Abstract 1316: Molecular features of complete response to neoadjuvant anti-androgen therapy in high risk localized prostate cancer

Though often curable, high-risk localized prostate cancer has a significant chance of recurring either biochemically, locoregionally, or as distant metastatic disease. Efforts are ongoing to evaluate neoadjuvant strategies to reduce this risk of recurrence. Our recent clinical trial showed that intense androgen deprivation with enzalutamide, leuprolide, and abiraterone acetate with prednisone (ELAP) induced pathologic complete response or minimal residual disease (< 5mm) at prostatectomy in 30% of trial patients (exceptional responders). Though previous studies have identified the pathological and genomic heterogeneity of localized prostate cancer, the impact of this heterogeneity on treatment response is unknown. To address this, we performed multi-region whole-exome and whole transcriptome sequencing on tumor and normal prostate regions from 15 exceptional responders and 15 non-responders treated with intensive androgen deprivation prior to prostatectomy. Overall, we found heterogeneous somatic mutation patterns with strong evidence of intra-tumoral heterogeneity and no association between mutation frequency and response. However, when subsetting patients by treatment response, SPOP mutation and SPOPL copy number loss were only observed in exceptional responders, while TP53 mutations were only observed in the non-responders. We observed expression signature differences between exceptional responders and non-responders, with exceptional responders having an increase in Androgen Receptor related gene signatures. Though underpowered to identify statistically significant genomic correlates of response to neoadjuvant ADT, our findings may inform future studies to identify clinically relevant features of high-risk localized prostate cancers to stratify therapies to reduce the risk of disease recurrence.

Citation Format: Alok Tewari, Alexander T. Cheung, Jake Conway, Jihye Park, Stephanie Wankowicz, Rosina T. Lis, Zhenwei Zhang, Saud AlDubayan, Rana R. McKay, Mary-Ellen Taplin, Eliezer M. Van Allen. Molecular features of complete response to neoadjuvant anti-androgen therapy in high risk localized prostate cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1316.

CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer

Androgen-receptor (AR) inhibitors, including enzalutamide, are used for treatment of all metastatic castration-resistant prostate cancers (mCRPCs). However, some patients develop resistance or never respond. We find that the transcription factor CREB5 confers enzalutamide resistance in an open reading frame (ORF) expression screen and in tumor xenografts. CREB5 overexpression is essential for an enzalutamide-resistant patient-derived organoid. In AR-expressing prostate cancer cells, CREB5 interactions enhance AR activity at a subset of promoters and enhancers upon enzalutamide treatment, including MYC and genes involved in the cell cycle. In mCRPC, we found recurrent amplification and overexpression of CREB5. Our observations identify CREB5 as one mechanism that drives resistance to AR antagonists in prostate cancers.

Abstract SY05-03: Dissecting genomic correlates of response and resistance to chemotherapy in bladder cancer through clinical computational oncology

