Search

Supplemental Table 1. Overall cohort characteristics of AAPC whole exome sequencing cohort (n=102) Supplemental Table 2. Clinical and pathological characteristics of AAPC WES discovery cohort (n=102) Supplemental Table 3. Comparison of numbers of tumors by Gleason grade between the TCGA and AAPC cohorts Supplemental Table 4. Germline pathogenic variants in genes in the DNA repair pathway and list of 20 DNA repair genes assessed in targeted analysis Supplemental Table 5. Alteration file of somatic variants detected in the AAPC WES discovery cohort (n=102) Supplemental Table 6. Focal deletion and amplification peaks and genes located within peaks by GISTIC2.0 analysis of AAPC WES cohort Supplemental Table 7. ERF deletions and mutations in prostate tumors of the Weill Cornell Precision Medicine cohort Supplemental Table 8. Clinical and pathological characteristics of AAPC targeted sequencing extension cohort Supplemental Table 9. List of genes and intronic regions targeted with hybrid capture bait set used for AAPC extension cohort Supplemental Table 10. Alteration file of somatic variants detected in the AAPC extension cohort (n=90) using the targeted sequencing panel Supplemental Table 11. ERF mutation frequencies across published prostate cancer cohorts Supplemental Table 12. Germline ERF variant detected in the AAPC WES cohort Supplemental Table 13. Mutations in cytochrome P450 genes in the AAPC exome discovery cohort Supplemental Table 14. ERF oligonucleotides used for RNA in situ hybridization Supplemental Table 15. Gene sets shERF_VCAP_UP_LnCAP_UP_overlap_UP and shERF_vs_CNTRL.LHSAR_UP Supplemental Table 16. Tumor purity estimates for AAPC exome discovery cohort

Supplemental Methods

Supplemental Figure Legends

Purpose: Platinum-based chemotherapy remains the standard treatment for advanced urothelial carcinoma by inducing DNA damage. We hypothesize that somatic alterations in DNA damage response and repair (DDR) genes are associated with improved sensitivity to platinum-based chemotherapy.Experimental Design: Patients with diagnosis of locally advanced and metastatic urothelial carcinoma treated with platinum-based chemotherapy who had exon sequencing with the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay were identified. Patients were dichotomized based on the presence/absence of alterations in a panel of 34 DDR genes. DDR alteration status was correlated with clinical outcomes and disease features.Results: One hundred patients were identified, of which 47 harbored alterations in DDR genes. Patients with DDR alterations had improved progression-free survival (9.3 vs. 6.0 months, log-rank P = 0.007) and overall survival (23.7 vs. 13.0 months, log-rank P = 0.006). DDR alterations were also associated with higher number mutations and copy-number alterations. A trend toward positive correlation between DDR status and nodal metastases and inverse correlation with visceral metastases were observed. Different DDR pathways also suggested variable impact on clinical outcomes.Conclusions: Somatic DDR alteration is associated with improved clinical outcomes in platinum-treated patients with advanced urothelial carcinoma. Once validated, it can improve patient selection for clinical practice and future study enrollment. Clin Cancer Res; 23(14); 3610–8. ©2017 AACR.

Supplemental Figure 1: The association between deleterious DDR (DNA damage response and repair) alteration status as determined by in silico analysis and (A) Progression-free survival and (B) overall survival, and the association between deleterious DDR alteration status as determined by literature review, and (C) progression-free survival and (D) overall survival. DDRwt: wild type DDR; DDRalt: altered DDR not considered deleterious per methodologies employed. Supplemental Figure 2: Mutation load estimates based on MSK-IMPACT assay recapitulates whole exome sequencing data. Correlation between mutation counts generated from all sequences produced by TGCA bladder cancer whole exome sequencing and counts generated after first subsetting TCGA data to only those reads that coincide with the MSK-IMPACT capture regions. Supplemental Figure 3: (A) Mean number of total mutations, (B) number of copy number alterations and (C) fraction of copy number altered genome based on number of DNA Damage Response and Repair (DDR) alterations. (Whisker plot with Tukey method) Supplemental Figure 4: Influence of total mutation load on (A) Progression-free survival, (B) overall survival and (C) response rate. Total mutation load was divided into quartiles for the purpose of graphical representation. Supplemental Table 1: DDR Gene Panel Supplemental Table 2: All identified DDR alterations

Introduction Optimal end points in phase 2 trials evaluating salvage therapy for metastatic urothelial carcinoma are necessary to identify promising drugs, particularly immunotherapeutics, where response and progression-free survival may be unreliable. We developed a nomogram using data from phase 2 trials of historical agents to estimate the 12-month overall survival (OS) for patients to which observed survival of nonrandomized data sets receiving immunotherapies could be compared. Patients and Methods Survival and data for major prognostic factors were obtained from phase 2 trials: hemoglobin, performance status, liver metastasis, treatment-free interval, and albumin. A nomogram was developed to estimate 12-month OS. Patients were randomly allotted to discovery:validation data sets in a 2:1 ratio. Calibration plots were constructed in the validation data set and data bootstrapped to assess performance. The nomogram was tested on external nonrandomized cohorts of patients receiving pemetrexed and atezolizumab. Results Data were available from 340 patients receiving sunitinib, everolimus, docetaxel + vandetanib, docetaxel + placebo, pazopanib, paclitaxel, or docetaxel. Calibration and prognostic ability were acceptable (c index = 0.634; 95% confidence interval [CI], 0.596-0.652). Observed 12-month survival for patients receiving pemetrexed (n = 127, 23.5%; 95% CI, 16.2-31.7) was similar to nomogram-predicted survival (19%; 95% CI, 16.5-21.5; P > .05), while observed results with atezolizumab (n = 403, 39.0%; 95% CI, 34.1-43.9) exceeded predicted results (24.6%; 95% CI, 23.4-25.8; P Conclusion This nomogram may be a useful tool to interpret results of nonrandomized phase 2 trials of salvage therapy for metastatic urothelial carcinoma by assessing the OS contributions of drug intervention independent of prognostic variables.

Purpose: Platinum-based chemotherapy remains the standard treatment for advanced urothelial carcinoma by inducing DNA damage. We hypothesize that somatic alterations in DNA damage response and repair (DDR) genes are associated with improved sensitivity to platinum-based chemotherapy. Experimental Design: Patients with diagnosis of locally advanced and metastatic urothelial carcinoma treated with platinum-based chemotherapy who had exon sequencing with the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay were identified. Patients were dichotomized based on the presence/absence of alterations in a panel of 34 DDR genes. DDR alteration status was correlated with clinical outcomes and disease features. Results: One hundred patients were identified, of which 47 harbored alterations in DDR genes. Patients with DDR alterations had improved progression-free survival (9.3 vs. 6.0 months, log-rank P = 0.007) and overall survival (23.7 vs. 13.0 months, log-rank P = 0.006). DDR alterations were also associated with higher number mutations and copy-number alterations. A trend toward positive correlation between DDR status and nodal metastases and inverse correlation with visceral metastases were observed. Different DDR pathways also suggested variable impact on clinical outcomes. Conclusions: Somatic DDR alteration is associated with improved clinical outcomes in platinum-treated patients with advanced urothelial carcinoma. Once validated, it can improve patient selection for clinical practice and future study enrollment. Clin Cancer Res; 23(14); 3610–8. ©2017 AACR.

Immunotherapy in urological cancer has made substantial progress during the last 20 years, but recent advances in immunotherapy have completely transformed the present treatment landscape. In this review, we summarize major clinical achievements of immunotherapy in genitourinary cancers, as well as address potential new directions for these therapies, including new agents, combinations, and biomarkers.Recently, nivolumab and atezolizumab have joined sipuleucel-T as Food and Drug Administration-approved therapies in urological malignancies. Additional checkpoint inhibitors and vaccines are being tested in clinical trials. Furthermore, significant work has been done exploring predictors of response to therapy.Immunotherapy has changed the treatment of urologic malignancies. New immunotherapies and novel combinations will continue to create new treatment options in urologic tumors.

