Targeted Next-generation Sequencing of Advanced Prostate Cancer Identifies Potential Therapeutic Targets and Disease Heterogeneity

Abstract

Background Most personalized cancer care strategies involving DNA sequencing are highly reliant on acquiring sufficient fresh or frozen tissue. It has been challenging to comprehensively evaluate the genome of advanced prostate cancer (PCa) because of limited access to metastatic tissue. Objective To demonstrate the feasibility of a novel next-generation sequencing (NGS) based platform that can be used with archival formalin-fixed paraffin-embedded (FFPE) biopsy tissue to evaluate the spectrum of DNA alterations seen in advanced PCa. Design, setting, and participants FFPE samples (including archival prostatectomies and prostate needle biopsies) were obtained from 45 patients representing the spectrum of disease: localized PCa, metastatic hormone-naive PCa, and metastatic castration-resistant PCa (CRPC). We also assessed paired primaries and metastases to understand disease heterogeneity and disease progression. Intervention At least 50 ng of tumor DNA was extracted from FFPE samples and used for hybridization capture and NGS using the Illumina HiSeq 2000 platform. Outcome measurements and statistical analysis A total of 3320 exons of 182 cancer-associated genes and 37 introns of 14 commonly rearranged genes were evaluated for genomic alterations. Results and limitations We obtained an average sequencing depth of >900X. Overall, 44% of CRPCs harbored genomic alterations involving the androgen receptor gene (AR), including AR copy number gain (24% of CRPCs) or AR point mutation (20% of CRPCs). Other recurrent mutations included transmembrane protease, serine 2 gene (TMPRSS2):v-ets erythroblastosis virus E26 oncogene homolog (avian) gene (ERG) fusion (44%); phosphatase and tensin homolog gene (PTEN) loss (44%); tumor protein p53 gene (TP53) mutation (40%); retinoblastoma gene (RB) loss (28%); v-myc myelocytomatosis viral oncogene homolog (avian) gene (MYC) gain (12%); and phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit α gene (PIK3CA) mutation (4%). There was a high incidence of genomic alterations involving key genes important for DNA repair, including breast cancer 2, early onset gene (BRCA2) loss (12%) and ataxia telangiectasia mutated gene (ATM) mutations (8%); these alterations are potentially targetable with poly(adenosine diphosphate-ribose)polymerase inhibitors. A novel and actionable rearrangement involving the v-raf murine sarcoma viral oncogene homolog B1 gene (BRAF) was also detected. Conclusions This first-in-principle study demonstrates the feasibility of performing in-depth DNA analyses using FFPE tissue and brings new insight toward understanding the genomic landscape within advanced PCa.

Androgen receptor antagonism drives cytochrome P450 17A1 inhibitor efficacy in prostate cancer

“…The data were subjected to exponential growth-curve analysis constrained to share an initial value and to 2-way ANOVA analysis followed by Bonferroni's multiple comparisons test. Significant differences as compared with the vehicle-treated control group (P < 0.05) were detected only for seviteronel at a dose of 100 mg/kg (days [14][15][16][17][18][19][20][21][22][23][24][25][26][27][28].…”

“…In addition to enhanced AR expression, there is considerable evidence to suggest that mutations in the AR that alter its response to pharmacological agents may also be important in CRPC (6,21,23). Specifically, treatment failure in patients progressing while on antiandrogens has been attributed to point mutations in the AR: flutamide, T877A; bicalutamide, W741C; and enzalutamide, F876L (6,21,(24)(25)(26)(27).…”

“…The most recent studies have attributed such resistance to continued AR overexpression, increased adrenal or intratumoral androgen synthesis, expression of constitutively active AR splice variants (AR-V7), glucocorticoid receptor (GR) expression, and AR mutations (5,(19)(20)(21)(22). AR point mutations are rare in early, untreated prostate tumors but commonly arise in treated CRPC tumors (23). These mutations occur most frequently in the AR ligand-binding domain (LBD) and lead to altered ligand pharmacology, such that antiandrogens function as agonists and drive the outgrowth of cells expressing the gain-of-function resistance mutation.…”

Stromal epigenetic dysregulation is sufficient to initiate mouse prostate cancer via paracrine Wnt signaling

“…Abnormal expression patterns of β-catenin have been observed in 20-71% of prostate cancer samples (51)(52)(53), and high levels of β-catenin are concomitantly associated with increasing Gleason score and castration resistance (53,54). Although recent studies showed that mutations in allophycocyanin and β-catenin can be detected in approximately 10% and 12% of castrationresistant prostate cancer, respectively (55)(56)(57), it seems that Wnt/ β-catenin signaling could play a more common role in prostate cancer than would be predicted by the point mutation rates of these downstream effectors (53,58,59). Alterations in Wnt ligands and their modulators that are secreted from prostate epithelia and the surrounding stroma may serve as the alternative mechanism for activation of Wnt signaling in a subset of human prostate cancer.…”

ATM Mutations in Cancer: Therapeutic Implications

“…In addition, a high rate of deletion or methylation of either ATM or MCPH1, a proximal regulator that recruits ATM to the sites of DNA DSBs, was reported in breast cancer samples (96%, 121 of 126). In prostate cancer, targeted next-generation sequencing has revealed an 8% incidence of ATM mutations (59). ATM is also one of the most commonly mutated genes in pancreatic cancer (60) or lung adenocarcinoma (61).…”