Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse.

Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identify pre-existing and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatment. We find distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent cells are able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal as yet unrecognized molecular predictors of treatment response. This suggests that the application of single-cell methods with high analytical resolution in pre-clinical models may powerfully inform clinical decision-making.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study.

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone. FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions. INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype.

Castration-resistant prostate cancer (CRPC) continues to pose a significant clinical challenge with new generation second-line hormonal therapies affording limited improvement in disease outcome. As the androgen receptor (AR) remains a critical driver in CRPC, understanding the determinants of its transcriptional activity is important for developing new AR-targeted therapies. FOXA1 is a key component of the AR transcriptional complex yet its role in prostate cancer progression and the relationship between AR and FOXA1 are not completely resolved. It is well established that FOXA1 levels are elevated in advanced prostate cancer and metastases. We mimicked these conditions by overexpressing FOXA1 in the androgen-responsive LNCaP prostate cancer cell line and observed a significant increase in AR genomic binding at novel regions that possess increased chromatin accessibility. High levels of FOXA1 resulted in increased proliferation at both sub-optimal and high 5α-dihydrotestosterone (DHT) concentrations. Immunohistochemical staining for FOXA1 in a clinical prostate cancer cohort revealed that high FOXA1 expression is associated with shorter time to biochemical recurrence after radical prostatectomy (hazard ratio (HR) 5.0, 95% confidence interval (CI) 1.2-21.1, P=0.028), positive surgical margins and higher stage disease at diagnosis. The gene expression program that results from FOXA1 overexpression is enriched for PTEN, Wnt and other pathways typically represented in CRPC gene signatures. Together, these results suggest that in an androgen-depleted state, elevated levels of FOXA1 enhance AR binding at genomic regions not normally occupied by AR, which in turn facilitates prostate cancer cell growth.

Plain radiography still is required in the planning of treatment for urolithiasis.

INTRODUCTION: Nonenhanced computed tomography (NCT) is recognised as the most sensitive tool in diagnosis of renal tract calculi. However, its role as the sole imaging investigation, for decisions regarding management is less clear. OBJECTIVE: To determine the proportion of new stone patient referrals in which management is altered by interpretation of a plain abdominal kidneys, ureters and bladder (KUB) radiograph in addition to NCT. METHODS: One hundred consecutive new referrals to a national lithotripsy centre were considered prospectively for treatment of renal tract calculi. RESULTS: A significant change in management was undertaken in 17 patients on the basis of KUB findings. Eleven patients had radio-lucent ureteric stones, for which Extracorporeal Shockwave Lithotripsy (ESWL) was consequently not possible and who required endoscopic management. There were six inaccuracies in measurement of size or positioning on NCT. In a further 43 patients it was not possible to confirm management until the KUB was reviewed, although in these cases ESWL or expectant management was still pursued. Thus additional imaging with a KUB was required in order to confirm optimum management in 60 patients. CONCLUSION: Additional plain radiography confers a significant advantage in the planning of treatment for urolithiasis once the diagnosis has been established by NCT because of information it provides regarding radio-opacity as well as stone size and visibility. This information cannot be delivered by NCT alone. We therefore recommend that KUB imaging is performed on all new stone patients referred for treatment.

Recurrence after totally extraperitoneal laparoscopic repair: implications for operative technique and surgical training.

BACKGROUND: The totally extraperitoneal (TEP) approach is increasingly favoured for inguinal hernia repair. The learning curve is slow with high, early recurrence rates but the exact cause of recurrence is unknown. OBJECTIVE: To determine the reasons for recurrence, identify the critical operative steps and examine the influence of surgical experience and training on results. PATIENTS AND METHODS: All patients undergoing TEP between 1993 and 2004 were included. Patients requiring re-operation for recurrence were identified and examined in detail. RESULTS: Eight surgical teams performed 1682 TEP repairs. Fifty five hernias recurred (3.27%) with a median follow-up of seven years (range 1-11 years). In six recurrences, the first repair was itself for recurrence and in 24, the initial repair was bilateral. The initial hernia was direct in 26 and indirect in 29 patients. These distributions were similar to a control sample. At re-operation, indirect recurrence was more common with 18 direct, and 37 indirect cases (P=0.020). At re-operation, when the original mesh could be identified (18 repairs), it appeared to have moved superiorly in 13 cases. Typically, recurrence occurred in 10% of a surgeon's first 20 cases, 4% of the next 60 cases and falling to below 2% thereafter. CONCLUSION: TEP repairs have a tendency for indirect recurrence even after direct repair. Meshes tend to migrate superiorly. Results suggest that recurrence occurs most often because of failure to fully expose the deep inguinal ring and/or to adequately spread the mesh inferiorly and laterally. We recommend particular attention be paid to these technical aspects. Acceptable results are obtainable after an experience of 20 cases but further improvement in results occurs as experience reaches 80 operations. With a large number of consultants having little or no experience in TEP surgery, there is an urgent need for 'hands-on' training courses so that all patients have access to TEP, particularly those with bilateral or recurrent inguinal herniae.