NGS-based molecular panel analysis of metastatic prostate cancer for daily routine: How often do we detect druggable mutations?

Abstract

203 Background: Guidelines recommend molecular analysis to identify druggable mutations after failure of the first-line systemic therapy for metastatic prostate cancer (mPCA). We report our results of molecular diagnostics in mCRPC patients. Methods: From 2018 to 2023, 311 mCRPC patients underwent molecular panel analysis of archived prostatectomy samples (n=96) or CT-guided biopsies of progressive metastases (n=215) using standardized NGS procedures after the failure of first- or second-line systemic therapy. Mutation analysis was initially performed using NGS with a custom "Prostate Cancer Panel" of 18 multiplex PCR amplicons (AR, ATM, AURKA/MYC, BRCA1/2, CDK12, CTNNB1, DLL3, ETS family, FOXA1, FOXO1, MED12, PIK3CA, PTEN, RAD51C, TP53, Wnt-Pathway), generated using a GeneRead DNAseq Custom Panel V2 (Qiagen). Since 2023, we perform apply the TSO500 panel in selected cases. Analysis of HRD was performed by combining BRCA1 and BRCA2 mutations with the HRD score (Genomic ScarScore GSS) using the HANDLE HRD Focus Panel (Halo-shape Annealing and Defer-Ligation Enrichment, AmoyDx). The data were evaluated using the following thresholds: tumor cell content ≥ 30%, GScore positive at ≥ 50, HRD positive: GScore at ≥ 50 or BRCA1/2 category 4/5 mutation. In addition MSI-high and mutations of MSH2, MSH6, PMS2, and MLH1 were analysed. The following databases were reviewed to identify druggable mutations: OncoKB, ClinVar, JAX-CKB, COSMIC, and My Cancer Genome. Results: Out of 311 biopsies, 299 (96%) had sufficient DNA content for NGS. NGS was performed from prostate (31%), lymph node (30%), visceral (15%), and bone (24%) metastases with informative DNA retrival in 95%, 95%, 92%, and 85%, respectively. Overall, 157 patients (50.5%) had no or non druggable mutations, while 154 patients (49.5%) exhibited druggable mutations. HRD gene mutations (BRCA1/2, ATM, CDK12, CHEK2, FANCA, Rad51C) and inactivating p53 mutations were observed in 66 patients (22%). 3 patients had p53 mutations with gain-of-function resulting in ATM inactivation. 50% HRD gene mutations including a positive HRD score were pathogen and treated with PARPi resulting in a progression-free survival of 3-28 months. Activating androgen receptor mutations and inactivating PTEN/activating PIK3Ca mutations were found in 42 (14%) and 24 (8%) patients, resp. Switch of treatment for AR mutation resulted in PFS of 6-9 months. Mismatch repair deficiency/MSI high mutations were identified in 3 cases who received pembrolizumab with a PFS of 4-8 months. Conclusions: NGS analysis in mCRPC reveals mutations in two-thirds of patients, of which 41% are already druggable. Only 50% of druggable mutations are based on BRCA1/2 or ATM. NGS analysis should be integrated into the diagnostic armamentarium following failure of first-line systemic therapy for mCRPC.