A MUCINs expression signature impacts overall survival in patients with clear cell renal cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34327857", "kind": "science-record", "revision": 8, "content_hash": "sha256:dfa3305f66408b82d5e1140d6fd637781009c7373a04335e5e95673dd4a0c057", "created_at": "2026-11-01T15:41:45Z", "updated_at": "2026-11-01T22:47:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A MUCINs expression signature impacts overall survival in patients with clear cell renal cell carcinoma.", "doi": "10.1002/cam4.4128", "pmid": "34327857", "authors": ["Hui Meng", "Xuewen Jiang", "Huangwei Huang", "Neng Shen", "Changsheng Guo", "Chunxiao Yu", "Gang Yin", "Yu Wang"], "journal": "Cancer medicine", "year": 2021, "abstract": "BACKGROUND: Kidney cancer, especially clear cell renal cell carcinoma (ccRCC), is one of the most common cancers in the urinary system. Previous studies suggested that certain members of MUCINs could serve as independent predictors for the survival of ccRCC patients. None of them, however, is robust enough to predict prognosis accurately.\nOBJECTIVE: To analyze the correlation of MUCINs alterations and their expression levels with the prognosis of ccRCC patients and develop a prognosis-related predictor.\nMETHODS: We applied whole-exome sequencing in samples from 22 Chinese ccRCC patients to identify genetic alterations in MUCIN genes and analyzed their genetic alterations, expression, and correlation with survival using the TCGA, GSE73731, and GSE29069 datasets.\nRESULT: Genetic alternations in MUCINs were identified in 91% and 51% of ccRCC patients in our cohort and the TCGA database, respectively. No correlation with survival was found for the genetic alterations. Using unsupervised clustering analysis of gene expression, we identified two major clusters of MUCIN expression patterns. Cluster 1 was characterized by a global overexpression of MUC1, MUC12, MUC13, MUC16, and OVGP1; and cluster 2 was characterized by a global overexpression of MUC4, MUC5B, MUC6, MUC20, EMCN, and MCAM. Patients with cluster 1 expression pattern had significantly shorter overall survival time and worse clinical features, including higher tumor grades and metastasis. Meanwhile, they had a higher level of mutation counts and more infiltrated immune cells, but lower enrichment in angiogenesis signature genes. A five-MUCINs expression signature was constructed from cluster 1, and notably, it was demonstrated to be associated with shorter overall survival. A similar worse clinical feature, lower angiogenesis but the more immune signature, was identified in samples presented with signature 1. In the validation data set GSE29069, patients with signature 1 were also associated with a trend of poor survival outcomes.\nCONCLUSION: We established a five-MUCINs expression signature as a new prognostic marker for ccRCC. The distinct tumor microenvironment feature between the two signatures may further affect ccRCC patients' clinical management.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier survival curves and Cox survival analysis were generated by the “survival” package and “survminer” package in R. The Cox proportional hazard ratio and the 95% confidence interval were included in the survival plot. A log‐rank test was used to evaluate the survival curves between different groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34327857", "locator": "sections[6] \"Survival analysis\" paragraph 2", "quote": "Kaplan–Meier survival curves and Cox survival analysis were generated by the “survival” package and “survminer” package in R."}, {"asset": "source:pmid:34327857", "locator": "sections[6] \"Survival analysis\" paragraph 2", "quote": "The Cox proportional hazard ratio and the 95% confidence interval were included in the survival plot."}, {"asset": "source:pmid:34327857", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "A log‐rank test was used to evaluate the survival curves between different groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw sequencing data files were deposited in the Chinese National Genomics Data Center(https://bigd.big.ac.cn/). Left biospecimens may be shared for academic research under prior approval from the government of China.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34327857", "locator": "sections[20] \"DATA AND MATERIAL AVAILABILITY STATEMENT\" paragraph 2", "quote": "The raw sequencing data files were deposited in the Chinese National Genomics Data Center(https://bigd.big.ac.cn/). Left biospecimens may be shared for academic research under prior approval from the government of China."}], "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:34327857"], "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:GSE29069"], "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:GSE29069"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34327857", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/cam4.4128", "sha256": "sha256:9af66604d9e85c595e6700751b5c33ebb2eb17886d8daec753225328252b9236", "bytes": 29071, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/cam4.4128", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8419780", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29069", "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=GSE29069", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29069", "version": null, "note": "The raw sequencing data files were deposited in the Chinese National Genomics Data Center(https://bigd.big.ac.cn/). Left biospecimens may be shared for academic research under prior approval from the government of China.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw sequencing data files were deposited in the Chinese National Genomics Data Center(https://bigd.big.ac.cn/). 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"taxon": "Homo sapiens", "title": "Clear cell renal cell carcinoma (ccRCC) samples", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34327857:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:46f62d6e9707c2f65f3fe8c1339c690103ca5db1d7e3c7f9115029947aade5d0", "bytes": 1230, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#cam44128-tbl-0001", "version": null, "note": "Positive correlation of Mucin gene expression in ccRCC‐TCGA", "structure": {"pmcid": "PMC8419780", "section_index": 14, "section_title": "Correlation of MUCINS expression levels in CCRCC", "row_count": 26, "column_count": 4}, "table": {"label": "TABLE 1", "caption": "Positive correlation of Mucin gene expression in 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"rows": [["Mucins", "Mucins", "Pearson r", "p"], ["EMCN", "MUC12", "−0.37185", "0"], ["EMCN", "MUC13", "−0.34702", "0"], ["MUC20", "MUC13", "−0.23436", "4.26E−08"], ["EMCN", "OVGP1", "−0.2261", "1.28E−07"], ["MCAM", "OVGP1", "−0.21355", "6.33E−07"], ["MUC13", "MUC4", "−0.21301", "6.77E−07"], ["EMCN", "MUC1", "−0.18511", "1.67E−05"], ["MUC4", "MUC1", "−0.15292", "0.000391"], ["MUC20", "MUC12", "−0.15079", "0.000472"], ["EMCN", "MUC16", "−0.14453", "0.000809"], ["EMCN", "MUC5B", "−0.10878", "0.011892"], ["MUC12", "MUC4", "−0.08943", "0.038836"]], "row_count": 13, "column_count": 4, "numeric_cells": 33, "header_rows": 1, "locator": "section[14]/table-wrap[2]#cam44128-tbl-0002"}}], "gaps": ["asset:data:geo:GSE29069 not downloaded", "asset:data:geo:GSE29069 licence not read", "asset:data:geo:GSE73731 not downloaded", "asset:data:geo:GSE73731 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE73731", "GSE29069"], "resolved_accessions": ["GSE73731", "GSE29069"], "statements": ["The raw sequencing data files were deposited in the Chinese National Genomics Data Center(https://bigd.big.ac.cn/). Left biospecimens may be shared for academic research under prior approval from the government of China."], "basis": "The paper names GSE73731, GSE29069 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. 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The Cox proportional hazard ratio and the 95% confidence interval were included in the survival plot. A log‐rank test was used to evaluate the survival curves between different groups."], "order_basis": "analysis_only", "id": "assay:1"}]}