A Signature Based on Chromatin Regulation and Tumor Microenvironment Infiltration in Clear Cell Renal Cell Carcinoma

Abstract

Aims: This research aimed to construct a signature based on chromatin regulation in localized clear cell renal cell carcinoma (ccRCC). Materials & methods: Non-negative matrix factorization clustering was performed on 438 localized ccRCC cases. The immune infiltration was generated by the single-sample gene set enrichment analysis algorithm. Survival analyses were performed using the Kaplan–Meier method, and the significance of the differences was determined using the log-rank test. The risk score was constructed based on the expression of chromatin regulators to quantify chromatin modification. Results: A score system based on chromatin modification was established. The high-risk subtype was characterized by increased tumor mutation burden, whereas a low-risk score was characterized by an increase in chromatin regulator expression and better overall survival. Conclusion: This research has constructed a signature based on chromatin regulation in localized ccRCC.

Plain language summary

This research aimed to construct a prognostic model based on chromatin regulation in localized clear cell renal cell carcinoma (ccRCC). There were 438 localized ccRCC patients included. Patients were classified into different chromatin groups and risk groups. The immune infiltration and survival analyses were performed on distinct groups. The prognostic model was constructed by including clinical characteristics and risk scores. Three different chromatin groups and two risk groups were established. Remarkable differences in immunity and survival were found in distinct chromatin groups and risk groups. A nomogram was plotted to visualize the predictive survival rate based on risk and clinical characteristics. This research has constructed a prognostic model based on chromatin regulation in localized ccRCC.

Keywords::

• ccRCC
• chromatin
• immunotherapy
• tumor microenvironment
• tumor mutation burden

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2022-0202

Author contributions

C Yang conceived the idea. C Yang and T Yu designed the study. C Yang collected the data, finished the content analysis and edited the article pictures. T Yu helped edit the article pictures. C Yang drafted the manuscript. T Yu and Q Lin reviewed and corrected the manuscript. All authors contributed to the article and approved the submitted version.

Financial & competing interests disclosure

This study was supported by the Natural Science Foundation of Fujian Province (grant nos. 2020J011220 and 2020J011236), the Key Medical and Health Projects in Xiamen (grant no. 3502Z20209002) and the National Natural Science Foundation of China (grant no. 81772893). The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

This study was supported by the Natural Science Foundation of Fujian Province (grant nos. 2020J011220 and 2020J011236), the Key Medical and Health Projects in Xiamen (grant no. 3502Z20209002) and the National Natural Science Foundation of China (grant no. 81772893). The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.