Prostate cancer follows a long and heterogeneous disease course with incompletely understood aetiology1. Here we dissect the mutational processes shaping the genomes of 959 donors from the Pan Prostate Cancer Group and assess their clinical relevance. By integrating de novo extracted single-base substitution, insertion–deletion and copy-number signatures with six novel complex structural variant signatures, we identify eight integrated mutational footprints (IMFs) that collectively explain the mutational processes in 85% of primary prostate cancer genomes. IMFs were strongly influenced by regional biases in the genome, most prevalently androgen receptor-mediated mutagenesis and replication stress. Four IMFs, present in 37% of primary tumours, were significantly associated with shorter time to metastasis. These included reactive oxygen-species-driven mutagenesis and both canonical and non-canonical homologous recombination deficiency, the latter being enriched in patients of African ancestry. Extending to the metastatic setting, we found that IMFs predicted sensitivity to androgen receptor pathway inhibitors. Taken together, our study delineates the aetiologies and mutational processes that drive the genomic and clinical heterogeneity of prostate cancer, introduces IMFs as a unifying framework, and highlights their potential to improve both risk stratification and biomarker-guided treatment selection. Eight integrated mutational footprints collectively explain the mutational processes in 85% of primary prostate cancer genomes.

The inactivation of tumour suppressor genes is a key step in cancer development, and is usually achieved by homozygous loss. In prostate cancer, however, large genomic regions are often hemizygously lost, which complicates the identification of putative tumour suppressors in these regions. Here, we develop Epi2Hit, an integrative computational method that leverages whole genome sequencing, epigenomic profiling and gene expression to identify biallelic inactivation of tumour suppressor genes involving DNA methylation of promoter and enhancer regions of one allele and genomic loss of the other allele. We apply Epi2Hit to a cohort of 2,021 prostate cancers to discover tumour suppressor genes. In particular, we identify epigenetic biallelic inactivation of ZFHX3 at a recurrence level similar to TP53. Biallelic inactivation of ZFHX3, a transcriptional repressor, leads to upregulation of oncogenes, including MYC and a shorter time to metastasis. Finally, we provide evidence that epigenetic silencing as 2nd hit is particularly enriched in regions with nearby essential genes, precluding homozygous loss. Epigenetic biallelic inactivation in prostate cancer remains to be explored. Here, the authors develop a computational method Epi2Hit that integrates the hemizygous genomic disruptions with patterns of hypermethylation at regulatory CpG sites to identify biallelic inactivation in tumour suppressor genes.

Newly diagnosed prostate cancers differ dramatically in mutational composition and lethality. The most accurate clinical predictor of lethality is tumor tissue architecture, quantified as tumor grade. To interrogate the evolutionary origins of prostate cancer heterogeneity, we analyzed 666 prostate tumor whole genomes. We identified a compendium of 223 recurrently mutated driver regions, most influencing downstream mutational processes and gene expression. We identified and validated individual germline variants that predispose tumors to acquire specific somatic driver mutations: these explain heterogeneity in disease presentation and ancestry differences. High-grade tumors have a superset of the drivers in lower-grade tumors, including increased frequency of BRCA2 and MYC mutations. Grade-associated driver mutations occur early in tumor evolution, and their earlier occurrence strongly predicts cancer relapse and metastasis. Our data suggest high- and low-grade prostate tumors both emerge from a common premalignant field, influenced by germline genomic context and stochastic mutation timing.Significance: This study uncovered 223 recurrently mutated driver regions using the largest cohort of prostate tumors to date. It reveals associations between germline SNPs, somatic drivers, and tumor aggression, offering significant insights into how prostate tumor evolution is shaped by germline factors and the timing of somatic mutations.

