A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36968596", "kind": "science-record", "revision": 3, "content_hash": "sha256:0497c59f5df5e7653f77343af070a029fba82676d878ac74d093ce9611f6dd1e", "created_at": "2026-11-01T20:26:10Z", "updated_at": "2026-11-01T22:09:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma.", "doi": "10.3389/fgene.2023.1096491", "pmid": "36968596", "authors": ["Deng-Xiong Li", "Qing-Xin Yu", "Chui-Xuan Zeng", "Lu-Xia Ye", "Yi-Qing Guo", "Jun-Fei Liu", "Hai-Hong Zheng", "Dechao Feng", "Wuran Wei"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Background: Endothelial cells in the tumor microenvironment play an important role in the development of kidney renal clear cell carcinoma (KIRC). We wanted to further identify the function of endothelial cells in KIRC patients by integrating single-cell and bulk RNA sequencing data. Methods: Online databases provide the original data of this study. An endothelial-related prognostic index (ERPI) was constructed and validated by R version 3.6.3 and relative packages. Results: The ERPI consisted of three genes (CCND1, MALL, and VWF). Patients with high ERPI scores were significantly correlated with worse prognosis than those with low ERPI scores in the TCGA training group, TCGA test group, and GSE29609 group. A positive correlation was identified between the ERPI score and poor clinical features. The results of functional analysis indicated that ERPI was significantly associated with immune-related activities. We suggested that patients with high ERPI scores were more likely to benefit from immunotherapy based on the results of immune checkpoints, tumor microenvironment, stemness index, and TCIA, while patients with low ERPI scores were sensitive to gemcitabine, docetaxel, paclitaxel, axitinib, pazopanib, sorafenib, and temsirolimus according to the results of the \"pRRophetic\" algorithm. Therefore, this ERPI may help doctors choose the optimal treatment for patients with KIRC. Conclusion: By integrating single-cell and bulk RNA sequencing data from KIRC patients, we successfully identified the key genes from the perspective of endothelial cells in the tumor microenvironment and constructed ERPIs that had positive implications in precision medicine.", "claims": [{"id": "claim-method", "statement": "Then, by following a minimum standard of 10-fold cross-validation, the lasso regression model applied penalties to these genes based on the TCGA training group. The prognostic value of the selected genes in the lasso regression model was assessed by a univariate Cox regression model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36968596", "locator": "sections[4] \"Construction of the endothelial-related prognostic index\" paragraph 2", "quote": "Then, by following a minimum standard of 10-fold cross-validation, the lasso regression model applied penalties to these genes based on the TCGA training group. The prognostic value of the selected genes in the lasso regression model was assessed by a univariate Cox regression model."}], "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 authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36968596", "locator": "sections[17] \"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 authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The endothelial-related prognostic index consisted of three genes: CCND1, MALL, and VWF.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36968596", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The ERPI consisted of three genes (CCND1, MALL, and VWF)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The endothelial-related prognostic index consisted of three genes: CCND1, MALL, and VWF.", "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:36968596"], "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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