Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers

The 30th Annual Prostate Cancer Foundation Scientific Retreat Report

BACKGROUND

The 30th Annual Prostate Cancer Foundation (PCF) Scientific Retreat was held at the Omni La Costa Resort in Carlsbad, CA, from October 26 to 28, 2023. A hybrid component was included for virtual attendees.

METHODS

The Annual PCF Scientific Retreat is a leading international scientific conference focused on pioneering, unpublished, and impactful studies across the spectrum of basic through clinical prostate cancer research, as well as research from related fields with significant potential for improving prostate cancer research and patient outcomes.

RESULTS

The 2023 PCF Retreat concentrated on key areas of research, including: (i) the biology of cancer stem cells and prostate cancer lineage plasticity; (ii) mechanisms of treatment resistance; (iii) emerging AI applications in diagnostic medicine; (iv) analytical and computational biology approaches in cancer research; (v) the role of nerves in prostate cancer; (vi) the biology of prostate cancer bone metastases; (vii) the contribution of ancestry and genomics to prostate cancer disparities; (viii) prostate cancer 3D genomics; (ix) progress in new targets and treatments for prostate cancer; (x) the biology and translational applications of tumor extracellular vesicles; (xi) updates from PCF TACTICAL Award teams; (xii) novel platforms for small molecule molecular glues and binding inhibitors; and (xiii) diversity, equity and inclusion strategies for advancing cancer care equity.

CONCLUSIONS

This meeting report summarizes the presentations and discussions from the 2023 PCF Scientific Retreat. We hope that sharing this information will deepen our understanding of current and emerging research and drive future advancements in prostate cancer patient care.

MicroRNAs Associated with IgLON Cell Adhesion Molecule Expression

The IgLON family of cell adhesion molecules consists of five members (LSAMP, OPCML, neurotrimin, NEGR1, and IgLON5) discovered as supporters of neuronal development, axon growth and guidance, and synapse formation and maintenance. Tumour suppression properties have recently been emerging based on antiproliferative effects through the modulation of oncogenic pathways. Available evidence endorses a role for non-coding RNAs or microRNAs as relevant controllers of IgLON molecule expression that can impact their critical physiological and pathological roles. Current findings support a function for long non-coding RNAs and microRNAs in the modulation of LSAMP expression in cell senescence, cancer biogenesis, addiction, and pulmonary hypertension. For OPCML, data point to a role for several microRNAs in the control of tumorigenesis. MicroRNAs were detected in neurotrimin-mediated functions in cancer biogenesis and in Schwann cell responses to peripheral nerve injury. For NEGR1, studies have mainly investigated microRNA involvement in neuronal responses to ischaemic injury, although data also exist about tumorigenesis and endothelial cell dysfunction. For IgLON5, information is only available about microRNA involved in myocardial infarction. In conclusion, despite much information being still missing and further research needed, the emerging picture favours a model in which non-coding RNAs exert a crucial role in modulating IgLON expression, ultimately affecting their important physiological functions.

Exploring the tumor genomic landscape of aggressive prostate cancer by whole-genome sequencing of tissue or liquid biopsies

Treatment resistance remains a major issue in aggressive prostate cancer (PC), and novel genomic biomarkers may guide better treatment selection. Circulating tumor DNA (ctDNA) can provide minimally invasive information about tumor genomes, but the genomic landscape of aggressive PC based on whole-genome sequencing (WGS) of ctDNA remains incompletely characterized. Thus, we here performed WGS of tumor tissue (n = 31) or plasma ctDNA (n = 10) from a total of 41 aggressive PC patients, including 11 hormone-naïve, 15 hormone-sensitive, and 15 castration-resistant patients. Across all variant types, we found progressively more altered tumor genomic profiles in later stages of aggressive PC. The potential driver genes most frequently affected by single-nucleotide variants or insertions/deletions included the known PC-related genes TP53, CDK12, and PTEN and the novel genes COL13A1, KCNH3, and SENP3. Etiologically, aggressive PC was associated with age-related and DNA repair-related mutational signatures. Copy number variants most frequently affected 14q11.2 and 8p21.2, where no well-recognized PC-related genes are located, and also frequently affected regions near the known PC-related genes MYC, AR, TP53, PTEN, and BRCA1. Structural variants most frequently involved not only the known PC-related genes TMPRSS2 and ERG but also the less extensively studied gene in this context, PTPRD. Finally, clinically actionable variants were detected throughout all stages of aggressive PC and in both plasma and tissue samples, emphasizing the potential clinical applicability of WGS of minimally invasive plasma samples. Overall, our study highlights the feasibility of using liquid biopsies for comprehensive genomic characterization as an alternative to tissue biopsies in advanced/aggressive PC.