Background: Tumour expression of selected microRNAs (miRs) correlates with cisplatin efficacy in multiple cancers. We investigated the role of selected miRs in patients receiving cisplatin-based therapy for advanced urothelial carcinoma (UC). Methods: RNA was extracted from formalin-fixed paraffin-embedded tumour from 83 advanced UC patients who received cisplatin. A miR panel based on relevance for platinum sensitivity and UC was studied by quantitative reverse transcription quantitative PCR (RT–qPCR). Association of progression-free survival (PFS) with miR expression was analysed using cox regression. Selected TFs were chosen by association with the panel of miRs using the Transcription Regulation algorithm (GeneGo MetaCore+MetaDrug version 6.23 build 67496). Bladder cancer (BC) cell lines were used to investigate the previously described role of miR-21 mediating cisplatin sensitivity. Results: The 83 patients had a median PFS of 8 months. In multivariate analysis, higher levels of E2F1 (P=0.01, HR: 1.95 (1.14, 3.33)), miR-21 (P=0.01, HR: 2.01 (1.17, 3.45)) and miR-372 (P=0.05, HR: 1.70 (1.00, 2.89)) were associated with a shorter PFS. In the 8 BC cell lines, miR-21 was not shown to be necessary nor sufficient for modulating cisplatin sensitivity. Conclusions: In metastatic UC patients treated with cisplatin-based therapy, high primary tumour levels of E2F1, miR-21 and miR-372 are associated with poor PFS independent of clinical prognostic factors. The in vitro study could not confirm miR-21 levels role in modulating platinum sensitivity.

Background: Single-agent taxanes are commonly used as salvage systemic therapy for patients with advanced urothelial carcinoma (UC). Objective: To study the impact of combination chemotherapy delivering a taxane plus other chemotherapeutic agents compared with single-agent taxane as salvage therapy. Design, setting, and participants: Individual patient-level data from phase 2 trials of salvage systemic therapy were used. Interventions: Trials evaluating either single agents (paclitaxel or docetaxel) or combination chemotherapy (taxane plus one other chemotherapeutic agent or more) following prior platinum-based therapy were used. Outcome measurements and statistical analysis: Information regarding the known major baseline prognostic factors was required: time from prior chemotherapy, hemoglobin, performance status, albumin, and liver metastasis status. Cox proportional hazards regression was used to evaluate the association of prognostic factors and combination versus single-agent chemotherapy with overall survival (OS). Results and limitations: Data were available from eight trials including 370 patients; two trials (n = 109) evaluated single-agent chemotherapy with docetaxel (n = 72) and cremophor-free paclitaxel (n = 37), and six trials (n = 261) evaluated combination chemotherapy with gemcitabine-paclitaxel (two trials, with n = 99 and n = 24), paclitaxel-cyclophosphamide (n = 32), paclitaxel-ifosfamide-nedaplatin (n = 45), docetaxelifosfamide-cisplatin (n = 26), and paclitaxel-epirubicin (n = 35). On multivariable analysis after adjustment for baseline prognostic factors, combination chemotherapy was independently and significantly associated with improved OS (hazard ratio: 0.60; 95% confidence interval, 0.45-0.82; p = 0.001). The retrospective design of this analysis and the trial-eligible population were inherent limitations. Conclusions: Patients enrolled in trials of combination chemotherapy exhibited improved OS compared with patients enrolled in trials of single-agent chemotherapy as salvage therapy for advanced UC. Prospective randomized trials are required to validate a potential role for rational and tolerable combination chemotherapeutic regimens for the salvage therapy of advanced UC. Patient summary: This retrospective study suggests that a combination of chemotherapy agents may extend survival compared with single-agent chemotherapy in selected patients with metastatic urothelial cancer progressing after prior chemotherapy. (C) 2015 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Purpose Platinum-based chemotherapy remains the standard treatment for advanced urothelial carcinoma by inducing DNA damage. We hypothesize that somatic alterations in DNA damage response and repair (DDR) genes are associated with improved sensitivity to platinum-based chemotherapy. Experimental design Patients with diagnosis of locally advanced and metastatic urothelial carcinoma treated with platinum-based chemotherapy who had exon sequencing with the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay were identified. Patients were dichotomized based on the presence/absence of alterations in a panel of 34 DDR genes. DDR alteration status was correlated with clinical outcomes and disease features. Results One hundred patients were identified, of which 47 harbored alterations in DDR genes. Patients with DDR alterations had improved progression-free survival (9.3 vs. 6.0 months, log-rank P = 0.007) and overall survival (23.7 vs. 13.0 months, log-rank P = 0.006). DDR alterations were also associated with higher number mutations and copy-number alterations. A trend toward positive correlation between DDR status and nodal metastases and inverse correlation with visceral metastases were observed. Different DDR pathways also suggested variable effect on clinical outcomes. Conclusions Somatic DDR alteration is associated with improved clinical outcomes in platinum-treated patients with advanced urothelial carcinoma. Once validated, it can improve patient selection for clinical practice and future study enrollment.

We evaluated primary tumors from two cohorts, Spain (N = 111) and Greece (N = 102), for patients who were treated with platinum-based chemotherapy. Patients were tested for HER2 status (IHC score of 3+ or FISH ratio of ≥2.2) by immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), DNA copy number, mRNA expression, and mutation status in patients with metastatic urothelial carcinoma (UC), and its impact on survival. ERBB2 mutation was determined by hotspot sequencing. mRNA expression was assessed using NanoString counting. Association of overall survival (OS) and HER2 status was assessed by a Cox regression model. NIH-3T3 cells containing HER2 V777L were assessed for growth, invasion, and HER2 kinase activation. In all, 22% of Spanish and 4% of Greek cohorts had 3+ HER2 staining by IHC. FISH amplification was identified in 20% of Spanish and 4% of Greek cohorts. Kappa coefficient between FISH and IHC was 0.47. HER2 status was not associated with OS in univariate (Spanish P = 0.34; Greek P = 0.11) or multivariate (Spanish P = 0.49; Greek P = 0.12) analysis. HER2-positive tumors expressed higher levels of HER2 mRNA than HER2-negative tumors (P < 0.001). HER2 mutations (V777L and L755S) were identified in two (2%) patients. In vitro analysis of V777L results in transformation of NIH-3T3 cells, leading to increased growth, invasion on soft agar, and HER2 kinase constitutive activation. In summary, HER2 overexpression or amplification in the primary tumor did not predict OS in patients with metastatic UC. HER2 positivity rates can differ between different populations. Further trials in genomically screened patients are needed to assess HER2-targeted therapies in UC This work has been supported by PI061513 (Spanish Health Ministry Grant “Fondo de/nInvestigacion Sanitaria”) and RTICC 06/0020/19 grants.

African-American men have the highest incidence of and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n = 102) and targeted validation (n = 90) of localized primary hormone-naïve prostate cancer in African-American men identified several gene mutations not previously observed in this context, including recurrent loss-of-function mutations in ERF, an ETS transcriptional repressor, in 5% of cases. Analysis of existing prostate cancer cohorts revealed ERF deletions in 3% of primary prostate cancers and mutations or deletions in ERF in 3% to 5% of lethal castration-resistant prostate cancers. Knockdown of ERF confers increased anchorage-independent growth and generates a gene expression signature associated with oncogenic ETS activation and androgen signaling. Together, these results suggest that ERF is a prostate cancer tumor-suppressor gene. More generally, our findings support the application of systematic cancer genomic characterization in settings of broader ancestral diversity to enhance discovery and, eventually, therapeutic applications. Significance: Systematic genomic sequencing of prostate cancer in African-American men revealed new insights into prostate cancer, including the identification of ERF as a prostate cancer gene; somatic copy-number alteration differences; and uncommon PIK3CA and PTEN alterations. This study highlights the importance of inclusion of underrepresented minorities in cancer sequencing studies. Cancer Discov; 7(9); 973–83. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 920

