Integrated Analysis of Single-Cell and Bulk RNA Sequencing Reveals HSD3B7 as a Prognostic Biomarker and Potential Therapeutic Target in ccRCC.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39684640", "kind": "science-record", "revision": 3, "content_hash": "sha256:fc2a7c8b362e5eb9ffdcc9849cd34ac88f513c8d03eb518da10603c648a56f9e", "created_at": "2026-11-01T20:29:58Z", "updated_at": "2026-11-01T22:13:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Analysis of Single-Cell and Bulk RNA Sequencing Reveals HSD3B7 as a Prognostic Biomarker and Potential Therapeutic Target in ccRCC.", "doi": "10.3390/ijms252312929", "pmid": "39684640", "authors": ["Guicen Liu", "Qichen Liu", "Jiawei Zhao", "Ruyue Luo", "Yuan Wan", "Zhongli Luo"], "journal": "International journal of molecular sciences", "year": 2024, "abstract": "Clear cell renal cell carcinoma (ccRCC) is the most common kidney malignancy, with a poor prognosis for advanced-stage patients. Identifying key biomarkers involved in tumor progression is crucial for improving treatment outcomes. In this study, we employed an integrated approach combining single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) to identify biomarkers associated with ccRCC progression and prognosis. Single-cell transcriptomic data were obtained from publicly available datasets, and genes related to tumor progression were screened using Monocle2. Bulk RNA-seq data for ccRCC were retrieved from The Cancer Genome Atlas (TCGA) and integrated with scRNA-seq data to explore tumor heterogeneity. We identified 3 beta-hydroxy steroid dehydrogenase type 7 (HSD3B7) as a candidate biomarker for ccRCC, associated with poor overall survival, disease-specific survival, and progression-free interval. Elevated HSD3B7 expression correlated with aggressive clinical features such as advanced TNM stages, histologic grades, and metastasis. Functional studies demonstrated that HSD3B7 promotes cell proliferation, migration, and invasion in vitro, while its silencing significantly inhibits tumor growth in vivo. Our findings reveal that HSD3B7 is a novel biomarker for ccRCC, providing insights into its role in tumor progression and potential as a target for therapy. This study highlights the value of integrating scRNA-seq and bulk RNA-seq data to uncover key regulators of tumor biology and lays the foundation for developing personalized therapeutic strategies for ccRCC patients.", "claims": [{"id": "claim-method", "statement": "Univariate Cox regression analysis was performed using the R package “survival” (v3.3.1, https://cran.r-project.org/web/packages/survival/index.html, accessed on 24 November 2023) and “survminer” (v0.4.9, https://cran.r-project.org/web/packages/survminer/index.html, accessed on 24 November 2023) to evaluate and visualize the association between patient survival and gene expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39684640", "locator": "sections[12] \"4.3. 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The ccRCC bulk RNA-seq and clinical data were retrieved from the Genomic Data Commons (GDC) data portal (https://portal.gdc.cancer.gov/ (accessed on 28 October 2024)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39684640", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. scRNA-seq datasets (GSE131685, GSE152938, GSE156632, and GSE159115) were obtained from the Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo (accessed on 28 October 2024)). The ccRCC bulk RNA-seq and clinical data were retrieved from the Genomic Data Commons (GDC) data portal (https://portal.gdc.cancer.gov/ (accessed on 28 October 2024))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Figure 4A shows that patients with high HSD3B7 expression had significantly poorer overall survival (OS; HR = 1.71, 95% CI: 1.25–2.32, p < 0.001), disease-specific survival (DSS; HR = 1.75, 95% CI: 1.18–2.59, p = 0.005), and progress free interval (PFI; HR = 1.70, 95% CI: 1.23–2.34, p = 0.001).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Figure 4A shows that patients with high HSD3B7 expression had significantly poorer overall survival (OS; HR = 1.71, 95% CI: 1.25–2.32, p < 0.001), disease-specific survival (DSS; HR = 1.75, 95% CI: 1.18–2.59, p = 0.005), and progress free interval (PFI; HR = 1.70, 95% CI: 1.23–2.34, p = 0.001)."}, "evidence": [{"asset": "source:pmid:39684640", "locator": "sections[5] \"2.3. 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