{
  "abstract": "In this retrospective public-cohort observational study, we evaluated a biologically motivated extracellular matrix (ECM)-high/immune-low transcriptomic score for association with pathological complete response (pCR) after neoadjuvant therapy in breast cancer. The score contrasted standardized ECM/fibroblast and immune-response components. Cohort-specific logistic models adjusted for available clinical covariates; their performance was evaluated separately and was not validation of a locked transported model. In I-SPY2/GSE194040 (n = 987; 319 pCR events), a one-standard-deviation higher score was associated with lower pCR odds (odds ratio [OR] 0.687, 95% confidence interval [CI] 0.588–0.803). Inverse adjusted estimates were also observed in GSE25066 (OR 0.744, 95% CI 0.568–0.975) and GSE20271 (OR 0.407, 95% CI 0.232–0.715). Apparent areas under the receiver operating characteristic curve (AUCs) for these multivariable models were 0.750, 0.732 and 0.798; corresponding 500-bootstrap optimism-corrected estimates were 0.731, 0.713 and 0.765, conditional on processed scores. GSE20194 estimates were nonsignificant, and substantial record overlap with GSE25066 prevented interpretation as additional independent confirmation. A GSE25066 sensitivity restricted to deposited human epidermal growth factor receptor 2 (HER2)-negative status retained direction but had a confidence interval crossing unity. Higher scores correlated with lower immune-related reverse-phase protein array signals in matched I-SPY2 samples. The findings support a hypothesis-generating bulk-transcriptomic response association, with limited cross-cohort robustness. Heterogeneous treatment, sampling, assay and endpoint annotations, together with absent spatial and prospective validation, preclude claims of causality or clinical treatment-selection utility.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Thyroid and Breast Surgery, Hubei No. 3 People’s Hospital of Jianghan University, Wuhan, Hubei, China",
    "Department of Cardiothoracic, Thyroid and Breast Surgery, Enshi Central Hospital, Enshi, Hubei, China"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Tao Wang"
    },
    {
      "affs": [
        1
      ],
      "name": "Xiaoyun Wu"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fh7pqgw2wh0wa.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0357532",
  "fulltext_url": null,
  "id": "fh7pqgw2wh0wa",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0357532",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Hormones"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Hormones/Estrogens"
    ],
    [
      "plos",
      "/Biology and life sciences/Cell biology/Cellular structures and organelles/Extracellular matrix"
    ],
    [
      "plos",
      "/Biology and life sciences/Computational biology/Genome analysis/Transcriptome analysis"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Genome analysis/Transcriptome analysis"
    ],
    [
      "plos",
      "/Biology and life sciences/Physiology/Endocrine physiology/Growth factors/Epidermal growth factor"
    ],
    [
      "plos",
      "/Computer and information sciences/Software engineering/Preprocessing"
    ],
    [
      "plos",
      "/Engineering and technology/Software engineering/Preprocessing"
    ],
    [
      "plos",
      "/Medicine and health sciences/Endocrinology/Endocrine physiology/Growth factors/Epidermal growth factor"
    ],
    [
      "plos",
      "/Medicine and health sciences/Oncology/Cancer treatment"
    ],
    [
      "plos",
      "/Medicine and health sciences/Oncology/Cancers and neoplasms/Breast tumors/Breast cancer"
    ]
  ],
  "openalex": null,
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-05",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/fh7pqgw2wh0wa.ris",
  "sources": [
    {
      "first_seen": "2026-11-06T12:20:42Z",
      "native_id": "10.1371/journal.pone.0357532",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0357532"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "plos:computational biology",
      "subfield": "bioinformatics"
    },
    {
      "field": "biology",
      "origin": "plos:cell biology",
      "subfield": "cell-biology"
    },
    {
      "field": "medicine",
      "origin": "plos:oncology",
      "subfield": "oncology"
    }
  ],
  "title": "A pretreatment ECM-high/immune-low transcriptomic score is associated with pathological complete response after neoadjuvant therapy in breast cancer",
  "title_text": "A pretreatment ECM-high/immune-low transcriptomic score is associated with pathological complete response after neoadjuvant therapy in breast cancer",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T12:20:24Z",
  "url": "https://research.draconitic.com/paper/fh7pqgw2wh0wa",
  "venue": "PLOS One",
  "versions": []
}