Single-Cell Sequencing to Identify Six Heat Shock Protein (HSP) Genes-Mediated Progression Subtypes of Clear Cell Renal Cell Carcinoma

Abstract

Background

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 <0.05). Survival analysis showed that C1 patients had a better overall survival (p <0.001). TIMER 2.0 analysis showed that three HSP genes were significantly correlated with the infiltration of CD4+ T cells and CD4+ Th1 cells (|cor|>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

Abbreviations

AJCC, American Joint Committee on Cancer; B-NHL, B-cell non-Hodgkin lymphoma; BP, biological processes; CC, cellular component; ccRCC, clear cell renal cell carcinoma; CTL, cytotoxic T lymphocyte; CTLA4, cytotoxic T-lymphocyte associated protein 4; DISC, death-inducing signaling complex; DR4, death receptors 4; DR5, death receptors 5; GEO, Gene Expression Omnibus; HSP, Heat shock protein; MF, Molecular function; MHC, major histocompatibility complex; PCA, Principal component analysis; PD1, programmed cell death 1; PD_L1, programmed death-ligand 1; TCGA, The Cancer Genome Atlas; TSS, transcription start site.

Data Sharing Statement

All data can be obtained from the corresponding author in a reasonable reasons.

Ethics

The original data required for this research were collected from public databases, so no medical ethics review is required.

Consent for Publication

All authors approved publication.

Acknowledgments

We are grateful to the uploader of the original data and the public database.

Author Contributions

All authors contributed to data analysis, drafting or revising the article, gave final approval of the version to be published, and agree to be accountable for all aspects of the work.

Disclosure

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Additional information

Funding

The study was sponsored by Research on the Frontiers and Application of Chongqing Science and Technology, Commission No. cstc2015jcyjA10030.