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pmid:33850736
Identification and validation of a six immune-related gene signature for prediction of biochemical recurrence in localized prostate cancer following radical prostatectomy.
Jiaochen Luan · Qijie Zhang · Lebin Song · Yichun Wang · Chengjian Ji · Rong Cong · Qitong Zheng · Zhenggang Xu · Jiadong Xia · Ninghong Song
Translational andrology and urology · 2021 doi:10.21037/tau-20-1231
Paper
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Experiment
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Data
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Complete file
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This study is aimed to identify the immune-related gene signature that can predict BCR in localized PCa following RP.\nMETHODS: Expression profile of genes together with clinical parameters from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus database (GEO) and the immune-related genes from the Molecular Signatures Database v4.0 were applied to construct and validate the gene signature. The Cox regression analyses were conducted to identify the candidate genes and establish the gene signature. To estimate the prognostic power of the risk score, the time-dependent receiver operating characteristic (ROC) analysis and Harrell's index of concordance (C-index) were utilized. We also established a nomogram to forecast the probability of patients' survival.\nRESULTS: A total of 268 patients from the TCGA and 77 patients from GSE70770 and six immune-related genes (SCIN, THY1, TBX1, NOTCH4, MAL, BNIP3L) were eventually selected. The Kaplan-Meier analysis demonstrated that patients in the low-risk group had a significantly longer recurrence-free survival (RFS) compared to those in the high-risk group. In the multivariate Cox model, the signature was identified as an independent prognostic factor, which was significantly associated with RFS (TCGA: HR =5.232, 95% CI: 1.762-15.538, P=0.003; GSE70770: HR =2.158, 95% CI: 1.051-4.432, P=0.036). Moreover, the C-index got improved after incorporating the risk score into original clinicopathological parameters. In addition, the novel nomogram was constructed to better predict the 1-, 3- and 5-year RFS.\nCONCLUSIONS: This signature could serve as an independent prognostic factor for BCR. Incorporation of our signature into traditional risk classification might further stratify patients with different prognosis, which could assist practitioners in developing clinical decision-making.", "claims": [{"id": "claim-data-access", "statement": "Expression profile of genes together with clinical follow-up parameters, including age, PSA, stage, GS and outcomes (BCR) for localized PCa patients were acquired from The Cancer Genome Atlas (TCGA) RNA-seq in our retrospective study. The discovery set (TCGA) and the validation set (GSE70770) included 268 and 77 localized PCa patients undergoing RP, separately.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33850736", "locator": "sections[3] \"Mining and processing of sample databases and immune-related genes\" paragraph 2", "quote": "Expression profile of genes together with clinical follow-up parameters, including age, PSA, stage, GS and outcomes (BCR) for localized PCa patients were acquired from The Cancer Genome Atlas (TCGA) RNA-seq in our retrospective study."}, {"asset": "source:pmid:33850736", "locator": "sections[8] \"Acquisition of the eligible databases\" paragraph 2", "quote": "The discovery set (TCGA) and the validation set (GSE70770) included 268 and 77 localized PCa patients undergoing RP, separately."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33850736"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE70770"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE70770"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33850736", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tau-20-1231", "sha256": "sha256:daf0421999647e01416213134b6d7f1e2ec09527117b3e480ef15e7a07931851", "bytes": 28668, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tau-20-1231", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8039594", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE70770", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70770", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70770", "version": null, "note": "Expression profile of genes together with clinical follow-up parameters, including age, PSA, stage, GS and outcomes (BCR) for localized PCa patients were acquired from The Cancer Genome Atlas (TCGA) RNA-seq in our retrospective study. 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