Objective To study the subsequent therapy and disease outcomes of patients with advanced urothelial carcinoma (UC) after discontinuation of programmed death-1 (PD-1) or programmed death ligand 1 (PD-L1) inhibitors. Patients and Methods We performed a retrospective analysis to examine outcomes and systemic therapy administration after PD-1/PD-L1 inhibitor therapy in patients with advanced UC. Data on demographics and therapy administered were collected from the institutions involved in the study. Univariable Cox regression analyses were performed to examine the clinical factors potentially associated with overall survival (OS) after PD-1/PD-L1 inhibitor therapy. Results Data from 62 patients were available from four institutions, with capture of subsequent therapy and outcomes after checkpoint inhibitor immunotherapy. The median patient age was 65.5 years and 51 patients (82.3%) were male. The median (range) duration of PD-1/PD-L1 inhibitor therapy in 55 patients for whom these data were available was 64 (7–669) days. Of these, 22 patients (35.5%) received post-PD-1/PD-L1 inhibitor therapy through a variety of different chemotherapy regimens (n = 16), chemobiological combination (n = 1), biological agents (n = 4) and immunotherapy (n = 1). The median (range) time from last PD-1/PD-L1 inhibitor therapy to subsequent therapy was 58 (14–242) days. The median OS of all patients after completion of PD-1/PD-L1 inhibitor therapy was 149 days (95% confidence interval [CI]: 75–359). Among those who received some post-PD-1/PD-L1 inhibitor therapy, the median OS was 182 days (95% CI: 121–372), and the median time to progression was 124 days (95% CI: 61–273) from the start of post-PD-1/PD-L1 therapy. Among these 22 patients, the only significant baseline prognostic factor associated with OS was performance status. Conclusions In this dataset, 35.5% of patients with advanced UC received systemic therapy after salvage therapy with PD-1/PD-L1 inhibitors. Outcomes after subsequent therapy appear similar to those historically observed in patients who had not received prior PD-1/PD-L1 inhibitor therapy. Further study of patients receiving post-PD-1/PD-L1 inhibitor therapy is warranted to identify factors associated with outcomes and potentially synergistic sequences.

African-American men have the highest incidence and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n=102) and targeted validation (n = 90) of localized primary hormone-naïve prostate cancer in African-American men identified several gene mutations not previously observed in this context, including recurrent loss-of-function mutations in ERF, an ETS transcriptional repressor, in 5% of cases. Analysis of existing prostate cancer cohorts revealed ERF deletions in 3% of primary prostate cancers and mutations or deletions in ERF in 3–5% of lethal castration-resistant prostate cancers. Knockdown of ERF confers increased anchorage-independent growth and generates a gene expression signature associated with oncogenic ETS activation and androgen signaling. Together, these results suggest that ERF is a prostate cancer tumor suppressor gene. More generally, our findings support the application of systematic cancer genomic characterization in settings of broader ancestral diversity to enhance discovery and, eventually, therapeutic applications.

Metastatic urothelial carcinoma (mUC) has a very high mutational rate and is associated with an APOBEC mutation signature. We examined the correlation of APOBEC expression with overall survival (OS) and PD-L1 expression in a cohort of 73 mUC patients. mRNA expression of APOBEC3 family of genes (A3A, A3B, A3C, A3F_a, A3F_b, A3G, A3H) was measured using Nanostring. PD-L1 expression, evaluated by immunohistochemistry, on tumor infiltrating mononuclear cells (TIMCs) and tumor cells was scored from 0 to 4, with 2-4 being positive. Wilcoxon's non-parametric tests assessed the association of APOBEC and PD-L1. The Cox regression model assessed the association of APOBEC with OS. All APOBEC genes were expressed in mUC. Increased A3A, A3D, and A3H expression associates with PD-L1 positive TIMCs (p = 0.0009, 0.009, 0.06). Decreased A3B expression was marginally associated with PD-L1 positive TIMCs expression (p = 0.05). Increased A3F_a and A3F_b expression was associated with increased expression of PD-L1 on tumor cells (p = 0.05). Increased expression of A3D and A3H was associated with longer OS (p = 0.0009). Specific APOBEC genes have different effects on mUC in terms of survival and PD-L1 expression. A3D and A3H may have the most important role in mUC as they are associated with OS and PD-L1 TIMC expression. This work has been supported by FIS PI10/02112 (microRNAS) (Spanish Health Ministry Grant “Fondo de Investigacion Sanitaria”) and RTICC 06/0020/19 grants. Fundació Cellex (Barcelona) provided a generous donation to the Group of Molecular Therapeutics and Biomarkers, Hospital del Mar. The Tumor Bank of the Department of Pathology of Hospital del Mar (RD09/0076/0036) and the Xarxa de Bancs de Tumors sponsored by Pla Director d’Oncologia de Catalunya (XBTC) provided tissue samples. This study was also possible thanks to a grant from Friends of Dana-Farber, the Retired Professional Fire Fighters Cancer Fund, and the generous support of Whole Foods Golf Classic for bladder cancer research in memoriam of Christopher Snell. Also a private donation in the memory of Rich Beaudoin. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscrip

Precision cancer medicine, the use of genomic profiling of patient tumors at the point-of-care to inform treatment decisions, is rapidly changing treatment strategies across cancer types. Precision medicine for advanced prostate cancer may identify new treatment strategies and change clinical practice. In this review, we discuss the potential and challenges of precision medicine in advanced prostate cancer.Although primary prostate cancers do not harbor highly recurrent targetable genomic alterations, recent reports on the genomics of metastatic castration-resistant prostate cancer has shown multiple targetable alterations in castration-resistant prostate cancer metastatic biopsies. Therapeutic implications include targeting prevalent DNA repair pathway alterations with PARP-1 inhibition in genomically defined subsets of patients, among other genomically stratified targets. In addition, multiple recent efforts have demonstrated the promise of liquid tumor profiling (e.g., profiling circulating tumor cells or cell-free tumor DNA) and highlighted the necessary steps to scale these approaches in prostate cancer.Although still in the initial phase of precision medicine for prostate cancer, there is extraordinary potential for clinical impact. Efforts to overcome current scientific and clinical barriers will enable widespread use of precision medicine approaches for advanced prostate cancer patients.

Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation.

Prior platinum-versus non-platinum-based chemotherapy did not affect survival after controlling for major prognostic factors in patients receiving salvage systemic chemotherapy for advanced urothelial carcinoma. Exposure to prior platinum therapy should not be required for the inclusion of patients in trials of salvage systemic therapy. Background: Trials of salvage therapy for advanced urothelial carcinoma have required prior platinum-based therapy. This practice requires scrutiny because non-platinum-based first-line therapy may be offered to cisplatin-ineligible patients. Patients and Methods: Data of patients receiving salvage systemic chemotherapy were collected. Data on prior first-line platinum exposure were required in addition to treatment-free interval, hemoglobin, Eastern Cooperative Oncology Group performance status, albumin, and liver metastasis status. Cox proportional hazard regression was used to evaluate their association with overall survival (OS) after accounting for salvage single-agent or combination chemotherapy. Results: Data were obtained from 455 patients previously exposed to platinum-based therapy and 37 not exposed to platinum. In the group exposed to prior platinum therapy, salvage therapy consisted of a single agent taxane (n = 184) or a taxane-containing combination chemotherapy (n = 271). In the group not exposed to prior platinum therapy, salvage therapy consisted of taxane or vinflunine (n = 20), 5-fluorouracil (n = 1), taxane-containing combination chemotherapy (n = 12), carboplatin-based combinations (n = 2), and cisplatin-based combinations (n = 2). The median OS for the prior platinum therapy group was 7.8 months (95% confidence interval, 7.0, 8.1), and for the group that had not received prior platinum therapy was 9.0 months (95% confidence interval, 6.0, 11.0; P = .50). In the multivariable analysis, prior platinum therapy versus no prior platinum exposure did not confer an independent impact on OS (hazard ratio, 1.10; 95% confidence interval, 0.75, 1.64; P = .62). Conclusion: Prior platinum-versus non-platinum-based chemotherapy did not have a prognostic impact on OS after accounting for major prognostic factors in patients receiving salvage systemic chemotherapy for advanced urothelial carcinoma. Lack of prior platinum therapy should not disqualify patients from inclusion onto trials of salvage therapy. (C) 2016 Elsevier Inc. All rights reserved.