Approximately 20,000 new cases of muscle-invasive bladder cancer (MIBC), a localized but potentially lethal stage of disease, are diagnosed annually in the US alone. Standard-of-care therapy for MIBC includes neoadjuvant cisplatin-based chemotherapy followed by definitive bladder resection. In prior work, we identified and validated genomic alterations in DNA repair genes such as ERCC2, which predict response to cisplatin-based chemotherapy (Van Allen et al. Cancer Discovery 2014; Liu et al. JAMA Oncology 2016). However, the majority of patients have disease resistant to chemotherapy with a poor prognosis of <40% survival at 5 years, and the genomic basis of chemotherapy resistance has not been well-characterized. In this study, our goal was to analyze matched pre-treatment and resistant post-chemotherapy cystectomy tumor samples to identify genomic correlates of cisplatin-based chemotherapy exposure and resistance. We identified 56 MIBC patients with matched pre-chemotherapy biopsy samples and resistant tumor samples from cystectomy. Along with matched normal samples (blood), we performed whole exome sequencing (WES) on these “trios” of pre, post, and normal tissue, and called somatic variants using standardized pipelines including single nucleotide variants (SNVs), short insertions and deletions, allelic copy number alterations (CNAs), tumor purity and ploidy, and purity- and ploidy-corrected copy number variants. After quality control, including contamination estimation < 5%, mean target coverage > 50x, and a tumor purity minimum threshold of 10%, we had data from 30 trios available for analysis. We hypothesized that DNA-damaging chemotherapy may lead to increased mutational load in the post-treatment tumor. However, we observed that while some tumors gained mutations, others lost mutations, with no overall change (mean change = -17.3 mutations, paired t-test p = 0.20) in total mutational load. We found that clonal mutations (found in all tumor cells) were virtually unchanged from matched pre- to post-treatment tumors. In contrast, subclonal mutations (found only in a subset of tumor cells) were private to pre- and post-treatment tumors. These pre- and post-treatment mutation differences may reflect tumor sampling heterogeneity (i.e. taking from different parts of the tumor), but may be also due to selection pressure from therapy (e.g. loss of subclones) and cisplatin-induced mutations.To investigate the latter possibility, we adapted a non-negative matrix factorization (NMF) approach (Lee and Seung Nature 1999) to discover mutational signatures (Alexandrov et al Nature 2013) in the mutations unique to post-treatment tumors. Along with signatures known to be operant in bladder cancers, we discovered a mutational signature dissimilar to any other previously described mutational signature which accounted for ~15% of post-treatment mutations. This signature exhibited a transcriptional strand bias consistent with known mechanisms of cisplatin-induced DNA damage and repair, and was enriched in subclonal mutations consistent with the relatively short time frame between cisplatin exposure and cystectomy. This signature also exhibited similar activity to a cisplatin-induced mutational signature derived in a preclinical model (DT40) exposed to cisplatin therapy (Pearson rho = 0.95, empiric p = 0.004). Finally, we were able to validate this signature in a separate cohort of pre- and post-cisplatin treated bladder cancers (Faltas et al Nature Genetics 2016). We further hypothesized that the degree of tumor heterogeneity itself may be a prognostic factor. We calculated two different measures of intratumor heterogeneity: (1) the proportion of mutations in each tumor that was subclonal; and (2) the number of unique subclones in each tumor, and examined the association of survival with these measures of intratumor heterogeneity using Cox survival analyses. We found that overall survival was associated with heterogeneity, with a 6.6% increase in mortality rate for each 10% increase in post-treatment proportion of subclonal mutations (p=0.013), and 64% increase in mortality rate for each additional inferred subclone (p=0.02). Tumor heterogeneity continued to be associated with survival after adjusting for clinical covariates (p=0.03, p=0.014, respectively).Finally, we analyzed our tumors for genomic alterations associated with resistance. While we did not discover highly recurrent post-treatment mutations in specific genes, we found drivers of cell cycle progression (E2F3 amplification, JUN amplification), biallelic loss of FBXW7 (regulator of protein degradation of multiple onco-proteins including c-MYC, Notch, Cyclin E, and c-JUN), and focal amplification of PD-L1/2 in individual post-treatment resistant tumors.In this study, we found that cisplatin-based chemotherapy did not induce a large increase in the number of mutations. Thus, while there is good empiric data for the efficacy of combination of chemotherapy and immune checkpoint inhibition in specific tumor type and clinical settings (e.g. platinum-doublet therapy + ICB in first-line therapy of non-small cell lung cancer (NSCLC)), our data suggests that alternative mechanisms other than increased neoantigen burden are responsible. We discovered a cisplatin-induced mutational signature in post-treatment tumors which has subsequently been found in other cisplatin-treated tumors (e.g. NSCLC and ovarian cancer). Interestingly, the proportion of mutations inferred to be cisplatin-induced was quite different between resistant tumors, and an area for further inquiry is whether these differences could be associated with different mechanisms of resistance (e.g. upregulation of efflux pumps vs. anti-apoptotic adaptations). Tumor heterogeneity, which has been associated with worse outcomes and resistance in multiple contexts, was prognostic for survival in our cohort, suggesting that this may be clinically useful as part of a prognostic biomarker. We discovered additional association of drivers of cell-cycle progression with resistance, and further identified acquisition of a focal amplification in a region containing PD-L1/PD-L2, suggesting a potential biomarker for a subset of bladder cancers for response to immune checkpoint blockade. Broadly, this study represents the development of algorithms to dissect genomic features associated with survival and resistance in a carefully curated cohort of matched patient tumors within a specific clinical context. These types of approaches can be applied across tumor types, therapies, and clinical contexts to shed light onto biological mechanisms underpinning response and resistance and inform the development of biomarkers to guide clinical management.

Citation Format: David Liu, Philip Abbosh, Daniel Keliher, Brendan Reardon, Diana Miao, Kent Mouw, Amaro Weiner-Taylor, Stephanie Wankowicz, Garam Han, Min-Yuen Teo, Catharine Cipolla, Jaegil Kim, Gopa Iyer, Hikmat Al-Ahmadie, Essel Dulaimi, David Y.T. Chen, R. Katherine Alpaugh, Jean Hoffman-Censits, Levi A. Garraway, Gad Getz, Scott L. Carter, Joaquim Bellmunt, Elizabeth Plimack, Jonathan E. Rosenberg, Eliezer M. Van Allen. Dissecting genomic correlates of response and resistance to chemotherapy in bladder cancer through clinical computational oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY05-03.