Kataegis associated mutational processes linked to adverse prostate cancer presentation in African men

Kataegis, the focal hypermutation of single base substitutions (SBS) in tumour genomes, has received little attention with respect to prostate cancer (PCa) associated molecular and clinical features. Most notably, data is lacking with regards to this tumour evolutionary phenomenon and PCa racial disparities, with African men disproportionately impacted. Here through comparison between African (n = 109) and non-African (n = 79) whole genome sequenced treatment naïve primary tumours, using a single analytical workflow we assessed for shared and unique features of kataegis. Linking kataegis to aggressive presentation, structural variant burden and copy number loss, we attributed APOBEC3 activity through higher rates of SBS2 to high-risk African tumours. While kataegis positive African patients presented with elevated prostate specific antigen levels, their tumours showed evolutionary unique trajectories marked by increased subclonal and structural variant-independent kataegis. The potential to exacerbate tumour heterogeneity emphases the significance of continued exploration of biological behaviours and environmental exposures for African patients.

Rare pathogenic structural variants show potential to enhance prostate cancer germline testing for African men

Prostate cancer (PCa) is highly heritable, with men of African ancestry at greatest risk and associated lethality. Lack of representation in genomic data means germline testing guidelines exclude for African men. Established that structural variations (SVs) are major contributors to human disease and prostate tumourigenesis, their role is under-appreciated in familial and therapeutic testing. Utilising a clinico-methodologically matched African (n = 113) versus European (n = 57) deep-sequenced PCa resource, we interrogated 42,966 high-quality germline SVs using a best-fit pathogenicity prediction workflow. We identified 15 potentially pathogenic SVs representing 12.4% African and 7.0% European patients, of which 72% and 86% met germline testing standard-of-care recommendations, respectively. Notable African-specific loss-of-function gene candidates include DNA damage repair MLH1 and BARD1 and tumour suppressors FOXP1, WASF1 and RB1. Representing only a fraction of the vast African diaspora, this study raises considerations with respect to the contribution of kilo-to-mega-base rare variants to PCa pathogenicity and African associated disparity.

Prostate cancer metastasis and health disparities: a systematic review

BACKGROUND

Prostate cancer (PCa), one of the most prevalent malignancies affecting men, significantly contributes to increased mortality rates worldwide. While the causative death is due to advanced metastatic disease, this occurrence disproportionately impacts men of African descent compared to men of European descent. In this review, we describe potential mechanisms underlying PCa metastases disparities and current treatments for metastatic disease among these populations, differences in treatment outcomes, and survival rates, in hopes of highlighting a need to address disparities in PCa metastases.

METHODS

We reviewed existing literature using databases such as PubMed, Google Scholar, and Science Direct using the following keywords: "prostate cancer metastases", "metastatic prostate cancer disparity", "metastatic prostate cancer diagnosis and treatment", "prostate cancer genetic differences and mechanisms", "genetic differences and prostate tumor microenvironment", and "men of African descent and access to clinical treatments". The inclusion criteria for literature usage were original research articles and review articles.

RESULTS

Studies indicate unique genetic signatures and molecular mechanisms such as Epithelial-Mesenchymal Transition (EMT), inflammation, and growth hormone signaling involved in metastatic PCa disparities. Clinical studies also demonstrate differences in treatment outcomes that are race-specific, for example, patients of African descent have a better response to enzalutamide and immunotherapy yet have less access to these drugs as compared to patients of European descent.

CONCLUSIONS

Growing evidence suggests a connection between a patient's genetic profile, the prostate tumor microenvironment, and social determinants of health that contribute to the aggressiveness of metastatic disease and treatment outcomes. With several potential pathways highlighted, the limitations in current diagnostic and therapeutic applications that target disparity in PCa metastases warrant rigorous research attention.

Optical genome mapping reveals balanced and unbalanced genetic changes associated with tumor-forming potential in an early-stage prostate cancer epithelial subline (M2205)

BACKGROUND

Identifying cytogenetic changes in tumors can aid in diagnosis/prognosis and disease management. Complete cytogenetic characterization has historically required a multimethod/time-consuming approach. Optical genome mapping (OGM) offers a potential solution to this challenge by detecting both balanced and unbalanced abnormalities in a single assay.

