An epithelial-mesenchymal transition-related mRNA signature associated with the prognosis, immune infiltration and therapeutic response of colon adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36910014", "kind": "science-record", "revision": 3, "content_hash": "sha256:a207e8a4a9b4d0537fe799cc6c3331ab4567a7e391958857dd540def509a0622", "created_at": "2026-11-01T19:01:32Z", "updated_at": "2026-11-01T22:09:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An epithelial-mesenchymal transition-related mRNA signature associated with the prognosis, immune infiltration and therapeutic response of colon adenocarcinoma.", "doi": "10.3389/pore.2023.1611016", "pmid": "36910014", "authors": ["Yu Zhang", "Yan Li", "Zan Zuo", "Ting Li", "Ying An", "Wenjing Zhang"], "journal": "Pathology oncology research : POR", "year": 2023, "abstract": "Background: Epithelial-mesenchymal transition (EMT) is closely associated with cancer cell metastasis. Colon adenocarcinoma (COAD) is one of the most common malignancies in the world, and its metastasis leading to poor prognosis remains a challenge for clinicians. The purpose of this study was to explore the prognostic value of EMT-related genes (EMTRGs) by bioinformatics analysis and to develop a new EMTRGs prognostic signature for COAD. Methods: The TCGA-COAD dataset was downloaded from the TCGA portal as the training cohort, and the GSE17538 and GSE29621 datasets were obtained from the GEO database as the validation cohort. The best EMTRGs prognostic signature was constructed by differential expression analysis, Cox, and LASSO regression analysis. Gene set enrichment analysis (GSEA) is used to reveal pathways that are enriched in high-risk and low-risk groups. Differences in tumor immune cell levels were analyzed using microenvironmental cell population counter and single sample gene set enrichment analysis. Subclass mapping analysis and Genomics of Drug Sensitivity in Cancer were applied for prediction of immunotherapy response and chemotherapy response, respectively. Results: A total of 77 differentially expressed EMTRGs were identified in the TCGA-COAD cohort, and they were significantly associated with functions and pathways related to cancer cell metastasis, proliferation, and apoptosis. We constructed EMTRGs prognostic signature with COMP, MYL9, PCOLCE2, SCG2, and TIMP1 as new COAD prognostic biomarkers. The high-risk group had a poorer prognosis with enhanced immune cell infiltration. The GSEA demonstrated that the high-risk group was involved in \"ECM Receptor Interaction,\" \"WNT Signaling Pathway\" and \"Colorectal Cancer.\" Furthermore, patients with high risk scores may respond to anti-CTLA4 therapy and may be more resistant to targeted therapy agents BI 2536 and ABT-888. Conclusion: Together, we developed a new EMTRGs prognostic signature that can be an independent prognostic factor for COAD. This study has guiding implications for individualized counseling and treatment of COAD patients.", "claims": [{"id": "claim-method", "statement": "The best EMTRGs prognostic signature was constructed by differential expression analysis, Cox, and LASSO regression analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36910014", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The best EMTRGs prognostic signature was constructed by differential expression analysis, Cox, and LASSO regression analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36910014", "locator": "sections[23] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Together, we developed a new EMTRGs prognostic signature that can be an independent prognostic factor for COAD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36910014", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We constructed EMTRGs prognostic signature with COMP, MYL9, PCOLCE2, SCG2, and TIMP1 as new COAD prognostic biomarkers."}, {"asset": "source:pmid:36910014", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Together, we developed a new EMTRGs prognostic signature that can be an independent prognostic factor for COAD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Together, we developed a new EMTRGs prognostic signature that can be an independent prognostic factor for COAD.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:36910014"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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