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Clear Cell Renal Cell Carcinoma with Biallelic Inactivation of CDKN2A/B on 9p21 have Distinct Gene Expression Signature and are Associated with Poor Prognosis

Purpose The clinical implications of biallelic inactivation of CDKN2A/B in clear cell renal cell carcinoma (ccRCC) and relevant dysregulated biological pathways and gene signatures were investigated. Materials and Methods Data were obtained from the TCGA data set and validated using Project GENIE and previously published dataset. CDKN2A/B allelic status was classified into 3 groups, including biallelic CDKN2A/B inactivation (homozygous deletion or combined heterozygous deletion and mutation), monoallelic CDKN2A/B loss (heterozygous deletion or mutation) and absent CDKN2A/B allelic loss. Univariate and multivariate cancer-specific survival and disease-free survival analyses were performed. Integrated analyses of copy number, gene expression (mRNA and miRNA), protein expression and methylation changes were conducted. Results Of 440 patients with ccRCC 17 (3.9%) had biallelic CDKN2A/B inactivation and 116 (26.4%) had monoallelic CDKN2A/B loss. CDKN2A/B allelic inactivation was associated with late tumor stage, high histological grade, presence of metastasis and greater tumor size. Patients with biallelic deletion of CDKN2A/B showed significantly worse cancer-specific survival and disease-free survival (p<0.0001). Significant co-occurrence of MTAP homozygous deletion was observed in CDKN2A/B biallic inactivated tumors (46.7%; p<0.001). Significant underexpression of CDKN2A/B was observed in biallelic inactivated tumors at the mRNA and protein levels. miR-21 was the most highly expressed miRNA in biallelic inactivated tumors. Biallelic inactivated tumors were significantly enriched for genes related to activation of ATR in response to replication stress and miR-21 target genes. Conclusions CDKN2A/B biallelic inactivation may be a prognostic marker for ccRCC and is associated with distinct dysregulation of gene expression signatures.