Genomic and epigenomic analysis of plasma cell-free DNA identifies stemness features associated with worse survival in lethal prostate cancer.

PURPOSE: Metastatic castration-resistant prostate cancer (mCRPC) resistant to androgen receptor signaling inhibitors (ARSIs) is often lethal. Liquid biopsy biomarkers for this deadly form of disease remain under investigation, and underpinning mechanisms remain ill-understood. EXPERIMENTAL DESIGN: We applied targeted cell-free DNA sequencing to 126 mCRPC patients from three academic cancer centers, and separately performed genome-wide cell-free DNA methylation sequencing on 43 plasma samples collected prior to the initiation of first-line ARSI treatment. To analyze the genome-wide sequencing data, we performed nucleosome-positioning and differential methylated region analysis. We additionally analyzed single-cell and bulk RNA sequencing data from 14 and 80 mCRPC patients, respectively, to develop and validate a stem-like signature, which we inferred from cell-free DNA. RESULTS: Targeted cell-free DNA sequencing detected AR/enhancer alterations prior to first-line ARSIs which correlated with significantly worse PFS (p = 0.01; HR = 2.12) and OS (p = 0.02; HR = 2.48). Plasma methylome analysis revealed that AR/enhancer lethal mCRPC patients have significantly higher promoter-level hypomethylation than AR/enhancer wild-type mCRPC patients (p < 0.0001). Moreover, gene ontology and CytoTRACE analysis of nucleosomally more accessible transcription factors in cell-free DNA revealed enrichment for stemness-associated transcription factors in lethal mCRPC patients. The resulting stemness signature was then validated in a completely held-out cohort of 80 mCRPC patients profiled by tumor RNA sequencing. CONCLUSIONS: We analyzed a total of 220 mCRPC patients, validated the importance of cell-free AR/enhancer alterations as a prognostic biomarker in lethal mCRPC and showed that the underlying mechanism for lethality involves reprogramming developmental states toward increased stemness.

Genomic and epigenomic analysis of plasma cell-free DNA identifies stemness features associated with worse survival in AR -altered lethal prostate cancer.

Metastatic castration-resistant prostate cancer (mCRPC) resistant to androgen receptor (AR)-targeted agents is often lethal. Unfortunately, biomarkers for this deadly disease remain under investigation, and underpinning mechanisms are ill-understood. Here, we applied deep sequencing to ∼100 mCRPC patients prior to the initiation of first-line AR-targeted therapy, which detected AR /enhancer alterations in over a third of patients, which correlated with lethality. To delve into the mechanism underlying why these patients with cell-free AR /enhancer alterations developed more lethal prostate cancer, we next performed genome-wide cell-free DNA epigenomics. Strikingly, we found that binding sites for transcription factors associated with developmental stemness were nucleosomally more accessible. These results were corroborated using cell-free DNA methylation data, as well as tumor RNA sequencing from a held-out cohort of mCRPC patients. Thus, we validated the importance of AR /enhancer alterations as a prognostic biomarker in lethal mCRPC, and showed that the underlying mechanism for lethality involves reprogramming developmental states toward increased stemness.

Circulating tumor DNA based minimal residual disease detection and adjuvant treatment decision-making for muscle-invasive bladder cancer guided by modern clinical trials.

Up to 430,000 cases of bladder cancer are diagnosed each year worldwide. A proposed method for non-invasive monitoring has been to utilize a "liquid biopsy." Liquid biopsy has been proposed as a non-invasive method of testing biomarkers in bodily fluids in order to detect and survey cancer. The liquid biopsy could be utilized to obtain information regarding circulating tumor cells, circulating cell-free tumor DNA, circulating cell-free tumor RNA, and more. It is currently being investigated to help guide adjuvant therapy and improve oncological outcomes. We highlight an array of exciting past and ongoing clinical trials regarding ctDNA and adjuvant therapy in regard to urothelial carcinoma which we believe to be amongst the leaders in the field.

Enhanced popcorning using polyanionic chelating solutions as irrigation.

Poly-anionic compounds can chelate divalent cations and dissolve calcium oxalate stone. Our objective was to assess how much concurrent irrigation with poly-anionic chelating solutions during non-contact laser lithotripsy or popcorning could improve stone ablation rate. A popcorning model was created by lowering a ureteroscope with thulium fiber laser into a test tube calyx. Begostones of matching size and mass were placed in the test tube and treated with the laser while irrigating with different iso-osmolar poly-anionic solutions. We compared 0.9% sodium chloride (NaCl), sodium citrate, sodium hexa-metaphosphate, and sodium ethylenediaminetetraacetate (EDTA) solutions. After treatment, residual stones were passed through a 1 mm sieve, and remaining fragments greater than 1 mm were weighed as remaining stone mass. Average remaining stone mass after lithotripsy with NaCl irrigation was 27.8% (± 10.0%). The average remaining stone mass after lithotripsy with hexa-metaphosphate, sodium citrate, and EDTA irrigation was 28.9% (± 13.4%), 17.5% (± 10.5%), and 9.8% (± 5.7%) respectively. Compared with NaCl, there was a 37% reduction in remaining stone mass when using citrate (p = 0.008) and a 64.7% reduction when using EDTA irrigation during lithotripsy (p < 0.001). Concurrent irrigation with citrate or EDTA solutions synergistically enhances the efficacy laser lithotripsy in this in vitro popcorning model. This may lead to tangible improvements in endoscopic stone removal outcomes; however, the effectiveness on different stone types and safety during short duration lithotripsy should be further investigated.

Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients.

Circulating tumor DNA (ctDNA) sensitivity remains subpar for molecular residual disease (MRD) detection in bladder cancer patients. To remedy this problem, we focused on the biofluid most proximal to the disease, urine, and analyzed urine tumor DNA in 74 localized bladder cancer patients. We integrated ultra-low-pass whole genome sequencing (ULP-WGS) with urine cancer personalized profiling by deep sequencing (uCAPP-Seq) to achieve sensitive MRD detection and predict overall survival. Variant allele frequency, inferred tumor mutational burden, and copy number-derived tumor fraction levels in urine cell-free DNA (cfDNA) significantly predicted pathologic complete response status, far better than plasma ctDNA was able to. A random forest model incorporating these urine cfDNA-derived factors with leave-one-out cross-validation was 87% sensitive for predicting residual disease in reference to gold-standard surgical pathology. Both progression-free survival (HR = 3.00, p = 0.01) and overall survival (HR = 4.81, p = 0.009) were dramatically worse by Kaplan-Meier analysis for patients predicted by the model to have MRD, which was corroborated by Cox regression analysis. Additional survival analyses performed on muscle-invasive, neoadjuvant chemotherapy, and held-out validation subgroups corroborated these findings. In summary, we profiled urine samples from 74 patients with localized bladder cancer and used urine cfDNA multi-omics to detect MRD sensitively and predict survival accurately.

Feasibility and safety of same-day discharge following single-port robotic-assisted laparoscopic prostatectomy.

PURPOSE: The standard discharge pathway following robotic-assisted laparoscopic prostatectomy (RALP) involves overnight hospital admission. Models for same-day discharge (SDD) have been explored for multiport RALP, however, less is known regarding SDD for single-port RALP, especially in terms of patient experience. METHODS: Patient enrollment, based on preoperative determination of potential SDD eligibility, commenced March 2020 and ended March 2021. Day-of-surgery criteria were utilized to determine which enrolled patients underwent SDD. Differences in preoperative characteristics and perioperative outcomes between patients undergoing SDD and patients undergoing standard discharge were evaluated. A prospectively administered questionnaire was designed to characterize patient-centered factors informing SDD perception. RESULTS: Fifteen patients underwent SDD and 36 underwent standard discharge. Overall mean ± SD age and BMI were 63.6 ± 7.0 years and 29.7 ± 4.4 kg/m2, respectively. Mean operative time was shorter in the SDD cohort than the standard discharge cohort (188 min vs 217 min, p = 0.011). A higher proportion of cases that underwent SDD were performed using the Retzius-sparing approach, 80% (12/15) vs 33% (12/36) in the standard discharge cohort (p = 0.005). Rates of 90 day complication (p = 0.343), 90 day readmission (p = 0.144), and 90 day emergency department visits (p = 0.343) rates were all not significantly different between cohorts. Of questionnaire respondents undergoing standard discharge, 32% (8/25) cited pain as a reason for not undergoing SDD. CONCLUSIONS: With comparable outcomes to the standard discharge pathway, SDD is safe and effective in single-port RALP. Post-operative pain and perceptions of distance are implicated as patient-centered barriers to SDD; proactive pain management and patient education strategies may facilitate SDD.

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.

Patient Factors Affect Ergonomic Strain of Endoscopists During Colonoscopy.

INTRODUCTION: Endoscopic procedures place a great deal of muscular strain on providers, especially over the span of their careers. In this study we quantitatively analyzed the effects of patient factors such as age, body mass index, and sex on the ergonomics of endoscopists performing colonoscopies. METHODS: Surface electromyography (sEMG) was used to measure ergonomic strain of physicians while performing colonoscopies in several key muscle groups. The percent of the maximum voluntary contraction (%MVC) was used as a measure of muscular strain. Data was then analyzed based on the patient characteristics above. RESULTS: Endoscopists performing colonoscopies on female patients (n = 47) experienced significantly higher ergonomic strain in their right trapezius and right posterior forearm muscle groups when compared to colonoscopies performed on males (n = 35) (%MVC R-trapezius: Male: 8.2; Female: 8.9; p = 0.048); (%MVC R-posterior forearm: Male: 10.4; Female: 11.6; p = 0.0006). Operators experienced greater strain in the same muscle groups when performing colonoscopies on patients with BMI ≤ 25 (n = 25) when compared to patients with BMI > 25 (n = 57) (%MVC R-trapezius: BMI < 25: 9.7; BMI ≥ 25: 8.2; p = 0.0002); (%MVC R-posterior forearm: BMI < 25: 11.9; BMI ≥ 25: 10.8; p = 0.0001). CONCLUSION: Physicians experienced greater ergonomic strain when performing colonoscopies on female patients and on patients with a BMI < 25. We believe that these factors potentially impact the tortuosity of the colon and therefore influence the difficulty of navigating the endoscope. These results may aid physicians in gauging the anticipated difficulty of colonoscopies based on patient factors. Increased awareness of their posturing and ergonomics during challenging cases will alleviate musculoskeletal injuries in the long run.

