International Journal of General Medicine (Jul 2021)
Single-Cell Sequencing to Identify Six Heat Shock Protein (HSP) Genes-Mediated Progression Subtypes of Clear Cell Renal Cell Carcinoma
Abstract
Qinke Li, Maoqing Lu, Zhechuan Zhang, Ronggui Zhang Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of ChinaCorrespondence: Ronggui ZhangDepartment of Urology, The Second Affiliated Hospital, Linjiang Road, Chongqing Medical University, Chongqing, 400010, People’s Republic of ChinaTel +86-23-13983790901Fax +23-63832133Email [email protected]: Heat shock proteins (HSPs) are widely involved in tumor occurrence and development and are prognostic markers for multiple tumors. However, the role of HSPs in clear cell renal cell carcinoma (ccRCC) remains unclear.Methods: We used Cytoscape to identify hub genes in the ccRCC single-cell sequencing data set from the Gene Expression Omnibus (GEO) data repository. We identified subtypes, C1 and C2, of The Cancer Genome Atlas (TCGA) patients based on the expression of hub genes using unsupervised consensus clustering. Principal component analysis (PCA) was used to verify the clustering differences, and Kaplan–Meier (K-M) estimate was used to verify the survival differences between C1 and C2 patients. We used TIMER 2.0 and CIBERSORT to evaluate the immune cell infiltration of HSP genes and C1 and C2 patients. The R package “pRRophetic” was used to evaluate the sensitivity in C1 and C2 patients to the four first-line treatment drugs.Results: We identified six hub genes (HSP90AA1, HSPH1, HSPA1B, HSPA8, and HSPA1A) encoding HSP, five of which were significantly downregulated in TCGA group, and four had a protective effect on prognosis (p 0.5, p< 0.001). CIBERSORT showed significant differences in multiple infiltrating immune cells between C1 and C2 patients. Meanwhile, the expression of PD1 was significantly lower in C1 patients than in C2 patients, and the expression of PDL1 is the another way around. Drug sensitivity analysis showed that C1 patients were more sensitive to sorafenib, pazopanib, and axitinib (p < 0.001).Conclusion: Our research revealed two molecular subtypes of ccRCC based on 6 HSP genes, and revealed significant differences between the two subtypes in terms of clinical prognosis, immune infiltration, and drug sensitivity.Keywords: ccRCC, bioinformatics, immune, molecular subtypes, prognosis