Brain metastases pose a formidable challenge in oncology. While certain cancers like lung, breast, and melanoma are known to commonly metastasize to the brain, comprehensive studies spanning cancer types that uncommonly or rarely spread to the brain are limited. This study employs data from the Surveillance, Epidemiology, and End Results (SEER) database to examine incidence, prevalence, and clinical characteristics of brain metastases across nearly all cancers. We conducted a detailed review of SEER-derived patient data, focusing on brain metastases. Statistical analyses, including Kaplan-Meier plots and Gehan-Breslow-Wilcoxon tests, were utilized to compare survival rates and clinical features between cancer types, integrating additional features such as staging. (i.e., T and N grades) Lung cancer is the most common primary source of brain metastases. (~80.5% of cases) Furthermore, cancers traditionally associated with brain metastasis—lung, melanoma, breast, renal, and colorectal—comprise 93% of all brain metastasis cases in SEER. Further analysis showed that brain metastasis patients had worse five-year survival than patients who developed metastasis elsewhere, and those patients with high grade glioma. Recent advancements in treatment have improved survival rates for patients diagnosed with brain metastases between 2015-2019, compared to those diagnosed during 2010-2014. This improvement appears to be driven disproportionately by cancers commonly associated with brain metastasis. Moreover, it can be revealed that there are notable differences in T/N grades and clinical features of the cancers that uncommonly or rarely spread to the brain, compared to those that commonly do so. This study suggests that the pattern of brain metastasis formation may differ between those primary malignancies that commonly, and uncommonly or rarely spread metastatically, highlighting the deficit of our clinical and scientific understanding of this pernicious cancer phenomenon, as well as the need to develop novel, innovative treatment paradigms for patients with brain metastases.

Abstract INTRODUCTION Brain metastases pose a significant and growing challenge in clinical practice, yet the molecular variants of this tumor type has not previously been examined comprehensively across multiple cancer types. In particular, there has been limited focus on contrasting the genetic profiles of common brain metastases originating from primary sites like lung, breast, melanoma, colorectal, and renal cancers, with those arising infrequently such as prostate and others. METHODS We have prospectively collected over 125 fresh frozen brain metastases and matching germline reference samples from 14 different primary tumor types and to date have performed WGS, RNA-Seq and Epic 850k methylation profiling on 60 of these samples spanning both common and rare brain metastases. We have employed machine learning algorithms, network analysis techniques, and integrative bioinformatics pipelines to extract meaningful insights into the biological underpinnings of brain metastasis formation. RESULTS We conducted an in-depth investigation into the genomic, transcriptomic, and epigenomic profiles of brain metastases, spanning both common and rare types. By merging these diverse datasets, we identified distinct molecular modifications linked to brain metastases with low incidence rates compared to those more frequently observed. Notably, we observed heightened alterations in the regulation of Golgi dynamics, sensing of lipid species, chromatin remodeling factors, and cytoskeletal remodeling in rare brain metastases. These changes likely influence cell migration and invasion dynamics, elucidating the potential for unique characteristics of less common brain metastasis types. CONCLUSIONS This research indicates that the molecular mechanisms driving the formation of brain metastases may vary depending on whether the primary malignancy frequently or infrequently spreads to the brain. Studies such as these, will aid in eventually driving innovations in precision oncology and ultimately improving patient outcomes.

BACKGROUND:Recent publications have shown patients with defects in the DNA mismatch repair (MMR) pathway driven by either MSH2 or MSH6 loss experience a significant increase in the incidence of prostate cancer. Moreover, this increased incidence of prostate cancer is accompanied by rapid disease progression and poor clinical outcomes.METHODS AND RESULTS:We show that androgen-receptor activation, a key driver of prostate carcinogenesis, can disrupt the MSH2 gene in prostate cancer. We screened tumours from two cohorts (recurrent/non-recurrent) of prostate cancer patients to confirm the loss of MSH2 protein expression and identified decreased MSH2 expression in recurrent cases. Stratifying the independent TCGA prostate cancer cohort for MSH2/6 expression revealed that patients with lower levels of MSH2/6 had significant worse outcomes, in contrast, endometrial and colorectal cancer patients with lower MSH2/6 levels. MMRd endometrial and colorectal tumours showed the expected increase in mutational burden, microsatellite instability and enhanced immune cell mobilisation but this was not evident in prostate tumours.CONCLUSIONS:We have shown that loss or reduced levels of MSH2/MSH6 protein in prostate cancer is associated with poor outcome. However, our data indicate that this is not associated with a statistically significant increase in mutational burden, microsatellite instability or immune cell mobilisation in a cohort of primary prostate cancers.

