Prostate cancer is a heterogeneous and multifocal disease. In general, it presents an indolent behavior, being asymptomatic in many cases. However, in some cases, the tumor rapidly progresses to metastatic disease leading to patient death. The Gleason score (GS) is the main prognostic factor for localized disease and its classification is based on the sum of the primary and the secondary histologic pattern, ranging from 2 to 10. Despite being the main classification method, GS alone does not provide accurate information about patient outcome, since patients with the same score can have different behaviors, particularly in intermediate GS (7-8). Therefore, in this study we investigated genomic alterations in patients with intermediate GS that presented biochemical recurrence (BCR) compared to patients without recurrence, aiming to improve prognosis and also to reveal biologic pathways involved with tumor aggressiveness. Forty-three prostate adenocarcinoma patients with intermediate GS (7-8) that underwent radical prostatectomy at the A.C. Camargo Cancer Center were selected and divided into 2 groups, 21 patients with and 22 patients without BCR, respectively. From these 43 patients we obtained genomic DNA from 35 paired tumor/normal samples and 8 tumors and performed targeted-sequencing of 58 carefully selected genes, including 24 genes frequently mutated in prostate cancer and 34 genes mutated in other solid tumors, using the TruSeq Custom Amplicon kit and the NextSeq platform (Illumina). Sequencing reads were aligned to reference human genome (hg19) using the BWA software, generating >1000X average coverage per sample. To identify somatic mutations, we used the MuTect variant caller followed by Varseq software for selecting SNVs (single nucleotide variants) and indels with a minimum coverage of 100X and minimum allele frequency of 2% in the tumor that leads to missense, nonsense, splice site, or frameshift alterations. A total of 292 variants were identified in prostate tumor samples, 250 SNVs and 42 indels, with an average of 8 alterations per tumor (ranging from 0 to 91). We detected 95 (77 SNVs and 18 Indels) somatic variants in the group of tumors with BCR and 197 (173 SNVs and 24 Indels) somatic variants in the group of tumors without BCR; however, no statistically significant difference in terms of number of variants was detected between the two groups (p-value = 0.30). Of the 58 genes investigated, 45 were affected in at least one patient (77.6%), suggesting that the custom panel is enriched in genes mutated in prostate cancer. Among the top mutated genes (affected by more than 10 variants) we detected genes involved with chromatin modification enzymes, such as KMT2D, KDM5C, KDM6A, CHD5, and BRCA2, as well as genes related to developmental gr In the next step we propose to investigate associations between somatic mutations and clinicopathologic characteristics, especially with the occurrence of biochemical relapse, in an attempt to improve prognosis and better estimate the risk of recurrence.
Citation Format: Isabella Meira, Bruna Barros, Rodrigo Ramalho, José Kroll, Renan Almeida, Sandro de Souza, Isabela da Cunha, Gustavo Guimarães, Dirce Carraro, Elisa Ferreira. Identification of somatic alterations in prostate adenocarcinoma with intermediate Gleason score with and without biochemical recurrence [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A19.