Background Combination platinum chemotherapy is standard first-line therapy for metastatic urothelial carcinoma (mUC). Defining the platinum response biomarkers for patients with mUC could establish personalize medicine and provide insights into mUC biology. Although DNA repair mechanisms have been hypothesized to mediate the platinum response, we sought to analyze whether increased expression of DNA damage genes would correlate with worse overall survival (OS) in patients with mUC. Patients and Methods We retrospectively identified a clinically annotated cohort of patients with mUC, who had been treated with first-line platinum combination chemotherapy. A tissue microarray was constructed from formalin-fixed paraffin-embedded tissue from the primary tumor before treatment. Immunohistochemical analysis of the following DNA repair proteins was performed: ERCC1, RAD51, BRCA1/2, PAR, and PARP-1. Nuclear and cytoplasmic expression was analyzed using multispectral imaging. Nuclear staining was used for the survival analysis. Cox regression analysis was used to evaluate the associations between the percentage of positive nuclear staining and OS in multivariable analysis, controlling for known prognostic variables. Results In a cohort of 104 patients with mUC, a greater percentage of nuclear staining of ERCC1 (hazard ratio [HR], 2.7; 95% confidence interval [CI], 1.5-4.9; P = .0007), RAD51 (HR, 5.6; 95% CI, 1.7-18.3; P = .005), and PAR (HR, 2.2; 95% CI, 1.1-4.4; P = .026) was associated with worse OS. BRCA1, BRCA2, and PARP-1 expression was not associated with OS (P = .76, P = .38, and P = .09, respectively). A greater percentage of combined ERCC1 and RAD51 nuclear staining was strongly associated with worse OS (P = .005). Conclusion A high percentage of nuclear staining of ERCC1, RAD51, and PAR, assessed by immunohistochemistry, correlated with worse OS for patients with mUC treated with first-line platinum combination chemotherapy, supporting the evidence of the DNA repair pathways' role in the prognosis of mUC. We also report new evidence that RAD51 and PAR might play a role in the platinum response. Additional prospective studies are required to determine the prognostic or predictive nature of these biomarkers in mUC.

Submitted by Biblioteca Suporte PUCRS (biblioteca.suporte@pucrs.br) on 2022-05-17T19:50:50Z No. of bitstreams: 2 Perioperative_Therapy_for_Muscle_Invasive_Bladder_Cancer.pdf: 264154 bytes, checksum: 441b261daf88efa6e824cda47225dfa2 (MD5) Perioperative_Therapy_for_Muscle_Invasive_Bladder_Cancer.pdf: 264154 bytes, checksum: 441b261daf88efa6e824cda47225dfa2 (MD5) Made available in DSpace on 2022-05-17T19:50:50Z (GMT). No. of bitstreams: 2 Perioperative_Therapy_for_Muscle_Invasive_Bladder_Cancer.pdf: 264154 bytes, checksum: 441b261daf88efa6e824cda47225dfa2 (MD5) Perioperative_Therapy_for_Muscle_Invasive_Bladder_Cancer.pdf: 264154 bytes, checksum: 441b261daf88efa6e824cda47225dfa2 (MD5) Previous issue date: 2015

279 Background: While there has been substantial advancement in the genomic understanding of metastatic prostate cancer (MPC), there is still much to be discovered. Additional progress is dependent upon obtaining a large amount of clinically-annotated genomic data. Therefore, we piloted a direct-to-patient nationwide research initiative where patients can contribute their medical records and biospecimens to accelerate research ( mpcproject.org ). Methods: In collaboration with patients and advocacy groups, we have developed a website ( mpcproject.org ). Participants are asked to complete a 17-question survey about their experiences with prostate cancer and an electronic informed consent. All participants receive a saliva kit for germline DNA and blood kit for circulating tumor DNA (ctDNA). Additionally, medical records are collected and archived tissue samples are requested if available. Ultra low pass whole genome sequencing (ULP-WGS) and whole exome sequencing (WES) are performed on the whole blood samples. WES is performed on saliva samples. Genomic, clinical, and patient-reported data will be shared widely with the research community. Aggregate study results will be reported to patients. Results: As of October 2017, 12 pilot patients aged 47-74 from 7 states, provided informed consent. 7 saliva kits, 4 blood kits, and 2 medical records were received. 4 patients were diagnosed with de novo metastatic disease, 8 reported a family history of breast and/or prostate cancer, 6 reported a secondary malignancy. All blood kits were submitted for ULP-WGS and WES. Updated genomic, clinical, and patient-reported data will be presented. Conclusions: We have provided preliminary evidence that partnering directly with MPC patients enabled the remote collection of saliva and blood samples, medical records, and patient-reported data. At the conclusion of the pilot phase, the MPC Project will open enrollment for all men with metastatic and advanced prostate cancer in the US and Canada.

Background An integrative analysis was conducted to identify genomic alterations at a pathway level that could predict overall survival (OS) in patients with advanced urothelial carcinoma (UC) treated with platinum-based chemotherapy. Patients and Methods DNA and RNA were extracted from 103 formalin-fixed paraffin embedded (FFPE) invasive high-grade UC samples and were screened for mutations, copy number variation (CNV) and gene expression analysis. Clinical data were available from 85 cases. Mutations were analyzed by mass-spectrometry based on genotyping platform (Oncomap 3) and genomic imbalances were detected by comparative genomic hybridization (CGH) analysis. Regions with threshold of log2 ratio ≥0.4, or ≤0.6 were defined as either having copy number gain or loss and significantly recurrent CNV across the set of samples were determined using a GISTIC analysis. Expression analysis on selected relevant UC genes was conducted using Nanostring. To define the co-occurrence pattern of mutations and CNV, we grouped genomic events into 5 core signal transduction pathways: 1) TP53 pathway, 2) RTK/RAS/RAF pathway, 3) PI3K/AKT/mTOR pathway, 4) WNT/CTNNB1, 5) RB1 pathway. Cox regression was used to assess pathways abnormalities with survival outcomes. Results 35 samples (41%) harbored mutations on at least one gene: TP53 (16%), PIK3CA (9%), FGFR3 (2%), HRAS/KRAS (5%), and CTNNB1 (1%). 66% of patients had some sort of CNV. PIK3CA/AKT/mTOR pathway alteration (mutations+CNV) had the greatest impact on OS (p=0.055). At a gene level, overexpression of CTNNB1 (p=0.0008) and PIK3CA (p=0.02) were associated with shorter OS. Mutational status on PIK3CA was not associated with survival. Among other individually found genomic alterations, TP53 mutations (p=0.07), mTOR gain (p=0.07) and PTEN overexpression (p=0.08) have a marginally significant negative impact on OS. Conclusions Our study suggests that targeted therapies focusing on the PIK3CA/AKT/mTOR pathway genomic alterations can generate the greatest impact in the overall patient population of high-grade advanced UC.