PURPOSE Androgen receptor (AR) signaling is important in prostate cancer progression, and therapies that target this pathway have been the mainstay of treatment for advanced disease for over 70 years. Tumors eventually progress despite castration through a number of well-characterized mechanisms; however, little is known about what determines the magnitude of response to short-term pathway inhibition. METHODS We evaluated a novel combination of AR-targeting therapies (degarelix, abiraterone, and bicalutamide) and noted that the objective patient response to therapy was highly variable. To investigate what was driving treatment resistance in poorly responding patients, as a secondary outcome we comprehensively characterized pre- and post-treatment samples using both whole-genome and RNA sequencing. RESULTS We find that resistance following short-term treatment differs molecularly from typical progressive castration-resistant disease, associated with transcriptional reprogramming, to a transitional epithelial-to-mesenchymal transition (EMT) phenotype rather than an upregulation of AR signaling. Unexpectedly, tolerance to therapy appears to be the default state, with treatment response correlating with the prevalence of tumor cells deficient for SNAI2, a key regulator of EMT reprogramming. CONCLUSION We show that EMT characterizes acutely resistant prostate tumors and that deletion of SNAI2, a key transcriptional regulator of EMT, correlates with clinical response.

Prostate cancer is caused by genomic aberrations in normal epithelial cells, however clinical translation of findings from analyses of cancer cells alone has been very limited. A deeper understanding of the tumour microenvironment is needed to identify the key drivers of disease progression and reveal novel therapeutic opportunities. In this study, the experimental enrichment of selected cell-types and the development of a Bayesian inference model for continuous differential transcript abundance permitted us to define the transcriptional landscape of the prostate cancer microenvironment along the disease progression axis. An important role of monocytes and macrophages in prostate cancer progression and disease recurrence was uncovered, supported by both transcriptional landscape findings and by differential tissue composition analyses. These findings were corroborated and validated by spatial analyses at the single-cell level using multiplex immunohistochemistry. This study advances our knowledge concerning the role of monocyte-derived recruitment in primary prostate cancer, and supports their key role in disease progression, patient survival and prostate microenvironment immune modulation.

You have accessJournal of UrologyProstate Cancer: Basic Research & Pathophysiology I (MP16)1 Apr 2020MP16-07 LOSS OF SNAI2 IN PROSTATE CANCER DEFINES PATIENT RESPONSE TO ANDROGEN DEPRIVATION THERAPY Niall Corcoran*, Mareck Cmero, Natalie Kurganovs, Patrick McCoy, Paul Ruljancich, Philip Dundee, David Clarke, Anthony Costello, Andrew Ryan, Phillip Parente, and Chris Hovens Niall Corcoran*Niall Corcoran* More articles by this author , Mareck CmeroMareck Cmero More articles by this author , Natalie KurganovsNatalie Kurganovs More articles by this author , Patrick McCoyPatrick McCoy More articles by this author , Paul RuljancichPaul Ruljancich More articles by this author , Philip DundeePhilip Dundee More articles by this author , David ClarkeDavid Clarke More articles by this author , Anthony CostelloAnthony Costello More articles by this author , Andrew RyanAndrew Ryan More articles by this author , Phillip ParentePhillip Parente More articles by this author , and Chris HovensChris Hovens More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000000841.07AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Androgen receptor (AR) signalling is important in prostate cancer progression, and therapies that specifically target this pathway are the mainstay of treatment for advanced disease. Treatment however is non-curative, and resistance develops inevitably with time. Although the mechanisms that drive castration resistant disease have been intensively analysed, how tumours survive and persist during the initial pathway inhibition is unclear. METHODS: To track this process in detail we performed a Phase II neo-adjuvant study of a novel combination of AR targeting therapies (degarelix & abiraterone & bicalutamide) for 6 months prior to prostatectomy in men with high risk, localised disease. To determine what was driving tumour persistence in poorly responding patients, we comprehensively characterised pre- and post-treatment samples using both whole genome and RNA-sequencing, validating pertinent findings by qRT-PCR, IHC and FISH. RESULTS: Despite universal ‘biochemical responses’, objective responses to treatment as measured by residual tumours volumes were highly variable. This state which we term ‘castration-persistence’, is molecularly distinct from ‘castration-resistance’, and is characterised by global transcriptional reprogramming leading to a transitional EMT state. Whole genome sequencing confirms tumour persistence is not associated with the emergence of a ‘driver’ lesion, rather treatment response is associated with regression of a ‘treatment sensitive’ subclonal population defined by deletion of the EMT master regulator SNAI2. The extent of treatment response observed was determined by the prevalence of cells harbouring SNAI2in pre-treatment biopsies. CONCLUSIONS: Cell plasticity with transition to a mesenchymal phenotype defines prostate cancer cell survival to acute AR signalling inhibition. Tumour response is determined by the proportion of cells present harbouring defects in this program. Source of Funding: National Health and Medical Research Council, AustraliaVictorian Cancer AgencyFerring (unrestricted grant for purchase of degarelix)Jannsen (supply of abiraterone) © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 203Issue Supplement 4April 2020Page: e216-e217 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Niall Corcoran* More articles by this author Mareck Cmero More articles by this author Natalie Kurganovs More articles by this author Patrick McCoy More articles by this author Paul Ruljancich More articles by this author Philip Dundee More articles by this author David Clarke More articles by this author Anthony Costello More articles by this author Andrew Ryan More articles by this author Phillip Parente More articles by this author Chris Hovens More articles by this author Expand All Advertisement PDF downloadLoading ...

