Infiltrating T-cell abundance combined with EMT-related gene expression as a prognostic factor of colon cancer.

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In this regard, RNA-seq and clinical data of 469 colon cancer samples derived from the Cancer Genome Atlas (TCGA) database were used to calculate infiltrating T-cell abundance (ITA), to illustrate a pathway enrichment analysis, and to construct Cox proportional hazards (CPH) regression models. Subsequently, the RNA-seq and clinical data of 177 colon cancer samples derived from the GSE17536 cohort were used to validate the CPH regression models. We found that ITA showed correlation with EMT-related gene expression, and that it was not an independent prognostic factor for colon cancer. However, upon comparison of two groups with the same ITA, higher EMT expression helped predicted a worse prognosis, whereas a higher ITA could help predict a better prognosis upon comparison of two groups with the same EMT. Additionally, seven genes were found to be statistically related to the prognosis of patients with colon cancer. These results suggest that the balance between ITA and EMT-related gene expression is conducive to the prognosis of patients with colon cancer, and TPM1 is necessary to further explore the common target genes of immune checkpoint blockade.", "claims": [{"id": "claim-method", "statement": "The Cox Proportional Hazards (CPH) regression model was used for assessing the dependence of overall survival (OS) on ITA and EMT-related gene expression levels for several patients with colon cancer using the R library ‘survival’ (version 3.2–7 https://cran.r-project.org/web/packages/survival/index.html) [22].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34180352", "locator": "sections[8] \"Survival analysis\" paragraph 2", "quote": "The Cox Proportional Hazards (CPH) regression model was used for assessing the dependence of overall survival (OS) on ITA and EMT-related gene expression levels for several patients with colon cancer using the R library ‘survival’ (version 3.2–7 https://cran.r-project.org/web/packages/survival/index.html) [22]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The clinical data and RNA sequencing data of the patients with colon cancer were retrieved from TCGA database (https://confluence.broadinstitute.org/display/GDAC/Home/), and our final dataset consisted of 469 cases consisting of both clinical information and corresponding RNA-seq data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34180352", "locator": "sections[3] \"Data sources\" paragraph 2", "quote": "The clinical data and RNA sequencing data of the patients with colon cancer were retrieved from TCGA database (https://confluence.broadinstitute.org/display/GDAC/Home/), and our final dataset consisted of 469 cases consisting of both clinical information and corresponding RNA-seq data."}], "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:34180352"], "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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