Background: The mutational landscapes of primary and metastatic prostate cancer (PCa) have been robustly analyzed in multiple whole exome sequencing (WES) studies. We hypothesized that an aggregate, uniform analysis of all data generated to date would enable discovery of new significantly mutated genes and pathways not previously associated with PCa, and shed more light onto the genetic differences between primary and metastatic PCa. Methods: We uniformly analyzed WES data of 1,021 tumor and matched germline primary and metastatic PCa (686 primary, 335 metastatic). We performed mutational significance analysis using statistical and biological approaches to determine recurrently altered genes and pathways. Results: We identified 117 significantly mutated genes (Mutsig q Our analysis also uncovered mutations in CUL3 (1.3%) and KLHL20, components of an E3-ubiquitin ligase complex that interacts with SPOP to promote the degradation of critical PCa genes (AR, SRC). KLHL20, CUL3, and SPOP mutations are mutually exclusive. Finally, a comparison of primary and metastatic samples identified alterations that are associated with metastatic disease, including AR amplifications and mutations, and loss of TP53, PTEN, and RB1. At lower frequency, metastatic tumors showed enrichment in mutations in MLLs (KMT2C/D), APC, CDK12, BRCA2, CTNNB1, and amplifications of MYC and CCND1. Conclusions: Through aggregation and uniform genomic analysis, we refined the map of somatic mutations in PCa and identified cancer genes and pathways not previously associated with this disease. Our findings may inform patient stratification and translational investigation. Citation Format: Joshua Armenia, Stephanie Mullane, Jianjiong Gao, Debyani Chakravarty, Ritika Kundra, Franklin Huang, Celine Han, Dan Robinson, Levi A. Garraway,, Peter Nelson, Mark Rubin, Mary-Ellen Taplin, Wassim Abida, Charles L. Sawyers, Arul M. Chinnaiyan, Philip W. Kantoff, Johann S. Bono, Nikolaus Schultz, Eliezer M. Van Allen. The long tail of significantly mutated genes in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3566. doi:10.1158/1538-7445.AM2017-3566

Background: Development of immune checkpoint inhibitors has substantially improved outcomes in patients diagnosed with metastatic melanoma. However, only a minority of patients treated experience long-term clinical benefit, and clinicians have limited ability to predict which patients will respond. Recent studies have demonstrated that the burden of tumor neoantigens generated by expressed somatic mutations is predictive of response to immunotherapy. Intron retention, which is widespread in cancer transcriptomes, represents a putative source of tumor neoantigens by generating peptides that are available for presentation through the MHC I pathway. Methods: We developed a neoantigen prediction pipeline to identify patient-specific neoantigens from transcriptome sequencing data, which enables identification of retained intron neoantigens from clinical cohorts receiving checkpoint inhibitor therapy. This pipeline incorporates published methods for detecting intron retention events from transcriptome data, detects open reading frames that extend from normal transcripts into intronic sequences, and identifies neoepitopes predicted as strong binders based on the patient’s HLA molecules. We applied this pipeline to a cohort of 41 melanoma patients receiving checkpoint inhibitor therapy and classified patient outcomes as receiving clinical benefit (CB) (n=14), no clinical benefit (NCB) (n=22), or long-term survival without clinical benefit (LS) (n=5). Results: Our initial analysis identified a mean retained intron neoantigen burden of 7709 per sample, without significant difference between response groups. In one patient who derived clinical benefit from checkpoint inhibition, neoantigen load from nonsynonymous mutations was low (407, 0.34 standard deviations (SD) below a mean of 1,015 among CB patients), while retained intron neoantigen load was high (14579, 1.7 SDs above a mean of 7517 among CB patients), suggesting that retained intron neoantigen load may explain response in some patients with low mutational burden. Preliminary analysis of specific neoantigens suggests that a retained intron in ZNF880 identified in patients expressing HLA-A01:01 is present in 6 of 6 patients experiencing clinical benefit, but only 2 of 7 patients not experiencing clinical benefit. The same analysis was performed on two additional cohorts of melanoma tumor samples to assess whether a larger sample size could aid in the identification of recurrent neoepitopes generated by retained introns. Conclusions: Application of this approach to data from patients receiving checkpoint blockade with selective response identifies response-associated neoantigens that may warrant further investigation. Identification of a novel source of neoantigens associated with immunotherapy response will provide valuable prognostic information to patients and inform the development of next generation immunotherapeutics. Citation Format: Alicia C. Smart, Claire Margolis, Diana Miao, David Liu, Jihye Park, Meng Xiao He, Brendan Reardon, Stephanie Mullane, Bastian Schilling, Levi A. Garraway, Dirk Schadendorf, Eliezer M. Van Allen. Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5647. doi:10.1158/1538-7445.AM2017-5647

Background Recent “next generation” androgen deprivation therapies (ADT), such as abiraterone and enzalutamide, have improved survival in patients with castrate-resistant prostate cancer (CRPC). Despite therapy, most patients develop resistance to these agents. We investigated the genetic basis of tumor evolution and clinical resistance to next generation ADT in CRPC by using whole exome sequencing (WES) on paired pretreatment and post-resistance biopsies from CRPC patients. Methods Matched “trios” of germline, pre-treatment and post-resistant tumor samples were obtained from 7 patients treated with abiraterone (n=4) and enzalutamide (n=3) and WES was performed. Clinical data, including PSA and radiographic measurements, was used to classify patients as intrinsically resistant or initially responsive to treatment. Quality control, mutation and indel calling, copy number variation identification were performed using analytical pipelines at the Broad Institute. Tumor purity and ploidy were inferred, and phylogenetic analysis was performed using ABSOLUTE and Phylogic, respectively to identify resistance associated alterations in the context of clinical phenotypes. Results We identified multiple putative mechanisms and genetic categories of resistance to next generation ADT in CRPC. One abiraterone patient acquired an AR mutation (L702H) in the post-treatment sample, previously reported to be associated with poor outcomes and to confer resistance to this therapy. Amplification of MYC was associated with resistance in two other abiraterone patients with pre-existing AR gain: one patient with initial response to therapy acquired a focal gain of MYC in the resistant sample, and the other harbored a pre-existing MYC amplification, but had no response to therapy. In three enzalutamide patients, all acquired alterations in cell cycle genes (CDKN2A mutation, focal amplifications in regions spanning CDK4/6, and CCND3 focal amplification) at the time of resistance that were absent in pre-treatment tumors. In parallel, we confirm CDK4/6 overexpression was sufficient to promote enzalutamide resistance in prostate cancer cell models. Additional candidate genomic events associated with CRPC were also implicated with this approach, such as RSPO3 amplification. Conclusion This study outlines an approach to identify clinical genetic resistance mechanisms of next generation ADT in CRPC through integration of genomic data from serial biopsies, clinical patient outcomes, and preclinical functional screening. These findings confirm previously known potential resistance mechanisms, such as AR and MYC activation, and suggest putative mechanisms linked to therapeutic agents, which may inform novel targets for treating CRPC patients. Citation Format: G. Celine Han, Justin Hwang, Stephanie A. Mullane, Carrie Cibulskis, Zhenwei Zhang, Rana R. McKay, PCF-SU2C Dream Team, Scott L. Carter, William C. Hahn, Mary-Ellen Taplin, Eliezer M. Van Allen. Clinical and genomic resistance to second generation androgen blockade in paired biopsies of metastatic castration-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2905. doi:10.1158/1538-7445.AM2017-2905

3016 Background: Immune checkpoint inhibitors targeting programmed cell death-1 (PD-1) substantially improve patient survival in clear-cell renal cell carcinoma (ccRCC), but predictive biomarkers for efficacy have not yet been identified. Methods: We analyzed whole exome sequencing (WES) from a clinical trial of anti-PD-1 monotherapy (nivolumab) for ccRCC (N = 34) to discover genomic predictors of response to immune checkpoint therapy, and validated our findings in 28 ccRCC patients from 2 institutions treated with anti-PD-1 or anti-PD-L1 therapies. We defined 3 response groups: clinical benefit (CB) – complete or partial response by RECIST or stable disease with objective decrease in tumor burden and progression free survival (PFS) > 6 months - and no clinical benefit (NCB) – progressive disease with PFS < 3 months, with all other patients in intermediate benefit (IB). We further validated our findings in WES from 212 melanoma patients treated with immune checkpoint therapies in 3 published cohorts. Results: Biallelic loss of the chromatin remodeling subunit PBRM1, mutated in 34/62 (55%) patients across both cohorts and up to 41% of ccRCC overall, was the only gene mutation associated with CB in both the training (p = 0.0064; Pearson’s chi-squared) and validation cohorts (p = 0.043), and predicted both PFS and overall survival (OS) (p = 0.042 and 0.014, respectively; Kaplan-Meier). In 212 melanomas, truncating alterations in ARID2 – a closely related chromatin remodeler - were also enriched in responders after correcting for tumor mutational burden (p = 0.036), and having a truncating alteration in either PBRM1 or ARID2 significantly predicted overall survival (p = 0.022). In this ccRCC cohort, tumor mutational burden and loss of antigen presentation machinery were not associated with CB or NCB. Conclusions: Loss of chromatin remodeling subunits may impact response to immune checkpoint therapy in both ccRCC and melanoma. Further study in larger cohorts of immunotherapy-treated patients and functional characterization of ARID2 and PBRM1 in the context of the tumor-immune microenvironment will help to determine potential for further biomarker development.

