Nature ImmunologyPub Date : 2026-10-07DOI: 10.1038/s41590-026-02665-6
Andrew Hart,Maria Merolle,Christian Howard,Breanne E. Haskins,Ian S. Cohn,Suhas Bobba,Rui Xiao,Yi Yang,Ken Cadwell,Junjie Ma,Hiroshi Yano,Xiaoxiao Hou,Bethan A. Wallbank,Daniel Cutillo,Ivaylo I. Ivanov,Boris Striepen,Sunny Shin,Igor E. Brodsky,David Artis,Christopher A. Hunter,Daniel P. Beiting,on behalf of the MIST Consortium,Ivaylo I. Ivanov,David Artis
{"title":"Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial–immune cell interactions","authors":"Andrew Hart,Maria Merolle,Christian Howard,Breanne E. Haskins,Ian S. Cohn,Suhas Bobba,Rui Xiao,Yi Yang,Ken Cadwell,Junjie Ma,Hiroshi Yano,Xiaoxiao Hou,Bethan A. Wallbank,Daniel Cutillo,Ivaylo I. Ivanov,Boris Striepen,Sunny Shin,Igor E. Brodsky,David Artis,Christopher A. Hunter,Daniel P. Beiting,on behalf of the MIST Consortium,Ivaylo I. Ivanov,David Artis","doi":"10.1038/s41590-026-02665-6","DOIUrl":"https://doi.org/10.1038/s41590-026-02665-6","url":null,"abstract":"","PeriodicalId":19032,"journal":{"name":"Nature Immunology","volume":"1 1","pages":""},"PeriodicalIF":30.5,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149090240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ImmunologyPub Date : 2026-09-30DOI: 10.1038/s41590-026-02656-7
C. Garrett Wilson, M. Pragun Acharya, Laura Karsch, Lennard W. Duck, Nana Twumasi-Ankrah, Yuanyou Wang, Hongxing Shen, Blake F. Frey, Annalisse R. McKee, Vishal H. Oza, Stacey N. Harbour, Yoshiko Nagaoka-Kamata, Jeffrey R. Singer, Robin D. Hatton, Jeffrey Moffitt, Matthias Gunzer, Carlene L. Zindl, Casey T. Weaver
{"title":"Barrier immune memory is programmed by intestinal epithelial cell presentation of cytosol-delivered bacterial antigens","authors":"C. Garrett Wilson, M. Pragun Acharya, Laura Karsch, Lennard W. Duck, Nana Twumasi-Ankrah, Yuanyou Wang, Hongxing Shen, Blake F. Frey, Annalisse R. McKee, Vishal H. Oza, Stacey N. Harbour, Yoshiko Nagaoka-Kamata, Jeffrey R. Singer, Robin D. Hatton, Jeffrey Moffitt, Matthias Gunzer, Carlene L. Zindl, Casey T. Weaver","doi":"10.1038/s41590-026-02656-7","DOIUrl":"10.1038/s41590-026-02656-7","url":null,"abstract":"Antigen compartmentalization is known to influence CD4 and CD8 T cell recognition but its impact on immune responses to different antigens expressed by the same pathogen is poorly understood. By tracking the clonal CD4 T cell response to a single epitope shuttled between different virulence proteins of Citrobacter rodentium, we found that response magnitude and quality depended on antigen localization. Antigens retained within bacteria elicited limited responses, whereas antigens injected into colonocyte cytosol through a type III secretion system generated robust mucosal CD4 T cell responses and promoted formation of epithelial-resident memory T cells. This process required direct presentation by infected epithelial cells. Single-cell transcriptomic analyses revealed that sustained, bidirectional communication between epithelial cells and T cells was essential to elicit both barrier-protective functions and transcriptional programs favoring tissue residency over central memory differentiation. These findings identify nonprofessional antigen-presenting cells as key regulators of CD4 T cell memory fate. Intestinal epithelial cells can present antigen to CD4 T cells. Here the authors show that epithelial cells must present translocated bacterial antigen for local CD4 resident memory T cells to be established.","PeriodicalId":19032,"journal":{"name":"Nature Immunology","volume":"27 10","pages":"2117-2133"},"PeriodicalIF":26.5,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41590-026-02656-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149078923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ImmunologyPub Date : 2026-09-30DOI: 10.1038/s41590-026-02622-3
Xi Lin, Richard S. Blumberg
