Identification and validation of a novel signature for prediction the prognosis and immunotherapy benefit in bladder cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35127296", "kind": "science-record", "revision": 5, "content_hash": "sha256:77b300a0dace555e87c388820399bec551f4126980cb6da9281eb224beca2a26", "created_at": "2026-11-01T17:36:52Z", "updated_at": "2026-11-01T22:05:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of a novel signature for prediction the prognosis and immunotherapy benefit in bladder cancer.", "doi": "10.7717/peerj.12843", "pmid": "35127296", "authors": ["Yichi Zhang", "Yifeng Lin", "Daojun Lv", "Xiangkun Wu", "Wenjie Li", "Xueqing Wang", "Dongmei Jiang"], "journal": "PeerJ", "year": 2022, "abstract": "BACKGROUND: Bladder cancer (BC) is a common urinary tract system tumor with high recurrence rate and different populations show distinct response to immunotherapy. Novel biomarkers that can accurately predict prognosis and therapeutic responses are urgently needed. Here, we aim to identify a novel prognostic and therapeutic responses immune-related gene signature of BC through a comprehensive bioinformatics analysis.\nMETHODS: The robust rank aggregation was conducted to integrate differently expressed genes (DEGs) in datasets of the Cancer Genome Atlas (TCGA) and the gene expression omnibus (GEO). Lasso and Cox regression analyses were performed to formulate a novel mRNA signature that could predict prognosis of BC patients. Subsequently, the prognostic value and predictive value of the signature was validated with two independent cohorts GSE13507 and IMvigor210. Finally, quantitative Real-time PCR (qRT-PCR) analysis was conducted to determine the expression of mRNAs in BC cell lines (UM-UC-3, EJ-1, SW780 and T24).\nRESULTS: We built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1. Our prognostic signature could be used to stratify BC population into two risk groups with distinct immune profile and responsiveness to immunotherapy. The results of qRT-PCR demonstrated that the eight mRNAs exhibited different expression levels in BC cell lines.\nCONCLUSION: Our study constructed a convenient and reliable 8-mRNA gene signature, which might provide prognostic prediction and aid treatment decision making of BC patients in clinical practice.", "claims": [{"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:The dataset of TCGA-BLCA generated and/or analyzed during the current study are available at the TCGA database (https://cancergenome.nih.gov/).The datasets generated and/or analyzed during the current study are available at GEO: GSE3167, GSE37815, GSE121711, GSE40355 and GSE13507.The dataset of IMvigor210 generated and/or analyzed during the current study are available in http://research-pub.gene.com/IMvigor210CoreBiologies/#transcriptome-wide-gene-expression-data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35127296", "locator": "sections[33] \"Data Availability\" paragraph 2", "quote": "The following information was supplied regarding data availability:The dataset of TCGA-BLCA generated and/or analyzed during the current study are available at the TCGA database (https://cancergenome.nih.gov/).The datasets generated and/or analyzed during the current study are available at GEO: GSE3167, GSE37815, GSE121711, GSE40355 and GSE13507.The dataset of IMvigor210 generated and/or analyzed during the current study are available in http://research-pub.gene.com/IMvigor210CoreBiologies/#transcriptome-wide-gene-expression-data."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35127296", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1.", "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:35127296"], "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:GSE121711"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE121711"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35127296", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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TCGA-BLCA generated and/or analyzed during the current study are available at the TCGA database (https://cancergenome.nih.gov/).The datasets generated and/or analyzed during the current study are available at GEO: GSE3167, GSE37815, GSE121711, GSE40355 and GSE13507.The dataset of IMvigor210 generated and/or analyzed during the current study are available in http://research-pub.gene.com/IMvigor210CoreBiologies/#transcriptome-wide-gene-expression-data.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The dataset of TCGA-BLCA generated and/or analyzed during the current study are available at the TCGA database (https://cancergenome.nih.gov/).The datasets generated and/or analyzed during the current study are available at GEO: GSE3167, GSE37815, GSE121711, GSE40355 and GSE13507.The dataset of IMvigor210 generated and/or analyzed during the current study are available in http://research-pub.gene.com/IMvigor210CoreBiologies/#transcriptome-wide-gene-expression-data.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3444310", "GSM3444311", "GSM3444312", "GSM3444313", "GSM3444314", "GSM3444315", "GSM3444316", "GSM3444317", "GSM3444318", "GSM3444319", "GSM3444320", "GSM3444321", "GSM3444322", "GSM3444323", "GSM3444324", "GSM3444325", "GSM3444326", "GSM3444327"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "Integrative metabolomic and transcriptomic analysis for the non-invasive study of bladder cancer", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE13507", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": 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