Comparison of Three Approaches to Single-Port Robot-Assisted Radical Prostatectomy: Our Institution's Initial Experience.

Background: We aimed to compare three robot-assisted radical prostatectomy (RARP) approaches-Retzius sparing (RS), extraperitoneal (EP), and transperitoneal (TP)-performed at our institution using the da Vinci® single-port (SP) platform (Intuitive Surgical, Sunnyvale, CA). Materials and Methods: We retrospectively reviewed the records of 101 patients who underwent SP-RARP at our institution and stratified them into three cohorts based on the RARP approach: RS (n = 32), EP (n = 30), and TP (n = 39). Data regarding preoperative patient characteristics, perioperative characteristics, oncologic outcomes, and early functional outcomes were collected. The Fisher's exact test and chi-square tests were utilized for categorical variables, and the Kruskal-Wallis test was utilized for numerical variables. Wilcoxon rank-sum tests were utilized for pairwise comparisons. A two-tailed p < 0.05 was considered significant. Results: All three cohorts were largely similar in terms of preoperative patient characteristics. Operative time was significantly different between cohorts (p < 0.001), with the RS approach having a faster mean operating time than the TP approach (208 ± 40 minutes vs 248 ± 36 minutes, p < 0.001). Clinically significant margin rates did not differ significantly between cohorts (p = 0.861). Postoperative continence differed significantly between cohorts (p < 0.001); higher continence rates were observed in RS vs EP-94% (30/32) vs 52% (15/29), respectively, p < 0.001. Return of erectile function also differed significantly between cohorts (p = <0.001); higher erectile function recovery rates were observed in RS vs EP-88% (28/32) vs 41% (11/27), respectively, p < 0.001-and in RS vs TP-88% (28/32) vs 60% (22/37), respectively, p = 0.014. Median (IQR) follow-up time was 150 (88-377) days. Conclusions: RS SP-RARP is associated with improved early functional outcomes when compared with both EP and TP approaches. These benefits are achieved while maintaining equivalent oncologic outcomes. Further research is needed to optimize the patient selection paradigm for the SP-RARP approach.

Smaller hands and less experience are associated with greater ergonomic strain during endoscopic procedures.

INTRODUCTION: Up to 89% of physicians who routinely perform endoscopy experience some type of musculoskeletal pain. In this study, we sought to quantitatively analyze provider factors that influence ergonomic strain during live endoscopic procedures. METHODS: Surface electromyography (sEMG) was used to measure ergonomic strain on physicians while performing upper and lower endoscopies. EMG data were normalized to a maximal voluntary contraction (MVC) recording for each muscle group, yielding a %MVC value. Subgroup analyses were performed based on glove size, physician training level, specialty, and handedness. RESULTS: A total of 165 upper (n = 68) and lower (n = 97) endoscopies were recorded. Endoscopists with small hand sizes had significantly higher ergonomic strain in the left anterior and posterior forearm muscle compartments as compared to endoscopists with medium or large hands (%MVC L-anterior: small: 9.1 ± 1.1; medium: 6.4 ± 1.2; large: 5.9 ± 1.6; p < 0.001); (%MVC L-posterior: small: 12.0 ± 0.8; medium: 9.4 ± 1.3; large: 8.8 ± 1.4; p < 0.001). Additionally, upper body muscle groups had significantly higher ergonomic strain in endoscopists with less lifetime endoscopic experience (%MVC R-trapezius: expert: 8.4 ± 1.2; novice: 9.3 ± 1.2; p < 0.05); (%MVC R-deltoid: expert: 6.1 ± 1.4; novice: 8.5 ± 1.3; p < 0.001). There were no significant ergonomic differences between surgeons or gastroenterologists and no differences between right- and left-handed dominant individuals. CONCLUSIONS: Endoscopists with small hands experienced great ergonomic strain in their left forearm. Our data support the widely held belief that "one size does not fit all" and will hopefully spark change in the design of future endoscopes by device manufacturers. Our data also support that the experience level of the endoscopist contributed significantly to ergonomic performance, likely due to postural differences leading to decreased upper body strain. Therefore, it remains critically important to educate young proceduralists on strategies for ergonomic relief early in his or her endoscopic training program that can ameliorate ergonomic strain that accrues over the lifetime of a physician's career.