{
  "abstract": "Background: Public transcriptomic cohort evaluation can be distorted by patient reuse, dependence among study sources, and cohort-relative normalization. Objective: To evaluate the association between a fixed 15-gene cohort-relative mitochondrial proteostasis score and source-study-defined pathological complete response (pCR) across four accession-defined cohorts from three principal study sources. Methods: The fixed score comprised 15 genes with equal positive weights, a specified expected direction, and a platform-coverage rule. After patient-level deduplication and duplicate-aliquot collapse, 285 patients with strict triple-negative breast cancer, including 104 with pCR, were analyzed. Cohort-specific odds ratios (ORs) per one-standard-deviation score increase were pooled by restricted maximum-likelihood random-effects meta-analysis with modified Hartung-Knapp inference. Sensitivity analyses summarized three study sources, used Paule-Mandel heterogeneity estimation, and applied one fixed single-sample RankScore implementation. Results: The primary four-cohort estimate was OR 0.958 (95% CI, 0.639–1.437; P = 0.760; tau^2 = 0). The three-source REML estimate was OR 0.971 (95% CI, 0.492–1.914; P = 0.868; tau^2 = 0.0201). The RankScore sensitivity was imprecise (OR 0.613 per 0.10 RankScore; 95% CI, 0.148–2.542; P = 0.354). The overlap assessment identified 57 strict-TNBC patients duplicated between GSE20194 and GSE25055; treating them as an additional accession effect increased nominal n from 285 to 342 without adding independent participants. Contextual NeoTRIP, single-cell, and I-SPY2 analyses were included to characterize biological and treatment context. Conclusions: Across four accession-defined cohorts from three principal study sources, the evaluated score implementations did not show a reproducible association with pCR. Source-level estimates remained imprecise. Patient overlap, reference dependence, and limited independent study sources are key considerations in cross-cohort biomarker evaluation.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Clinical Medicine, Quanzhou Medical College, Quanzhou, Fujian, China",
    "Department of Breast Surgery, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China",
    "Medical Research Center of Quanzhou Medical College, Quanzhou Medical College, Quanzhou, Fujian, China",
    "Thoracic Surgery Department, People’s Hospital Affiliated to Quanzhou Medical College, Quanzhou, Fujian, China"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
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        0
      ],
      "name": "Xiaoyuan Weng"
    },
    {
      "affs": [
        1
      ],
      "name": "Yanqi Tang"
    },
    {
      "affs": [
        2
      ],
      "name": "Caiji Wang"
    },
    {
      "affs": [
        3
      ],
      "name": "Zhaofeng Huang"
    },
    {
      "name": "Xiyin Huang"
    },
    {
      "name": "Jinsheng Wang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bs1wskbjyhz6w.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0355652",
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  "id": "bs1wskbjyhz6w",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0355652",
  "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": [
    [
      "openalex",
      "1306|Breast Cancer Treatment Studies"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Bioenergetics/Energy-producing organelles/Mitochondria"
    ],
    [
      "plos",
      "/Biology and life sciences/Cell biology/Cellular structures and organelles/Energy-producing organelles/Mitochondria"
    ],
    [
      "plos",
      "/Medicine and health sciences/Clinical medicine/Clinical oncology/Cancer chemotherapy"
    ],
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      "plos",
      "/Medicine and health sciences/Oncology/Cancer treatment"
    ],
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      "plos",
      "/Medicine and health sciences/Oncology/Cancer treatment/Cancer chemotherapy"
    ],
    [
      "plos",
      "/Medicine and health sciences/Oncology/Cancers and neoplasms"
    ],
    [
      "plos",
      "/Medicine and health sciences/Oncology/Cancers and neoplasms/Breast tumors/Breast cancer"
    ],
    [
      "plos",
      "/Medicine and health sciences/Oncology/Cancers and neoplasms/Malignant tumors"
    ],
    [
      "plos",
      "/Medicine and health sciences/Oncology/Clinical oncology/Cancer chemotherapy"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pharmaceutics/Drug therapy/Chemotherapy/Cancer chemotherapy"
    ],
    [
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      "/Physical sciences/Mathematics/Statistics/Statistical methods/Metaanalysis"
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      "/Research and analysis methods/Mathematical and statistical techniques/Statistical methods/Metaanalysis"
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      "/Research and analysis methods/Specimen preparation and treatment"
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  "openalex": "W7221167568",
  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0355652&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-09",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/bs1wskbjyhz6w.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:30Z",
      "native_id": "10.1371/journal.pone.0355652",
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      "url": "https://doi.org/10.1371/journal.pone.0355652"
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  "subjects": [
    {
      "field": "medicine",
      "origin": "plos:oncology",
      "subfield": "oncology"
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  "title": "Patient overlap, cohort-relative scaling, and biological context in cross-cohort evaluation of a mitochondrial proteostasis-associated score in triple-negative breast cancer",
  "title_text": "Patient overlap, cohort-relative scaling, and biological context in cross-cohort evaluation of a mitochondrial proteostasis-associated score in triple-negative breast cancer",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:30Z",
  "url": "https://research.draconitic.com/paper/bs1wskbjyhz6w",
  "venue": "PLOS One",
  "versions": []
}