Decreased expression and hypomethylation of HDAC9 lead to poor prognosis and inhibit immune cell infiltration in clear cell renal cell carcinoma.

INTRODUCTION & OBJECTIVES: To evaluate the expression and methylation levels of histone deacetylase 9 (HDAC9) in clear cell renal cell carcinoma (ccRCC), investigate the correlations between the prognosis of ccRCC patients and HDAC9, and examine the associations between immunological parameters and HDAC9. MATERIALS & METHODS: The differences between HDAC9 expression in ccRCC tissues and normal tissues were evaluated with reverse transcription­quantitative polymerase chain reaction (RT­qPCR), western blotting and immunohistochemistry. HDAC9 methylation levels in ccRCC tissues and normal tissues were evaluated via The Cancer Genome Atlas and University of California, Santa Cruz Xena. Kaplan-Meier curves were also obtained from University of California, Santa Cruz Xena. Then, cell proliferation was examined via colony formation assays and 5-ethynyl-2'-deoxyuridine assays, and cell metastasis was investigated via transwell assays. Gene set enrichment analysis was conducted to examine the biofunctions of HDAC9. The relationships between HDAC9 expression and immunological parameters were assessed via the Tumor Immune Estimation Resource database. RESULTS: HDAC9 down-regulation and hypomethylation were observed in ccRCC tissues and led to poor prognosis. HDAC9 up-regulation inhibited the proliferation and metastasis of ccRCC cells. A subset of the pathways identified by gene set enrichment analysis were associated with the immune response and inflammation, which were significantly positively correlated with HDAC9 expression in ccRCC. We confirmed that HDAC9 significantly promoted immune cell infiltration but was positively correlated with the expression of immune checkpoint molecules. CONCLUSION: Decreased expression and hypomethylation of HDAC9 lead to poor prognosis and inhibit immune cell infiltration in ccRCC.