Abstract 6698: Combinatorial genomic and epigenomic cell-free DNA analysis of high-risk metastatic castration resistant prostate cancer reveals prognostic liquid biopsy signatures

Background: Androgen receptor signaling inhibitors (ARSI) such abiraterone and enzalutamide have significantly improved clinical outcomes in metastatic castrate-resistant prostate cancer (mCRPC) patients. However, patients with genomic alterations in the androgen receptor (AR) and its enhancer region do not respond well and acquire resistance to these inhibitors. Here, we applied our previously developed cell-free DNA (cfDNA) liquid biopsy assay (EnhanceAR-Seq) to detect these high-risk mCRPC patients prior to the administration of first-line AR-directed therapy and correlated with survival. We also interrogated the plasma methylome to identify differentially methylated regions (DMRs) across these high-risk patients. Methodology: We applied EnhanceAR-Seq to plasma cfDNA isolated from 99 mCRPC patients enrolled from two institutions (n=52 Tulane; n=47 WashU). Plasma samples were collected prior to ARSI initiation (n=63) or during treatment (n=36). We also performed Enzymatic Methyl-seq in pre-treatment plasma from 43 patients. We split these 43 patients into cell-free genomically high-risk and low-risk groups using our EnhanceAR-seq results, and conducted DMR analysis using metilene. To identify significant DMRs, we performed multiple hypothesis testing and required q<0.05 using the Benjamini-Hochberg procedure, and further required at least 5 CpGs per DMR. Results: EnhanceAR-Seq detected AR/enhancer alterations in 35% of all plasma samples. Cell-free AR/enhancer detection was highly prognostic (PFS HR=2.80, p=0.0002; OS HR=2.6, p=0.01). When considering only pre-treatment plasma, AR/enhancer alterations detected in 44% (28/63) of samples correlated significantly with worse PFS (HR=2.21, p=0.009) and OS (HR=2.60, p=0.02). AR/enhancer alterations detected in 19% (7/36) of samples collected during ARSI were also associated with worse PFS (HR=15.6, p=0.0002) and OS (HR=8.09, p=0.05). Plasma methylome analysis revealed that for cell-free genomically high-risk mCRPC patients (based on AR/enhancer alterations detected in cfDNA), significantly hypomethylated DMRs were found in the AR promoter, upstream AR enhancer, and in AR-associated genes including FOXP1 and FOLH1. Significantly hypomethylated DMRs were also observed in DNA damage repair and cell cycle genes including MSH6, MSH3, FANCD2, CDK12 and RAD51B. Hypermethylated DMRs were seen in tumor suppressor genes including ZBTB16, BRCA2, WT1 and GNAS. Conclusions: AR/enhancer alterations detected in plasma cfDNA predicted inferior survival in mCRPC patients. Cell-free genomically high-risk mCRPC patients could be distinguished from low-risk patients based on distinct methylation signatures.

Citation Format: Irfan Alahi, Pradeep S. Chauhan, Alexander L. Shiang, Jace Webster, Ha X. Dang, Lilli Greiner, Breanna yang, Elisa M. Ledet, Ramandeep K. Babbra, Wenjia Feng, Peter K. Harris, Ellen B. Jaeger, Patrick J. Miller, Sydney A. Caputo, Giordano Cittolin Santos, Oliver Sartor, Russell K. Pachynski, Christopher A. Maher, Aadel A. Chaudhuri. Combinatorial genomic and epigenomic cell-free DNA analysis of high-risk metastatic castration resistant prostate cancer reveals prognostic liquid biopsy signatures [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6698.

Abstract 2219: Urine cell-free DNA multi-omics to detect molecular residual disease and predict survival in bladder cancer patients

Background: Circulating cell-free tumor DNA (ctDNA) analysis for minimal residual disease (MRD) detection is transforming cancer care. However, the sensitivity of these approaches remains subpar and there is significant risk of false negative results. We analyzed the most proximal biofluid (urine) in localized muscle-invasive bladder cancer (MIBC) patients, and performed two orthogonal ctDNA analytical techniques, one focusing on driver mutation detection, and another focusing on genome-wide copy number alterations. The primary objective of this combinatorial approach was to sensitively detect ctDNA MRD, predict pathologic complete response (pCR), and improve patient risk-stratification.