4512 Background: Biomarkers of survival and resistance in chemotherapy-resistant muscle-invasive bladder cancer (MIBC) are not well-characterized, but may inform management in this setting. Methods: Matched pre- and post-neoadjuvant cisplatin-based chemotherapy (NAC) tumor samples were obtained from 30 MIBC patients with gross residual disease (≥ pT2) at cystectomy, followed by whole exome sequencing of these “trios” (pre- and post-NAC tumor with matched germline samples). Phylogenetic analysis of matched tumor samples was performed to identify subclones, their associated mutations, and the corresponding enrichment in post-treatment tumors. Intratumoral heterogeneity was assessed by the proportion of mutations that were subclonal; the number of inferred subclones; and associated with overall survival using a Cox Proportional Hazards model. Results: Increased proportion of subclonal mutations in post-treatment tumors was associated with worse overall survival (HRR 1.86 [95% CI 1.12-3.06], p = 0.02), whereas pre-treatment proportion of subclonal mutations was only borderline statistically significant (HRR 1.48 [95% CI 0.99-2.20], p = 0.052). The total number of inferred tumor subclones in pre- or post-treatment tumor (or both) was associated with overall survival (HRR 1.60 [95% CI 1.05-2.43], p = 0.03), interpreted as a 60% increase in death rate per additional inferred subclone. While no single gene was statistically significantly enriched for new alterations in the post-chemotherapy resistant samples, we observed new post-treatment amplifications in cell-cycle genes ( E2F3, c-JUN), biallelic events in cell-cycle regulators ( FBXW7), and amplification of immune checkpoint genes ( PDL1/2). Conclusions: These results suggest that intratumoral heterogeneity (particularly post-therapy) predicts survival in a chemotherapy-resistant cohort. Further, alterations in cell cycle regulation may contribute to the mechanism of chemotherapy resistance. Finally, we observe evidence of immune checkpoint gene amplification post-treatment, suggesting that testing immune checkpoint blockade during NAC or, in high risk patients, following NAC may be warranted.

In this retrospective study, docetaxel treatment after previous paclitaxel treatment and the reverse sequence demonstrated outcomes and activity similar to salvage therapy for advanced urothelial carcinoma (UC). The clinical implications are that trials using a taxane can probably allow previous exposure to a different taxane, and patients treated off protocol may receive a taxane after previous exposure to a different taxane. Background: Taxanes such as paclitaxel and docetaxel are commonly used for second-or third-line salvage systemic therapy for metastatic UC. Although trials have generally excluded previous exposure to taxanes when using a taxane in a salvage therapy trial, taxanes might not be completely cross-resistant. Hence, we aimed to study outcomes with docetaxel after previous paclitaxel and the reverse sequence, to identify the level of cross-resistance between these taxanes. Patients and Methods: Data from a randomized phase II trial that compared salvage therapy with docetaxel combined with either placebo or vandetanib for advanced UC were analyzed. Both arms were combined for analysis because no differences in any outcomes were observed. Data were also requested from institutions for patients who received paclitaxel after previous docetaxel treatment. Descriptive statistics were used to summarize patient and treatment characteristics and outcomes. The primary clinical end point of interest was overall survival (OS). Results: Of 148 patients who received docetaxel with either vandetanib or placebo, 21 had received previous paclitaxel treatment. No difference in OS, progression-free survival, or response rate was observed with docetaxel based on previous paclitaxel treatment after adjusting for known prognostic factors. Among the 8 patients who received paclitaxel after previous docetaxel treatment, partial response was observed in 1 patient (12.5%) and stable disease in 2 patients (25%). Conclusion: Docetaxel treatment after previous paclitaxel treatment and the reverse sequence demonstrates activity in advanced UC. There is no strong evidence to disallow patients with previous exposure to a taxane to enroll in a clinical trial involving another taxane. (C) 2015 Elsevier Inc. All rights reserved.

Background: Management of high-grade T1 (HGT1) bladder cancer represents a major challenge. We studied a treatment strategy according to substaging by depth of lamina propria invasion. Methods: In this prospective observational cohort study, patients received initial transurethral resection (TUR), mitomycin-C, and BCG. Subjects with shallower lamina propria invasion (HGT1a) were followed without further surgery, whereas subjects with HGT1b received a second TUR. Association of clinical and histological features with outcomes (primary: progression; secondary: recurrence and cancer-specific survival) was assessed using Cox regression. Results: Median age was 71 years; 89.5% were males, with 89 (44.5%) cases T1a and 111 (55.5%) T1b. At median follow-up of 71 months, disease progression was observed in 31 (15.5%) and in univariate analysis, substaging, carcinoma in situ, tumour size, and tumour pattern predicted progression. On multivariate analysis only substaging, associated carcinoma in situ, and tumour size remained significant for progression. Conclusions: In HGT1 bladder cancer, the strategy of performing a second TUR only in T1b cases results in a global low progression rate of 15.5%. Tumours deeply invading the lamina propria (HGT1b) showed a three-fold increase in risk of progression. Substaging should be routinely evaluated, with HGT1b cases being thoroughly evaluated for cystectomy. Inclusion in the TNM system should also be carefully considered.

Blockade of the PD1/PD-L1 T cell immune checkpoint yields responses and survival benefits exceeding mTOR blockade alone in metastatic renal cell carcinoma (mRCC). However, predictors of response to anti-PD1/PD-L1 therapy are mostly unknown, and pathways of acquired resistance to immune checkpoint therapy are poorly understood. In this study, we undertook whole exome sequencing and neoantigen analysis of matched “trios” (primary tumor resection, immune-checkpoint-refractory metastasis, and germline tissue) from 3 patients treated with anti-PD1 or anti-PD-L1 therapy for mRCC. Patients RCC-001 and RC-002 received anti-PD1 therapy after VEGF-targeted therapy and patient RCC-003 received anti-PD-L1 first-line for mRCC. All 3 patients experienced tumor regression on immune checkpoint therapy, with treatment durations of 10 months, 2 years, and 3 months, respectively. Progressive disease samples were sequenced for analysis of genomic mechanisms of treatment resistance. Whole transcriptome sequencing was obtained on primary and metastatic tumors from RCC-003. Nonsynonymous mutation load was moderate in all samples (range: 33-46 primary, 36-67 resistant). Alterations in VHL were seen in RCC-001 and RCC-002 before and after treatment. RCC-003 had a frameshift deletion in the tumor suppressor NF2 and a nonsense mutation in the MHCI antigen-processing protein TAP1 in both primary and refractory tumors. Resistance-associated mutations in RCC-002 included a frameshift deletion in MR1, involved in MHC I antigen presentation, and missense mutations in TJP1, implicated in JAK/STAT signaling, and PIAS2, implicated in STAT2 and PTEN regulation. JAK2 amplifications have been found to upregulate PD-L1 expression (Green et al. 2010, Blood), and PTEN loss mediates resistance to T cell-mediated immmunotherapy in vitro (Peng et al. 2016, Cancer Discovery). None of the primary tumors harbored alterations in microsatellite-instability-associated genes, and loss of β2 microglobulin was not observed in any sample. Despite moderate mutational loads, each sample harbored a sizeable number of neoantigens (range: 24-76 primary, 50-104 resistant). Across the 6 samples, 28 to 69% of nonsynonymous mutations were predicted to yield at least one neoantigen, with one alteration yielding a maximum of 12 unique neoantigens. Up to 60% of neoantigens observed in the primary tumor were not seen in the resistant setting (range: 20.8-59.2%). Whole transcriptome sequencing in RCC-003 showed 18/24 predicted neoantigens were expressed in the primary tumor and 24/50 in the refractory sample. 13 neoantigens were shared between the two samples, while 5 were unique to the pre-treatment tumor. Integrated whole exome and whole transcriptome sequencing with matched germline profiling identified 5 neoantigens in RCC-003 that were found exclusively in the primary tumor (lost in the treatment-resistant tumor). This could represent immune evasion via deletion of immunogenic mutations, cytotoxic killing of immunogenic tumor clones, or intrinsic resistance to immune checkpoint therapy in heterogenous tumors. Ongoing in vitro analysis of reactivity of predicted neoantigens from all 3 samples with patient-derived T cells will further clarify the biological significance these putative tumor antigens. Citation Format: Diana Miao, Guillermo De Velasco, Dennis Adeegbe, Craig Norton, Dylan Martini, Stephanie Mullane, Raphael Moreira, Sabina Signoretti, Kwok-Kin Wong, Toni Choueiri, Eliezer Van Allen. Genomic and neoantigen evolution and resistance to immune checkpoint blockade in metastatic renal cell carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr A18.