{"title":"Epithelial antigen presentation shapes barrier memory","authors":"Xi Lin, Richard S. Blumberg","doi":"10.1038/s41590-026-02622-3","DOIUrl":"10.1038/s41590-026-02622-3","url":null,"abstract":"Bacterial antigens injected into the cytosol of intestinal epithelial cells are preferentially presented by MHC II for induction of antigen-specific T cell responses and long-term epithelial cell-associated CD4 tissue-resident memory T cells.","PeriodicalId":19032,"journal":{"name":"Nature Immunology","volume":"27 10","pages":"1972-1974"},"PeriodicalIF":26.5,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149078911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ImmunologyPub Date : 2026-09-30DOI: 10.1038/s41590-026-02668-3
Alicia G. Aguilar-Navarro, Gibran Edun, Mark Gower, Joan Kant, Ximing Li, Dustin Yang, Mursal Nader, Minerva Fernandez, Soheil Jahangiri, Emily Tsao, Pratik Joshi, Pathum Kossinna, Loic Cameron Caloren, John Roderick Davey, Michael G. Zywiel, R. Peter Suderman, Anoushka I. Kapoor, Margarete K. Akens, Adele Changoor, Minna Woo, Robert F. Stanley, Kira A. Young, Christine Tran, Valentin Sotov, Ben X. Wang, Sagi Abelson, Omar Abdel-Wahab, Shruti Naik, Jennifer J. Trowbridge, Robert Vanner, Kristin J. Hope, Hubert Tsui, Federico Gaiti, Anastasia N. Tikhonova
{"title":"Prefibrotic bone marrow microenvironment is a hallmark of clonal hematopoiesis","authors":"Alicia G. Aguilar-Navarro, Gibran Edun, Mark Gower, Joan Kant, Ximing Li, Dustin Yang, Mursal Nader, Minerva Fernandez, Soheil Jahangiri, Emily Tsao, Pratik Joshi, Pathum Kossinna, Loic Cameron Caloren, John Roderick Davey, Michael G. Zywiel, R. Peter Suderman, Anoushka I. Kapoor, Margarete K. Akens, Adele Changoor, Minna Woo, Robert F. Stanley, Kira A. Young, Christine Tran, Valentin Sotov, Ben X. Wang, Sagi Abelson, Omar Abdel-Wahab, Shruti Naik, Jennifer J. Trowbridge, Robert Vanner, Kristin J. Hope, Hubert Tsui, Federico Gaiti, Anastasia N. Tikhonova","doi":"10.1038/s41590-026-02668-3","DOIUrl":"https://doi.org/10.1038/s41590-026-02668-3","url":null,"abstract":"Clonal hematopoiesis of indeterminate potential is associated with systemic inflammation and increased malignant risk in humans, yet understanding of how it reshapes the bone marrow (BM) microenvironment has been limited. Using single-cell transcriptomic profiling of freshly isolated BM samples, combined with histological and spatial transcriptomic analyses, we identified fibro-inflammatory remodeling as a hallmark of clonal hematopoiesis of indeterminate potential. Fibroblasts were markedly expanded and acquired cancer-associated fibroblast-like transcriptional states, while mesenchymal and vascular cells upregulated collagen production and extracellular matrix remodeling pathways. Spatial transcriptomics revealed discrete fiber-enriched regions populated by active and CXCL12+ fibroblasts, macrophages and lymphoid cells. These regions exhibited major enrichment of proinflammatory pathways, including transforming growth factor-beta and tumor necrosis factor signaling, identifying them as spatially confined inflammatory hubs within the BM. Collectively, these findings establish fibro-inflammatory BM remodeling as a defining feature of clonal hematopoiesis of indeterminate potential, linking it to prefibrotic stromal changes and niche reorganization that may facilitate progression to overt malignancy.","PeriodicalId":19032,"journal":{"name":"Nature Immunology","volume":"3 1","pages":""},"PeriodicalIF":30.5,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ImmunologyPub Date : 2026-09-24DOI: 10.1038/s41590-026-02663-8
{"title":"Remodeling of a distal IRF4 element spurs human regulatory T cell instability under inflammatory conditions","authors":"","doi":"10.1038/s41590-026-02663-8","DOIUrl":"10.1038/s41590-026-02663-8","url":null,"abstract":"In an in vitro model, human regulatory T cells undergo inflammatory cytokine-driven reprogramming, resulting in increased chromatin accessibility at AP-1-binding sites, increased IRF4 expression and, ultimately, loss of lineage identity and suppressive function. Deletion of an open chromatin region distal to IRF4 protects cells from this cytokine-induced destabilization.","PeriodicalId":19032,"journal":{"name":"Nature Immunology","volume":"27 10","pages":"1992-1993"},"PeriodicalIF":26.5,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149040130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}