{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:50:29Z","timestamp":1792788629219,"version":"4.5.0"},"reference-count":20,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T00:00:00Z","timestamp":1791504000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fujian Provincial Young and Middle-Aged Teacher Education Research Project","award":["JZ240098"],"award-info":[{"award-number":["JZ240098"]}]},{"DOI":"10.13039\/501100018623","name":"Quanzhou City Science and Technology Program","doi-asserted-by":"publisher","award":["2025QZNY020 and 2021N152s"],"award-info":[{"award-number":["2025QZNY020 and 2021N152s"]}],"id":[{"id":"10.13039\/501100018623","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Quanzhou Medical College Research Project","award":["XJK2008B"],"award-info":[{"award-number":["XJK2008B"]}],"id":[{"id":"https:\/\/ror.org\/009xp3h24","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The primary four-cohort estimate was OR 0.958 (95% CI, 0.639\u20131.437; P\u2009=\u20090.760; tau^2\u2009=\u20090). The three-source REML estimate was OR 0.971 (95% CI, 0.492\u20131.914; P\u2009=\u20090.868; tau^2\u2009=\u20090.0201). The RankScore sensitivity was imprecise (OR 0.613 per 0.10 RankScore; 95% CI, 0.148\u20132.542; P\u2009=\u20090.354). 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0355652","type":"journal-article","created":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T17:27:06Z","timestamp":1791566826000},"page":"e0355652","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Patient overlap, cohort-relative scaling, and biological context in cross-cohort evaluation of a mitochondrial proteostasis-associated score in triple-negative breast cancer"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-9830-4771","authenticated-orcid":true,"given":"Xiaoyuan","family":"Weng","sequence":"first","affiliation":[{"name":"Quanzhou Medical College","place":["Quanzhou, Fujian, China"],"department":["Department of Clinical Medicine"]},{"name":"Second 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