346 Background: Early surrogate endpoints of benefit in mUC phase 2 salvage therapy trials are necessary to identify promising drugs, particularly for checkpoint inhibitors where response and progression-free survival are inadequate. We developed a nomogram using prognostic variables from phase 2 trials of historical agents to estimate 12 month survival to which observed survival in single arm trials could be compared. Methods: Data were obtained from phase II trials of salvage therapy for mUC for survival and 5 prognostic factors: hemoglobin, performance status, liver metastasis, treatment-free interval and albumin. Patients (pts) were randomly allotted to discovery:validation (DIS:VAL) datasets in a 2:1 ratio. A nomogram was developed for estimating 12-month survival. Calibration plots were constructed in the VAL dataset by plotting estimated vs. observed 12-mo survival and data bootstrapped to assess performance. The nomogram was applied to external nonrandomized salvage therapy data: 1) retrospective pemetrexed data or 2) trials of atezolizumab: PCD4989g and IMvigor210. Results: Data were available from 340 pts receiving sunitinib (n = 77), everolimus (n = 45), docetaxel + vandetanib or placebo (n = 109), pazopanib (n = 42), paclitaxel (n = 36) and docetaxel (n = 31). Calibration and prognostic ability of the model was acceptable (c-index = 0.634, 95% CI = 0.596-0.652). Observed 12-month survival for pts on pemetrexed (n = 127, 23.5% [95% CI: 16.2%-31.7%]) were similar to nomogram-predicted survival (19% [95% CI: 16.5-21.5], P> 0.05), while observed result with atezolizumab (n = 403, 39.0% [95% CI: 34.1-43.9]) exceeded predicted result (24.6% [95% CI: 23.4-25.8], P< 0.001). Conclusions: Atezolizumab was associated with a significantly longer 12-mo survival compared to nomogram-predicted survival while pemetrexed was not. This nomogram incorporates baseline prognostic factors to provide expected 12-mo survival of phase 2 patient cohorts with which to compare observed survival, thereby providing a useful tool to quantify benefit in phase II studies while controlling for the impact of clinical variables.

513 Background: Novel biomarkers are required to accurately assess response in renal cancer. Genomic alterations (GAs) in samples from primary (nephrectomy) (N) as compared distant metastases (M) in clear cell RCC (ccRCC) may have clinical implications as well as mutations in circulating tumour DNA (ctDNA). Methods: 237 primary ccRCC nephrectomy specimens and 156 samples from distant metastases were assayed by hybrid capture based comprehensive genomic profiling (CGP) in the course of clinical care to identify GAs suggesting benefit from targeted therapy. Tumor mutation burden (TMB) was assessed as the number of somatic coding point mutations per megabase of targeted territory. Aditionally, 17 patient-specific assays were developed to quantify ctDNA allele fraction (AF) in plasma of mRCC patients. Results: 1263 GAs and 34 clinically relevant GA (CRGAs) were identified. Most common GA identified were VHL (74%/72%), PBRM1 (40%/51%), SETD2 (28%/26%) in N and m respectively (Table). Additionally, most common CRGA identified were TP53 (8%/15%), PTEN (10%/10%), TSC1 (6%/6%), and TERT(5%/9%) in N and m respectively. No difference in TMB was seen between primary and metastatic samples. By site of metastases, soft tissue, and adrenal gland had the highest TMB and lymph node the lowest. In the 17 patients with available ctDNA, 15/17 (88.2%) have a maximum somatic AF < 1% (median 0.33% [0% - 22%]) suggesting generally low tumor content. Interestingly, ctDNA in 3 patients were successfully sequenced including a patient with an EML4-ALKfusion treated with alectinib. Conclusions: This data supports that both primary and metastatic RCC share the majority of common GA. Quantitation of ctDNA is a promising biomarker for response. [Table: see text]

353 Background: Currently, there are no FDA-approved blood biomarkers for the prognosis or prediction of outcomes in urothelial carcinoma (UC). The telomerase reverse transcriptase ( TERT) promoter is recurrently mutated at high frequency in UC (50%). These mutations have been correlated with tumor recurrence and survival. Tumor cell-free DNA (cfDNA) with somatic genomic alterations can be found in the plasma of cancer patients and has the potential for use as a non-invasive cancer biomarker. Detection of TERT promoter mutations in cfDNA might be used as a prognostic tool to monitor disease outcome in UC patients. We set out to detect tumor cfDNA and TERT promoter mutations in cfDNA from patients with UC at different stages. Methods: UC patients receiving chemotherapy in the neoadjuvant, first or second-line metastatic setting had blood collected either before or during therapy. cfDNA was isolated from ~1ml plasma samples using the QIAmp (Qiagen) kit. Samples underwent ultra-low pass whole genome sequencing (ULP-WGS) to determine whether tumor cfDNA could be detected in these samples. TERT promoter mutations were detected using a sensitive qPCR assay. Results: 40 plasma samples from a total of 32 patients with urothelial carcinoma were analyzed. Sufficient amounts of plasma cfDNA were obtained for library construction and ULP-WGS in 11 patients. 6 of these 11 patients were determined to be positive for detectable tumor cfDNA and of these, all were metastatic and 50% (3/6) were positive for a TERT promoter mutation. In total, 8 out of 40 samples (20%) were positive for a TERT promoter mutation, including samples from two patients where total cfDNA yield was insufficient for library construction. A total of ~20% of patients with metastatic disease were positive for TERT promoter mutations in cfDNA. The low percentage of samples having sufficient cfDNA most likely reflects the low volume of plasma used. Conclusions: TERT promoter mutations were identified in cfDNA of UC patients. ULP-WGS showed tumor cfDNA in patients with a high tumor burden and metastatic disease. TERTpromoter mutations in cfDNA could potentially be used as a non-invasive method for detection of disease. These results have implications for the use of cfDNA in the evaluation of advanced UC.