Abstract 1304: Whole-exome analysis of 1,135 melanomas reveals new significantly mutated cancer genes and copy number alterations

Introduction: Identifying driver mutations and significantly mutated genes (SMGs) is critical to characterize therapeutic targets and understand biological subtypes. Past studies in melanoma have identified ~20 SMGs and 4 genomic subtypes (BRAF, NRAS, and NF1, and triple wildtype). Critically, these studies have been powered to detect SMGs only at a frequency of >~10%. However, clinically targetable drivers can occur at much lower frequencies (e.g. ALK-rearrangmenet in lung cancer). Thus, we hypothesized that a uniform meta-analysis of all publicly available melanoma whole exome sequences would provide power to identify clinically SMGs not previously associated with melanoma. Methods: We assembled and uniformly analyzed a cohort of 1,135 tumor and matched germline primary and metastatic non-uveal melanoma whole exomes. All samples were realigned to hg19 using the Picard best practice realignment pipeline. These samples passed several QC metrics that included coverage (DepthOfCoverage, 50X tumor and 20X normal), cross sample contamination (ContEst, < 5%), tumor purity (FACETS, > 20%), and tumor-in-normal (deTiN, < 30%). Mutational significance analysis was performed using MutSigCV2 followed by filtering via biological priors using OncoKB. CNA profiles were generated using GATK4 best practices pipeline. Results: We identified 77 SMGs (MutSig q < 0.1) that were implicated in either melanoma or other cancer types according to OncoKB's curated list of 1,018 cancer genes, some of which that have not been considered SMGs or previously reported in melanoma. Novel genes were involved in immune response [B2M (1.7%) and PTPRC (12.1%)], DNA damage checkpoints [MDC1 (7.5%)], negative regulation of the MAPK pathway [CBL (4.6%)], MYC suppression [MGA (9.4%)], and the PI3K/AKT pathway [PIK3CA (3.4%) and PIK3CB (3.5%)]. Within the “triple-wt” subset of melanomas (n=212), we identified additional SMGs including IDH1, SF3B1, CTNNB1, and MAPK2K1 present in 3-5% of tumors, suggesting additional potential therapeutic targets. Copy number profiles of the cohort were consistent with previous findings. By increasing the resolution from cytobands to 1Mb regions, we identified a 1Mb region in chromosome 3 (chr3:138Mb-139Mb) that was enriched in amplifications (29.2%). Genes in this region include MRAS, PI3KCB, FOXL2, and FAIM. Conclusion: Through assembly and uniform analysis of the largest melanoma whole exome cohort to date, we identified significantly mutated known cancer genes not previously associated with the disease, and identified additional drivers within an incompletely characterized subtype of melanoma. This also enabled us to find genome regions enriched in copy number alterations. Taken together, our findings may inform the additional classification of melanoma and identification of novel drivers to shed light on biological subtypes and identify potential therapeutic targets.

Citation Format: Jake R. Conway, David Liu, Stephanie Wankowicz, Amaro Taylor-Weiner, Felix Dietlein, Eliezer Van Allen. Whole-exome analysis of 1,135 melanomas reveals new significantly mutated cancer genes and copy number alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1304.

Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer

Despite continued widespread use, the genomic effects of cisplatin-based chemotherapy and implications for subsequent treatment are incompletely characterized. Here, we analyze whole exome sequencing of matched pre- and post-neoadjuvant cisplatin-based chemotherapy primary bladder tumor samples from 30 muscle-invasive bladder cancer patients. We observe no overall increase in tumor mutational burden post-chemotherapy, though a significant proportion of subclonal mutations are unique to the matched pre- or post-treatment tumor, suggesting chemotherapy-induced and/or spatial heterogeneity. We subsequently identify and validate a novel mutational signature in post-treatment tumors consistent with known characteristics of cisplatin damage and repair. We find that post-treatment tumor heterogeneity predicts worse overall survival, and further observe alterations in cell-cycle and immune checkpoint regulation genes in post-treatment tumors. These results provide insight into the clinical and genomic dynamics of tumor evolution with cisplatin-based chemotherapy, suggest mechanisms of clinical resistance, and inform development of clinically relevant biomarkers and trials of combination therapies.

The impact of cisplatin-based chemotherapy on tumor genomes is complex. Here, the authors study matched pre- and post-chemotherapy primary samples in muscle-invasive bladder cancer, finding a cisplatin-based mutational signature, and highlighting the impact of intratumor heterogeneity on survival.