, IHC detection and quantification for stem and progenitor cells proliferation (BrdU, h), and intestinal crypts regeneration (OLFM4, i), in control-IgG and CD8αβ+ T cells depleted cohorts (n = 5 per group). Scale bar, 20 µm. Unpaired two-tailed Student’s t-tests (b, c, d, f, g, h, i). Data (b, d) are mean ± s.d. Box and whiskers (c, f) are plotted min to the max value.

Source data

Extended Data Fig. 6 Cysteine-rich diet stimulates IL-22 production from crypt-associated CD8αβ+ T cells.

a, Relative fold change of selected, highly expressed cytokines in small-intestinal tissue after 6 weeks of CysRD feeding, as measured with the Mouse XL cytokine array (n = 3 per group). b, Representative images of Cxcl10 ISH staining in the crypts from control- and CysRD-fed mice. Scale bar, 20 µm. c, Fraction of intraepithelial CD8αβ+ T cells in control-IgG and CXCL10 neutralized cohorts (n = 5 per group). d, Flow cytometry for intraepithelial CD8αβ+ T cell gating panel (up), and anti-IL-22-PE histogram (down) in control- and CysRD-fed mice. e, IHC for HMGCS2 in the intestinal crypts from control and IL-22 i.p. injected mice. Scale bar, 20 µm. f, Flow cytometry for intraepithelial IL-22-GFP+ cell gating panel (left), and CD8β+ T cells histogram (right) in control- and CysRD-fed mice. g-j, Fraction of IL22-GFP+ immune cells in the IEL and LPL compartments of control- and CysRD-fed mice, assessed in both unirradiated (g, h) and irradiated (i, j) cohorts (n = 5 per group). k, Schematic of the CD8αβ+ T cells isolation, transplantation into Rag2−/− mice, dietary regimen, and intestinal regeneration assay, including the timeline of diet treatment, irradiation (XRT, 7.5 Gy x 2) and tissue collection. l-m, Representative images and quantification of day-3 regenerating crypts stained with BrdU cell proliferation marker (l), and Lgr5 (ISH) (m) stem cell marker from 5 Rag2−/−, 5 Rag2−/− with CD8αβIL22-KO, and 5 Rag2−/− with CD8αβIL22-WT mice intestine. Scale bar, 20 µm. Related to Fig. 3g–i. Unpaired two-tailed Student’s t-tests (c, g, i, l, m). Data (h, j) are mean ± s.d. Box and whiskers (c, g, i) are plotted min to the max value.

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Extended Data Fig. 7 CoA supplementation elevates intraepithelial CD8αβ+ T cells accumulation, IL-22 production.

a-b, Bar graph quantifying the relative fold change of pantothenate (supplemented drinking water) (a) and CoA-related metabolites (b) in the small intestine after pantothenate treatment (n = 4 replicates per group). c, IHC for HMGCS2 in the intestinal crypts from control and pantothenate-treated mice. Scale bar, 20 µm. d, OLFM4 IHC to assess for ISCs regeneration after irradiation-induced injury in control and pantothenate-treated mice. Scale bar, 30 µm. e, Bar graph quantifying BrdU+ CD8αβ+ IELs in control-, CysRD-, and CoA-treated mice (n = 6 per group). f, Fraction of CD8αβ+ T cells in the IEL and LPL compartments of control-, CysRD-, and CoA-treated mice (n = 5 per group). g, Relative fold change of selected, highly expressed cytokines in small-intestinal tissue treated with CoA, as measured with the Mouse XL cytokine array (n = 2 per group). h, Small intestinal crypts IL-22 levels in control- and CoA-treat mice (n = 5 per group). i, Fraction of IL22-GFP+ cells in the small intestinal CD8αβ+ T cells population in control-, CysRD-, and CoA-treated mice (n = 5 per group). j, Immunoblots detection for the small intestinal phospho-Y705-STAT3 in control-, CysRD-, and CoA-treated mice. The BrdU assays for the control and CysRD groups (shown in Extended Data Fig. 5b) were performed alongside the CoA-treated group, and the complete results are presented together in Extended Data Fig. 7e. Unpaired two-tailed Student’s t-tests (a, b, e, f, h, i). Data (a, b, e, g, h) are mean ± s.d. Box and whiskers (f, i) are plotted min to the max value.