131 Background: The mutational landscapes of primary and metastatic PCa have been robustly analyzed in multiple whole exome sequencing (WES) studies. We hypothesized that an aggregate, uniform analysis of all data generated to date would enable discovery of new significantly mutated genes and pathways not previously associated with PCa, and shed more light onto the genetic differences between primary and metastatic PCa. Methods: We assembled and uniformly analyzed a cohort of 1,021 tumor and matched germline primary and metastatic PCa whole exomes (686 primary, 335 metastatic), and performed mutational significance analysis using statistical and biological approaches to determine which genes and pathways are recurrently altered. Results: We identified 117 significantly mutated genes (Mutsig q

199 Background: While there has been substantial advancement in the genomic understanding of prostate cancer (PCa), there is still much to be discovered. Additional progress is dependent upon obtaining a large amount of clinically annotated genomic data. As PCa is often treated in a community setting, where research samples are not collected, we are starting a direct-to-patient nationwide research initiative where patients can donate their medical records and biospecimens to accelerate research. Previously, we launched the metastatic breast cancer project (MBCproject; mbcproject.org) that leverages social media to engage the MBC community. Based on the initial success with this approach, we now aim to build out the PCproject. Methods: In collaboration with patients, we are developing a website to enable participation in the PCproject. Enrolled patients will be sent a saliva kit, used for germline DNA. We will also obtain medical records. Metastatic patients will also be sent a blood draw kit for circulating tumor DNA (ctDNA). Whole exome sequencing of the ctDNA will be performed. We will use the recruitment infrastructure, clinical record abstraction, and biospecimen processing developed for the MBC project. The data will be shared widely with the research community. Aggregate study results will be reported to patients. Results: In the first year of the MBCproject, 2912 MBC patients from all 50 states enrolled. 2766 (95.0%) completed the 16-question survey about their cancer, treatments, and demographic information. 1716 (58.9%) completed the online consent form permitting acquisition and analysis of medical records, tumor tissue, and saliva samples. 936 (68.8% success rate) saliva samples have been received. To date, we have obtained medical records from 155 patients (72.1% success rate) and tumor samples from 60 patients (72.3% success rate). Based on initial recruitment and surveys among PCa patients, we estimate that 500 patients will enroll in 2017. Conclusions: Based on experience from the MBC project, we will partner directly with patients to recruit and drive the PCproject forward. Remote acquisition of medical records, saliva samples, and tumor tissue for patients located throughout the US is feasible.

467 Background: Nivolumab, a monoclonal antibody against PD-1, has been shown to improve survival for pts with mRCC. The current standard of care is to administer treatment on a continuous basis until progression or toxicity. Outcomes of pts who experience a response to treatment and then discontinue therapy for irAEs have not been fully characterized. The purpose of this analysis was to evaluate outcomes of responders to PD-1/PD-L1 targeted therapy (TT) who discontinue treatment for irAEs. Methods: We identified pts with mRCC having experienced a response to PD-1/PD-L1 TT, which was subsequently discontinued for an irAE. Clinical characteristics, response, and survival data were collected. Results: We identified 9 mRCC pts who were treated with a PD-1/PD-L1 inhibitor, experienced a response to therapy, and subsequently discontinued treatment for an irAE. 8 had clear cell histology and 1 had translocation RCC. 7 pts were treatment naive. 2 pts had International mRCC Database Consortium favorable risk, 4 intermediate risk, and 3 poor risk disease. 44% (n = 4) of pts received PD-1/PD-L1 monotherapy and the overall median duration of therapy was 5 months (mos) (range 4-15). There was 1 complete response, 7 partial responses, and 1 stable disease (17% shrinkage). Treatment was discontinued for the following irAEs: arthritis, uveitis, arthropathy, hypophysitis, myositis, blepharitis, hepatitis, rash, pericarditis, and amylase and lipase elevations. After PD-1/PD-L1 treatment discontinuation, 4 (44%) pts remained progression free with a median time off therapy of 20 mos (range 10-44) and median time on therapy of 9 mos (range 4-15). 5 (56%) pts progressed within 6 mos (range 2-6) of treatment discontinuation and median time on therapy was 4 mos (range 3-10). Conclusions: We demonstrate that some pts can have persistent clinical benefit after discontinuation of PD-1/PD-L1 TT for irAEs. Larger studies are warranted to evaluate the need for continuous drug dosing in all pts, identify pts in which continuous dosing is not required, and evaluate long-term outcomes in this population.

4539Background: HGT1 NMI tumors have a 40% risk of R and 21% risk of P. Distinguishing aggressive versus indolent HGT1 disease is critical to decide which patients will benefit from early cystectom...

e16028Background: High grade T1 (HGT1) nonmuscle-invasive bladder cancer (NMIBC) represents a challenging and clinically heterogeneous subset of bladder cancer. Micropapillary carcinomas (MC), a ra...

4535Background: Programmed death-1 (PD-1) receptor negatively regulates T cell-mediated responses.PD-1 ligand (PD-L1) can be expressed on both tumor cells and mononuclear (MNC) infiltrates in MIUC....

4541Background: Application of ChIP-seq to the vast majority of clinical tissue samples has not been possible due to the extensive tissue fixation. We developed Fixed-Tissue chromatin immuno-precip...

386 Background: Trials of salvage therapy for advanced UC have required prior platinum-based therapy. This practice requires scrutiny since non-platinum-based first-line therapy may be offered to cisplatin-ineligible patients (pts). We examined the impact of prior exposure to first-line platinum vs. non-platinum based chemotherapy on overall survival (OS) with salvage systemic chemotherapy. Methods: Data of pts receiving salvage systemic chemotherapy were collected retrospectively or from trials. Data on prior first-line platinum exposure were required in addition to the known prognostic factors: treatment free interval, hemoglobin, performance status, albumin and liver metastasis status. Cox proportional hazards regression was used to evaluate their association with OS after accounting for salvage therapy with single agent chemotherapy or combination chemotherapy. Results: Data was obtained from 455 pts exposed to prior platinum and 37 pts not exposed to prior platinum. In the group exposed to prior platinum, salvage therapy consisted of a single agent taxane (n = 184) and taxane containing combination chemotherapy (n = 271). In the group not exposed to prior platinum, salvage therapy consisted of single agent taxane or vinflunine (n = 20), single agent 5-fluorouracil (n = 1), taxane containing combination chemotherapy (n = 12), carboplatin-based combinations (n = 2) and cisplatin-based combinations (n = 2). The median OS for the prior platinum group was 7.8 (95% CI: 7.0, 8.1) months (mo), and for the prior non-platinum group was 9.0 (6.0, 11.0) mo (p = 0.50). In a multivariable analysis including major prognostic factors and after controlling for single agent or combination salvage chemotherapy, prior platinum vs. no prior platinum exposure conferred no independent impact on OS (HR 1.10 [0.75, 1.64], p = 0.62). Conclusions: Prior platinum vs. non-platinum based chemotherapy did not confer a prognostic impact on OS after accounting for major prognostic factors in pts receiving salvage systemic chemotherapy for advanced UC. Lack of exposure to prior platinum should not disqualify pts from inclusion in trials of salvage therapy after accounting for the 5 known prognostic factors.

415 Background: Upper tract carcinoma (UTUC) is a poorly studied location amongst urothelial tumors. Treatment strategies are often extrapolated from bladder cancer and are not well defined. We aimed to retrospectively evaluate the chemotherapy (CT) treatment patterns and prognostic factors associated with outcome in patients (pts) with visceral metastatic UTUC. Methods: We collected clinical data on 102 UTUC pts treated at Dana-Farber Cancer Institute between Jan 2001 and Dec 2014. We focused our analysis on pts who recurred with visceral metastasis after radical nephroureterectomy and were subsequently treated with CT. Patients with lymph node only recurrence were excluded. Of 102 pts, 74 developed visceral metastasis from which 45 were treated. Overall survival (OS) was defined from date of first line CT for metastatic disease to date of death or censored at last follow up. Kaplan Meier method was used to estimate median OS. Cox regression model was used to summarize the association of OS and potential prognostic factors. Results: Overall, 45 pts received CT. The most common sites of metastases were lung (60%, n = 27), liver (49%, n = 22) and bone (36%, n = 16). 36 % of the pts (n = 16) received first line CT with cisplatin-based combinations. With a median follow up of 29.8 mo the median OS was 14.7 mo, with 32 pts having died at the time of analysis. PS, Hb ≤ 11 and other described known factors were analyzed as well as the impact on OS of the type of CT given cisplatin vs non cisplatin. 81% of the pts (n = 37) had PS < 2. PS 0-1 vs > 1 was included as an exploratory analysis being the number of pts small for grouping. Lower Hb was associated with shorter OS (p = 0.04). Cisplatin vs non cisplatin regimens had a trend on survival benefit in the analysis done in 11 pts (19,3 vs 13,2 mo). Further analysis is ongoing. Conclusions: Although only one third of patients were eligible, this study supports the use of cisplatin regimen to optimize survival in patients with UTUC and visceral metastasis. A significant correlation between Hb ≤11 and OS were observed. The exploratory analysis of PS 0-1 vs > 1 did not have an impact on survival. [Table: see text]