{
  "abstract": "Severe Coronavirus disease 2019 (COVID-19) can induce progressive diffuse alveolar damage (DAD) leading to fatal outcomes. Here, we leveraged data from Visium spatial transcriptomics for COVID-19 and control lung samples to unravel insights into cellular and molecular events driving lethal COVID-19. We report a progressive loss of endothelial cell types, pneumocytes type I and natural killer cells coupled with a continuous increase of myeloid and stromal cells, mostly peribronchial fibroblasts, across acute and proliferative DAD. Spatial organization analysis also identified specific compartmentalization including immune-specific clusters across DAD patterns. Importantly, spatially informed ligand-receptor interaction analysis revealed intercellular communication signatures defining COVID-19 induced DAD. Transcription factor activity enrichment analysis identified the TGF-β pathway as DAD driver, highlighting the antagonizing roles of SMAD3 and SMAD7 activity during fibrosis. Integration of these data yielded a signaling kinase pathway in peribronchial fibroblasts with amenable novel targets. Finally, spatio-temporal trajectory analysis characterized an alveolar epithelium regeneration program.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "research support, non u.s. gov't",
  "arxiv": null,
  "author_total": 12,
  "authors": [
    {
      "name": "Carlos A. Garcia-Prieto",
      "orcid": "0000-0001-5021-6916"
    },
    {
      "name": "Eva Musulen"
    },
    {
      "name": "Daniela Grases"
    },
    {
      "name": "Veronica Davalos",
      "orcid": "0000-0003-4077-5137"
    },
    {
      "name": "Gerardo Ferrer",
      "orcid": "0000-0002-4084-6815"
    },
    {
      "name": "Belén Pérez-Miés"
    },
    {
      "name": "Tamara Caniego-Casas"
    },
    {
      "name": "José Palacios"
    },
    {
      "name": "Xavier Saenz-Sardà"
    },
    {
      "name": "Elisabet Englund"
    },
    {
      "name": "Eduard Porta",
      "orcid": "0000-0001-7900-4239"
    },
    {
      "name": "Manel Esteller",
      "orcid": "0000-0003-4490-6093"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/079xsrdrfaebe.bib",
  "cited_by": 0,
  "doi": "10.1038/s41467-026-78188-3",
  "fulltext_url": "https://europepmc.org/articles/PMC13672299",
  "id": "079xsrdrfaebe",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://www.nature.com/articles/s41467-026-78188-3",
  "language": "eng",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7222292996",
  "pdf_url": "https://www.nature.com/articles/s41467-026-78188-3.pdf",
  "pmcid": "PMC13672299",
  "pmid": "42881179",
  "published": "2026-10-15",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/079xsrdrfaebe.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:38Z",
      "native_id": "10.1038/s41467-026-78188-3",
      "source": "crossref",
      "url": "https://www.nature.com/articles/s41467-026-78188-3"
    },
    {
      "first_seen": "2026-10-30T12:18:46Z",
      "native_id": "MED:42881179",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42881179"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19",
  "title_text": "Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:46Z",
  "url": "https://research.draconitic.com/paper/079xsrdrfaebe",
  "venue": "Nature Communications",
  "versions": []
}