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Extended Data Fig. 8 Cysteine-rich diet has no effect on intraepithelial CD8αβ+ T cells accumulation, CoA generation, or IL-22 production in the colon.

a, Relative fold changes of colon intraepithelial lymphocytes from control- and CysRD-fed mice (n = 5 per group). b, Heatmap highlighting the colon metabolites most significantly affected by CysRD treatment. c-d, Normalized cysteine (c) and cystine (d) levels in small intestinal and colonic tissues from control- and CysRD-fed mice (n = 5 per group). e, Plasma cysteine level from control- and CysRD-fed mice (n = 5 per group). f, Normalized CoA species levels in colonic tissues from control- and CysRD-fed mice (n = 5 per group). g-h, Immunoblots detection (g) and pixel intensity (h) for SLC7A11 in the small intestine and colon (n = 4 per group). i, Colonic IL-22 levels in control- and CysRD-fed mice (n = 5 per group). j, Immunoblots detection of the colonic phospho-Y705-STAT3 in control- and CysRD-fed mice. Unpaired two-tailed Student’s t-tests (a, c, d, e, f, h, i). Data (a, e, h, i) are mean ± s.d. Box and whiskers (c, d, f) are plotted min to the max value.

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Extended Data Fig. 9 Cystine uptake by CD8αβ+ T cells is not required for CysRD-induced enhancement of ISCs.

a, PCR gel blot of Slc7a11 genotyping in FACS enriched mesenteric lymph node CD8αβ+ T cells from WT, Slc7a11f/f, and Slc7a11-tKO mice. b, Normalized cystine level in flow cytometry enriched mesenteric lymph node CD8αβ+ T cells from control and Slc7a11-tKO mice (n = 5 per group). c-d, Fraction of intraepithelial CD8αβ+ T cells (a, n = 5) and normalized crypts IL-22 expression (b, n = 5) from small intestine of CD8-Cre; Slc7a11f/f (Slc7a11-tKO) mouse that fed with control and CysRD. e-j, Schematic of the intestinal regeneration assay, including the timeline of dietary regimen, irradiation (XRT, 7.5 Gy x 2), and tissue collection (e). Representative images of regenerating crypts by Lgr5 ISH (f), IHC staining with BrdU cell proliferation (g) and OLFM4 (h) stem cell markers. Scale bar, 20 µm. Quantification of day-3 BrdU+ cells (per crypt, i), OLFM4+ crypts (per 10 crypts, j) from 5 control and 5 CysRD diets treated mice. Unpaired two-tailed Student’s t-tests (b, c, d, f, i, j). Data (b, c, d) are mean ± s.d.

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Extended Data Fig. 10 IL-22 and epithelial SLC7A11, but not ketones are essential for the CysRD-induced ISCs enhancement.

a, Schematic of the intestinal regeneration assay, including the timeline of dietary regimen, irradiation (XRT, 7.5 Gy x 2), and tissue collection. b-g, Representative images (a, d, f) and quantification (c, e, g) of day-3 regenerating crypts stained with BrdU cell proliferation marker (b-c), and OLFM4 (IHC) (d-e), Lgr5 (ISH) (f-g) stem cell markers from WT, IL22-KO and SLC7A11-iKO mice that fed with control and CysRD (n = 5 per group). Scale bar, 20 µm. h, Bar plot quantifying the normalized levels of the dominant ketone body metabolite, 3-hydroxybutyrate, in the small intestine with control, CysRD, and ketogenic diet feeding. n = 7 biological replicates for control and CysRD, n = 5 biological replicates for control and ketogenic diets. i, RNAscope in situ hybridization (ISH) for detecting Notch pathway target Hes1 in each diet. j, Irradiation-induced intestinal regeneration assay in intestine epithelial specific Hmgcs2 knockout mouse model (Hmgcs2-iKO) fed with control and CysRD. Representative IHC images of regenerating crypts for BrdU+ cell proliferation, OLFM4+ stem cells, and post-mitotic Lysozyme+ Paneth cells. Scale bar, 20 µm. Unpaired two-tailed Student’s t-tests (c, e, g, h). Data (h) are mean ± s.d.

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Source data of western blot shown in main and extended data figures

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Supplementary Table 1 (download XLSX )

Small intestinal metabolites level from 6 weeks control- and CysRD-fed mice, shown in Fig. 4a

Supplementary Table 2 (download XLSX )

Colon metabolites level from 6 weeks control- and CysRD-fed mice, shown in Extended Data Fig. 8b

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Chi, F., Zhang, Q., Shay, J.E.S. et al. Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22. Nature 647, 706–715 (2025). https://doi.org/10.1038/s41586-025-09589-5

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