A novel m7G-related lncRNA risk model for predicting prognosis and evaluating the tumor immune microenvironment in colon carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35992788", "kind": "science-record", "revision": 4, "content_hash": "sha256:01b5c7a48d69c8e58f54ce8408fea37ace0c85679bd8d61e70046a651c0c75a5", "created_at": "2026-11-01T18:15:09Z", "updated_at": "2026-11-01T22:07:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A novel m7G-related lncRNA risk model for predicting prognosis and evaluating the tumor immune microenvironment in colon carcinoma.", "doi": "10.3389/fonc.2022.934928", "pmid": "35992788", "authors": ["Sheng Yang", "Jiahui Zhou", "Zhihao Chen", "Qingyang Sun", "Dongsheng Zhang", "Yifei Feng", "Xiaowei Wang", "Yueming Sun"], "journal": "Frontiers in oncology", "year": 2022, "abstract": "N7-Methylguanosine (m7G) modifications are a common type of posttranscriptional RNA modifications. Its function in the tumor microenvironment (TME) has garnered widespread focus in the past few years. Long non-coding RNAs (lncRNAs) played an essential part in tumor development and are closely associated with the tumor immune microenvironment. In this study, we employed a comprehensive bioinformatics approach to develop an m7G-associated lncRNA prognostic model based on the colon adenocarcinoma (COAD) database from The Cancer Genome Atlas (TCGA) database. Pearson's correlation analysis was performed to identify m7G-related lncRNAs. Differential gene expression analysis was used to screen lncRNAs. Then, we gained 88 differentially expressed m7G-related lncRNAs. Univariate Cox analysis and Lasso regression analysis were performed to build an eight-m7G-related-lncRNA (ELFN1-AS1, GABPB1-AS1, SNHG7, GS1-124K5.4, ZEB1-AS1, PCAT6, C1RL-AS1, MCM3AP-AS1) risk model. Consensus clustering analysis was applied to identify the m7G-related lncRNA subtypes. We also verified the risk prediction effect of a gene signature in the GSE17536 test set (177 patients). A nomogram was constructed to predict overall survival rates. Furthermore, we analyzed differentially expressed genes (DEGs) between high-risk and low-risk groups. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted with the analyzed DEGs. At last, single-sample gene set enrichment analysis (ssGSEA), CIBERSORT, MCP-COUNTER, and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithms were utilized to discover the relationship between the risk model and the TME. Consequently, the m7G-related lncRNA risk model for COAD patients could be a viable prognostic tool and treatment target.", "claims": [{"id": "claim-method", "statement": "In addition, through 1,000-fold cross-validation, the Lasso Cox regression method was used to identify the ideal penalty parameter lambda and the relevant coefficient criterion based on the minimal criterion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35992788", "locator": "sections[6] \"Construction of the prognostic m7G-related lncRNA risk model\" paragraph 2", "quote": "In addition, through 1,000-fold cross-validation, the Lasso Cox regression method was used to identify the ideal penalty parameter lambda and the relevant coefficient criterion based on the minimal criterion."}], "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/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35992788", "locator": "sections[24] \"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/s."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Consensus clustering identified three m7G-associated molecular subtypes among 452 COAD samples with significantly different overall survival between the subtypes (log-rank P = 0.007).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35992788", "locator": "sections[17] \"Identification of m7G-associated clusters and prognostic analysis between clusters\" paragraph 2", "quote": "After careful selection, the best K value was 3 and the samples were divided into three clusters."}, {"asset": "source:pmid:35992788", "locator": "sections[17] \"Identification of m7G-associated clusters and prognostic analysis between clusters\" paragraph 2", "quote": "The corresponding p value obtained by the log-rank test was 0.007."}, {"asset": "source:pmid:35992788", "locator": "sections[17] \"Identification of m7G-associated clusters and prognostic analysis between clusters\" paragraph 2", "quote": "There were significant differences in survival among the three subgroups. with cluster1 having a worse prognosis than clusters 2 and 3."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Consensus clustering identified three m7G-associated molecular subtypes among 452 COAD samples with significantly different overall survival between the subtypes (log-rank P = 0.007).", "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:35992788"], "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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