{
  "abstract": "The intestinal immune system must adapt as the neonatal gut shifts from milk to solid food and becomes densely colonized. How the T cell compartment is established under these conditions remains unclear. Using fate-mapping to timestamp naive T cells, with imaging, transcriptomic, and repertoire analyses, we tracked them from suckling to adulthood. Intestinal T cell entry peaked at weaning, coinciding with relocation from crypts to villi guided by the tissue microenvironment and, partly, the microbiota. T cells timestamped at suckling persisted into adulthood and, at weaning, adopted a transient cytotoxic-regulatory state in the lamina propria, with granzyme B expression microbiota-dependent only in the ileum. Clonal expansions at weaning were restricted to the small intestinal lamina propria and absent in germ-free mice. Most expanded clones recognized early-life commensals. Weaning is a physiological window of transient inflammation imprinting a hybrid CD4 T cell compartment, suggesting that early-life commensals modulate T cell selection.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 14,
  "authors": [
    {
      "name": "Marina Schernthanner"
    },
    {
      "name": "Rohit R. Gokhale"
    },
    {
      "name": "Alexandra Thoms"
    },
    {
      "name": "Gabriella Lima dos Reis"
    },
    {
      "name": "Marwa Saad"
    },
    {
      "name": "Mackenzie M. Clark"
    },
    {
      "name": "Yue S. Yin"
    },
    {
      "name": "Izabela Mamede",
      "orcid": "0000-0002-0707-5588"
    },
    {
      "name": "Bernardo S. Reis"
    },
    {
      "name": "Tiago B. R. Castro"
    },
    {
      "name": "Roham Parsa",
      "orcid": "0000-0002-0864-6098"
    },
    {
      "name": "Elaine Fuchs"
    },
    {
      "name": "Daniel Mucida",
      "orcid": "0000-0002-0000-0452"
    },
    {
      "name": "Angelina M. Bilate",
      "orcid": "0000-0003-4575-786X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/82ydkeyge6r7p.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.26.762022",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.26.762022v1.full",
  "id": "82ydkeyge6r7p",
  "issns": [
    "2692-8205"
  ],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.26.762022v1",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "immunology"
    ],
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "2403|T-cell and B-cell Immunology"
    ]
  ],
  "openalex": "W7223972669",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.26.762022v1.full.pdf",
  "pmcid": "PMC13733993",
  "pmid": "42990295",
  "published": "2026-10-26",
  "publisher": "Cold Spring Harbor Laboratory Preprints",
  "ris": "https://research.draconitic.com/paper/82ydkeyge6r7p.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:51Z",
      "native_id": "10.64898/2026.10.26.762022",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.26.762022v1"
    },
    {
      "first_seen": "2026-11-08T12:23:39Z",
      "native_id": "PMC13733993",
      "source": "pmc",
      "url": "https://doi.org/10.64898/2026.10.26.762022"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:immunology",
      "subfield": "immunology"
    }
  ],
  "title": "Weaning imprints a hybrid cytotoxic-regulatory identity on intestinal CD4+ T lymphocytes",
  "title_text": "Weaning imprints a hybrid cytotoxic-regulatory identity on intestinal CD4+ T lymphocytes",
  "type": "preprint",
  "updated_at": "2026-11-08T12:23:39Z",
  "url": "https://research.draconitic.com/paper/82ydkeyge6r7p",
  "venue": "bioRxiv",
  "versions": []
}