Background DNA originating from degenerate tumour cells can be detected in the circulation in many tumour types, where it can be used as a marker of disease burden as well as to monitor treatment response. Although circulating tumour DNA (ctDNA) measurement has prognostic/predictive value in metastatic prostate cancer, its utility in localised disease is unknown. Methods We performed whole-genome sequencing of tumour-normal pairs in eight patients with clinically localised disease undergoing prostatectomy, identifying high confidence genomic aberrations. A bespoke DNA capture and amplification panel against the highest prevalence, highest confidence aberrations for each individual was designed and used to interrogate ctDNA isolated from plasma prospectively obtained pre- and post- (24 h and 6 weeks) surgery. In a separate cohort ( n = 189), we identified the presence of ctDNA TP53 mutations in preoperative plasma in a retrospective cohort and determined its association with biochemical- and metastasis-free survival. Results Tumour variants in ctDNA were positively identified pre-treatment in two of eight patients, which in both cases remained detectable postoperatively. Patients with tumour variants in ctDNA had extremely rapid disease recurrence and progression compared to those where variants could not be detected. In terms of aberrations targeted, single nucleotide and structural variants outperformed indels and copy number aberrations. Detection of ctDNA TP53 mutations was associated with a significantly shorter metastasis-free survival (6.2 vs. 9.5 years (HR 2.4; 95% CIs 1.2–4.8, p = 0.014). Conclusions CtDNA is uncommonly detected in localised prostate cancer, but its presence portends more rapidly progressive disease.

338 Background: Androgen receptor (AR) signalling is important in prostate cancer progression, and therapies that specifically target this pathway are the mainstay of treatment for advanced disease. Treatment however is non-curative, and resistance develops inevitably with time. Although the mechanisms that drive castration resistant disease have been intensively analysed, how tumours survive and persist during the initial pathway inhibition is unclear. Methods: To track this process in detail we performed a Phase II neo-adjuvant study of a novel combination of AR targeting therapies (degarelix & abiraterone & bicalutamide) for 6 months prior to prostatectomy in men with high risk, localised disease. To determine what was driving tumour persistence in poorly responding patients, we comprehensively characterised pre- and post-treatment samples using both whole genome and RNA-sequencing, validating pertinent findings by qRT-PCR, IHC and FISH. Results: Despite universal ‘biochemical responses’, objective responses to treatment as measured by residual tumours volumes were highly variable. This state which we term ‘castration-persistence’, is molecularly distinct from ‘castration-resistance’, and is characterised by global transcriptional reprogramming leading to a transitional EMT state. Whole genome sequencing confirms tumour persistence is not associated with the emergence of a ‘driver’ lesion, rather treatment response is associated with regression of a ‘treatment sensitive’ subclonal population, defined by deletion of the EMT master regulator SNAI2. The extent of treatment response observed was determined by the prevalence of cells with loss of SNAI2 in pre-treatment biopsies. Conclusions: Cell plasticity with transition to a mesenchymal phenotype defines prostate cancer cell survival to acute AR signalling inhibition. Tumour response is determined by the proportion of cells present harbouring defects in this program.

You have accessJournal of UrologyProstate Cancer: Basic Research & Pathophysiology I (MP16)1 Apr 2020Prostate Cancer: Basic Research & Pathophysiology I (MP16) View All Author Informationhttps://doi.org/10.1097/JU.0000000000000841AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 203Issue Supplement 4April 2020 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Expand All Advertisement PDF downloadLoading ...

