Identification of a 5-gene-based signature to predict prognosis and correlate immunomodulators for rectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36130456", "kind": "science-record", "revision": 5, "content_hash": "sha256:db96cf865f09b7c952abdedd49442113dbe0c09e55e2226765d143e9c6d0e56f", "created_at": "2026-11-01T18:15:24Z", "updated_at": "2026-11-01T22:50:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a 5-gene-based signature to predict prognosis and correlate immunomodulators for rectal cancer.", "doi": "10.1016/j.tranon.2022.101529", "pmid": "36130456", "authors": ["Lin Yi", "Ji Qiang", "Peng Yichen", "Yu Chunna", "Zheng Yi", "Kang Xun", "Zheng Jianwei", "Bai Rixing", "Yan Wenmao", "Wang Xiaomin", "Li Parker", "Li Wenbin"], "journal": "Translational oncology", "year": 2022, "abstract": "BACKGROUND: Specific tumor markers have yet to be identified in rectal cancer. This study aims to identify a novel genetic signature in rectal cancer to provide clues for survival and immunotherapy.\nMETHODS: DEGs were obtained from two GEO datasets of rectal cancer. By using data from TCGA and GSE133057, two cohorts of rectal cancer were applied to establish and evaluate the signature. A nomogram was constructed for training and validation. We integrated the risk-score with clinicopathological features and assessed its interplay with immune cells and molecules. Finally, our study performed functional annotations, gene-targeted miRNAs, and single-cell analysis.\nRESULTS: A total of 468 DEGs were identified, and a signature consisting of 5 genes (CLIC5, ENTPD8, PACSIN3, HGD, and GNG7) was selected to calculate the risk-score. The model exhibited high performance in time-dependent ROC and a nomogram. Further results showed that overall survival was significantly worse in the high-risk group. As an independent prognostic factor, the risk-score was associated with vascular invasion. There was a dramatic difference in nonregulatory CD4+ and CD8+ T cells between the high and low-risk groups, and the 5 genes were correlated with immune inhibitors. There was a considerable difference in autophagy, immune, cell cycle, infection, and apoptosis-associated terms and pathways in GO and KEGG. The functional states of differentiation, apoptosis, and quiescence were closely related to the 5-gene signature in single-cell analysis.\nCONCLUSION: Our results suggest that the signature could serve as a novel prognostic biomarker in rectal cancer, which might benefit decision-making regarding immunotherapy.", "claims": [{"id": "claim-method", "statement": "Overall survival was plotted and calculated using the Kaplan–Meier method, and differences between groups were compared by the log-rank test. The Multivariate Cox analysis was carried out on the statistically significant variables in the univariate Cox regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36130456", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "Overall survival was plotted and calculated using the Kaplan–Meier method, and differences between groups were compared by the log-rank test. The Multivariate Cox analysis was carried out on the statistically significant variables in the univariate Cox regression."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The 5-gene signature (CLIC5, ENTPD8, PACSIN3, HGD, and GNG7) stratified rectal cancer patients into high- and low-risk groups with significantly different overall survival in the TCGA cohort.", "kind": "quantitative", "target": {"value": 0.0044, "unit": "p-value", "tolerance": null, "source": "It showed that overall survival is significantly low in the high-risk group (P = 0.0044, log-rank = 6.328)."}, "evidence": [{"asset": "source:pmid:36130456", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A signature consisting of 5 genes (CLIC5, ENTPD8, PACSIN3, HGD, and GNG7) was selected to construct a prognostic model in TCGA rectal cancer cohort and validated in the GSE133057 cohort."}, {"asset": "source:pmid:36130456", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "It showed that overall survival is significantly low in the high-risk group (P = 0.0044, log-rank = 6.328)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The 5-gene signature (CLIC5, ENTPD8, PACSIN3, HGD, and GNG7) stratified rectal cancer patients into high- and low-risk groups with significantly different overall survival in the TCGA cohort.", "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:36130456"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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