{
  "abstract": "The thymic medulla provides the microenvironment for negative selection, late thymocyte maturation, and thymocyte egress, and is generally characterized by widespread distribution of medullary thymic epithelial cells (mTECs). In contrast, the rat thymic medulla contains medullary epithelium-free areas (mEFAs), but the cellular composition and functional significance of these regions remain unclear. Here, to address these questions, we combined spatial transcriptomic data with thymocyte and stromal scRNA-seq reference datasets using robust cell-type decomposition (RCTD) to characterize mEFAs. These analyses revealed that more mature phenotypes within the CD4SP, CD8SP, and regulatory T-cell lineages were preferentially localized in mEFAs, whereas immature SP subsets were enriched in medullary epithelium-containing areas. The newly identified rat thymic mesenchymal cell subsets TMC3 and TMC4 were also enriched in mEFAs. These subsets were broadly similar to mouse medullary fibroblasts but displayed distinct predicted interactions with SP thymocytes, including costimulatory molecule–receptor, chemokine–receptor, and ECM–integrin axes. In addition, venous endothelial cells (vECs) expressing portal endothelial cell markers were enriched in mEFAs. Spns2 , which encodes a transporter that releases S1P from cells into the extracellular space, was preferentially expressed in both TMC4 and vEC subsets, suggesting that these cells may contribute to the formation of a local S1P gradient within mEFAs. These findings suggest that mEFAs may be specialized medullary niches associated with stromal organization, the localization of mature thymocytes, and thymic egress.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Anatomy, Dokkyo Medical University",
    "Laboratory for Molecular Pathobiology, Research Center for Advanced Medical Science, Dokkyo Medical University"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Yasushi Sawanobori"
    },
    {
      "affs": [
        1
      ],
      "name": "Tadayuki Ogawa"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2h1hjxaptzvqg.bib",
  "cited_by": 0,
  "doi": "10.3389/fimmu.2026.1945985",
  "fulltext_url": "https://europepmc.org/articles/PMC13713823",
  "id": "2h1hjxaptzvqg",
  "issns": [
    "1664-3224"
  ],
  "landing_url": "https://www.frontiersin.org/articles/10.3389/fimmu.2026.1945985/full",
  "language": "eng",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Original Research"
    ],
    [
      "openalex",
      "2403|T-cell and B-cell Immunology"
    ]
  ],
  "openalex": "W7221805017",
  "pdf_url": "https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2026.1945985/pdf",
  "pmcid": "PMC13713823",
  "pmid": "42953182",
  "published": "2026-10-14",
  "publisher": "Frontiers Media SA",
  "ris": "https://research.draconitic.com/paper/2h1hjxaptzvqg.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:17Z",
      "native_id": "10.3389/fimmu.2026.1945985",
      "source": "crossref",
      "url": "https://www.frontiersin.org/articles/10.3389/fimmu.2026.1945985/full"
    },
    {
      "first_seen": "2026-10-31T00:20:41Z",
      "native_id": "MED:42953182",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42953182"
    },
    {
      "first_seen": "2026-11-01T12:21:26Z",
      "native_id": "PMC13713823",
      "source": "pmc",
      "url": "https://doi.org/10.3389/fimmu.2026.1945985"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:2403|T-cell and B-cell Immunology",
      "subfield": "immunology"
    }
  ],
  "title": "Medullary epithelium-free areas in the rat thymus are specialized niches enriched for mature thymocytes and distinct stromal subsets",
  "title_text": "Medullary epithelium-free areas in the rat thymus are specialized niches enriched for mature thymocytes and distinct stromal subsets",
  "type": "peer-reviewed",
  "updated_at": "2026-11-01T12:21:26Z",
  "url": "https://research.draconitic.com/paper/2h1hjxaptzvqg",
  "venue": "Frontiers in Immunology",
  "versions": []
}