Prostate cancer is a leading cause of morbidity and cancer-related death worldwide. Androgen deprivation therapy (ADT) is the cornerstone of management for advanced disease. The use of these therapies is associated with multiple side effects, including metabolic syndrome and truncal obesity. At the same time, obesity has been associated with both prostate cancer development and disease progression, linked to its effects on chronic inflammation at a tissue level. The connection between ADT, obesity, inflammation and prostate cancer progression is well established in clinical settings; however, an understanding of the changes in adipose tissue at the molecular level induced by castration therapies is missing. Here, we investigated the transcriptional changes in periprostatic fat tissue induced by profound ADT in a group of patients with high-risk tumours compared to a matching untreated cohort. We find that the deprivation of androgen is associated with a pro-inflammatory and obesity-like adipose tissue microenvironment. This study suggests that the beneficial effect of therapies based on androgen deprivation may be partially counteracted by metabolic and inflammatory side effects in the adipose tissue surrounding the prostate.

Purpose To review the current understanding and recent developments regarding the concept of oligometastases in hormone-sensitive prostate cancer. Methods A comprehensive literature search of electronic databases, including PubMed and Embase was conducted for the search term ‘oligometastases’ in combinations with ‘prostate cancer’, ‘hormone sensitive’, ‘genetics’, and ‘molecular’. All articles relating to these search terms have been taken into account. Results Prostate cancer remains a major cause of morbidity and mortality worldwide. The majority of these cancer-related deaths result from metastases. Currently, there is a dichotomy in prostate cancer management where it is only deemed curable if it is localized, while any signs of metastasis relegate patients to systemic therapies to delay their inevitable death. A growing body of evidence supports the notion that aggressive treatments during the stable ‘oligometastatic’ state can have significant clinical benefits and potentially ‘reset’ prostate cancer to an earlier time point in cancer progression. This concept of oligometastases has been adopted in other cancer settings such as colorectal and non-small-cell lung cancers. Conclusion Multiple clinical and molecular biological studies have been influential in the support of a stable state in metastatic cancer progression coined ‘oligometastases’. As our understanding of oligometastases in hormone-sensitive prostate cancer develops, we will be able to molecularly define the oligometastatic state and develop clinically available diagnostic tests. In doing so, prostate cancer patients will experience significant clinical benefits and the burden of prostate cancer worldwide will likely be reduced.

Patients with defects in the mismatch repair (MMR) pathway driven by either MSH2 or MSH6 loss experience a significant increase in the incidence of prostate cancer, whilst germline MMR defects in either MLH1 or PMS2, exhibit no such increase. Prostatic carcinogenesis is driven by androgen signalling. Here we show that androgen-receptor activation can disrupt the MSH2 gene in prostate cancer model systems. We screened tumors from two contrasting risk cohorts of prostate cancer patients to confirm loss of MSH2 protein expression and surprisingly found a small but significant fraction of high risk cases exhibited reduced expression of MSH2. Stratifying a large independent TCGA prostate cancer cohort for MSH2 expression levels revealed that patients whose tumors exhibited either complete loss or aberrant levels of MSH2 had equally significant worse survival outcomes and accelerated clinical progression. In contrast, colorectal cancer patients with aberrant MSH2 levels had improved clinical survival. We show that reduced expression of MSH2 can also occur through androgen-induced miRNA regulatory mechanisms. Aberrant MSH2 expression in prostate tumors does not induce enhanced immune cell mobilisation seen in colorectal tumors suggesting that the prostate is an immune privileged site that is less likely to benefit from immunotherapies.

DNA-fluorescence in situ hybridisation (DNA-FISH) allows visualisation of chromosome organisation and rearrangement. FISH probes are pools of short fluorescently labelled DNA fragments that are often produced from template plasmids that contain large genomic inserts. For effective sample penetration and target hybridisation it is critical that probe fragments are between 200 and 500bp. Production of these short probes requires significant optimisation and can be confounded access to expensive sonication equipment or inherent sequence features that influence enzymatic fragmentation or amplification. Here we demonstrate that effective FISH probes can be prepared without the need for optimisation of fragmentation using a cocktail of two the 4bp recognition sequence restriction enzymes CviQI and AluI.

Key Points Prostate cancers are capable of intratumoural androgen biosynthesis, which is a potential mechanism of castration resistance Three possible competing androgen biosynthesis pathways exist, all of which might enable androgen biosynthesis in the presence of androgen-deprivation therapy Currently, investigations of androgen biosynthesis rely heavily on preclinical models, which generally do not accurately reflect human disease in this setting Identifying the dominant androgen biosynthetic pathway in each patient could have implications for treatment-related decisions