Methods: Urine samples from 74 localized bladder cancer patients were collected preoperatively on the day of curative-intent radical cystectomy (RC) to assess urine tumor DNA (utDNA). We performed ultra-low pass whole genome sequencing (ULP-WGS) of urine cfDNA from all 74 patients as well as 15 healthy adults. Tumor fraction (TFx) level based on genome-wide copy number alterations was estimated using ichorCNA. Variant allele frequency (VAF) based on single-nucleotide variants (SNVs) was estimated by uCAPP-Seq. We also noninvasively inferred tumor mutation burden (iTMB). pCR was determined by surgical pathology. A random forest (RF) model with leave-one-out cross-validation (LOOCV) was utilized to predict disease status. Kaplan-Meier (KM) and Cox proportional hazards model survival analyses were performed to assess overall survival (OS) and progression-free survival (PFS).

Results: Our study cohort consisted of 74 patients, of which 58 (78%) harbored localized MIBC, and 16 (22%) harbored treatment-refractory high-risk localized NMIBC. Among MIBC patients, 64% (37/58) received neo-adjuvant chemotherapy. VAF, iTMB and TFx levels significantly predicted pCR status. Our RF model incorporating these three utDNA parameters achieved a sensitivity of 87%, a negative predictive value of 77%, and a positive predictive value of 65% for predicting residual disease. AUC for the model was 0.80 (p<0.0001). KM analysis revealed that both PFS (HR = 3.00, P = 0.01) and OS (HR = 4.81, P = 0.009) were significantly worse for patients predicted by the model to have residual disease. Univariate and multivariate Cox proportional hazards models confirmed the significance of our MRD predictions. Survival analyses performed on MIBC, neoadjuvant chemotherapy, and held-out validation subgroups corroborated these findings.

Conclusions: Integration of ULP-WGS with uCAPP-Seq enabled robust detection of residual urine tumor DNA with high sensitivity and predicted survival in localized bladder cancer patients. In the future, this type of multimodal urine-based genomic analysis may lead to more precise risk stratification and nonoperative clinical decision-making for bladder cancer patients.

Citation Format: Pradeep Singh Chauhan, Alexander L. Shiang, Irfan Alahi, R. Taylor Sundby, Wenjia Feng, Bilge Gungoren, Cayce Nawaf, Kevin Chen, Ramandeep K. Babbra, Peter K. Harris, Faridi Qaium, Casey Hatscher, Anna Antiporda, Lindsey Brunt, Lindsey R. Mayer, Jack F. Shern, Brian C. Baumann, Eric H. Kim, Melissa A. Reimers, Zachary L. Smith, Aadel A. Chaudhuri. Urine cell-free DNA multi-omics to detect molecular residual disease and predict survival in bladder cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2219.

Comparison of single-port and multi-port Retzius-sparing robot-assisted laparoscopic prostatectomy

Dissemination of robotic surgical technology for robot-assisted laparoscopic prostatectomy (RALP) has yielded advancements including the Retzius-sparing (RS) approach and the single-port (SP) platform. The safety and feasibility of each individual advancement have been evaluated, yet there is a lack of literature comparing SP RS-RALP to conventional multi-port (MP) RS-RALP. All patients who underwent RS-RALP at our institution between January 2019 and February 2021 were retrospectively reviewed. Data regarding baseline patient and tumor characteristics, operative characteristics, and surgical outcomes were collected and analyzed using the Fisher's exact test and two-tailed unpaired t tests. 62 patients were evaluated: 31 received SP RS-RALP and 31 received MP RS-RALP. Differences in patient age, BMI, and initial PSA were not observed. Lower median lymph node yield (SP: 4 vs MP: 12, p < 0.01), lower estimated blood loss (SP: 111.2 vs. MP 157.8 mL, p < 0.01), shorter operative time (SP: 207.7 vs. MP: 255.9 min, p < 0.01) and decreased length of stay (SP: 0.39 vs. MP: 1.23 days, p < 0.01) were observed in the SP RS-RALP cohort. No differences in positive surgical margins, complications, or biochemical recurrence rates were observed. SP RS-RALP is non-inferior to MP RS-RALP in terms of both perioperative and early oncologic outcomes. Despite the small sample size, the SP platform is a safe and feasible option for RS-RALP and confers potential benefits in the form of shorter operative time and reduced length of stay.