METHODS

Genetic changes acquired with tumor-forming potential in a prostate xenograft subline [M2205] (derived from a Black male) that were detected using cytogenetic versus OGM analyses were compared to assess the utility of OGM for analyzing solid tumors.

RESULTS

Cytogenetic/OGM concordance was noted for (a) copy number gains (16, 1p, 3q, 5q, 7p, 8q, 9q, 11p, 11q, 15q, 20q), (b) copy number losses (Y, 3p, 4p, 6p, 7p, 9p, 11q), and (c) structural changes, including multibreak rearrangements. Discordance was noted for two structural findings, both of which had breakpoints localized to repetitive sequences. The OGM studies identified new findings and confirmed/further characterized 8q24 structural abnormalities. It also detected genes gained/disrupted in the 8q24 region (e.g., MYC, DEPTOR, and EXT1); but recognizing a jumping translocation required cytogenetic analyses.

CONCLUSION

These results support using OGM as a tool to analyze solid tumors in clinical/research settings. Moreover, this OGM analysis expanded the characterization of cytogenetic changes present in the M2205 subline, including alterations associated with tumors from Black males diagnosed with prostate cancer.

Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons

Veterans are at an increased risk for prostate cancer, a disease with extraordinary clinical and molecular heterogeneity, compared with the general population. However, little is known about the underlying molecular heterogeneity within the veteran population and its impact on patient management and treatment. Using clinical and targeted tumor sequencing data from the National Veterans Affairs health system, we conducted a retrospective cohort study on 45 patients with advanced prostate cancer in the Veterans Precision Oncology Data Commons (VPODC), most of whom were metastatic castration-resistant. We characterized the mutational burden in this cohort and conducted unsupervised clustering analysis to stratify patients by molecular alterations. Veterans with prostate cancer exhibited a mutational landscape broadly similar to prior studies, including KMT2A and NOTCH1 mutations associated with neuroendocrine prostate cancer phenotype, previously reported to be enriched in veterans. We also identified several potential novel mutations in PTEN, MSH6, VHL, SMO, and ABL1 Hierarchical clustering analysis revealed two subgroups containing therapeutically targetable molecular features with novel mutational signatures distinct from those reported in the Catalogue of Somatic Mutations in Cancer database. The clustering approach presented in this study can potentially be used to clinically stratify patients based on their distinct mutational profiles and identify actionable somatic mutations for precision oncology.

Survival Outcomes by Race and Ethnicity in Veterans With Nonmetastatic Castration-Resistant Prostate Cancer

Importance

Racial and ethnic disparities in prostate cancer are poorly understood. A given disparity-related factor may affect outcomes differently at each point along the highly variable trajectory of the disease.

Objective

To examine clinical outcomes by race and ethnicity in patients with nonmetastatic castration-resistant prostate cancer (nmCRPC) within the US Veterans Health Administration.

Design, Setting, and Participants

A retrospective, observational cohort study using electronic health care records (January 1, 2006, to December 31, 2021) in a nationwide equal-access health care system was conducted. Mean (SD) follow-up time was 4.3 (3.3) years. Patients included in the analysis were diagnosed with prostate cancer from January 1, 2006, to December 30, 2020, that progressed to nmCRPC defined by (1) increasing prostate-specific antigen levels, (2) ongoing androgen deprivation, and (3) no evidence of metastatic disease. Patients with metastatic disease or death within the landmark period (3 months after the first nmCRPC evidence) were excluded.

Main Outcomes and Measures

The primary outcome was time from the landmark period to death or metastasis; the secondary outcome was overall survival. A multivariate Cox proportional hazards model, Kaplan-Meier estimates, and adjusted survival curves were used to evaluate outcome differences by race and ethnicity.

Results

Of 12 992 patients in the cohort, 826 patients identified as Hispanic (6%), 3671 as non-Hispanic Black (28%; henceforth Black), 7323 as non-Hispanic White (56%; henceforth White), and 1172 of other race and ethnicity (9%; henceforth other, including American Indian or Alaska Native, Asian, Native Hawaiian or Other Pacific Islander, unknown by patient, and patient declined to answer). Median time elapsed from nmCRPC to metastasis or death was 5.96 (95% CI, 5.58-6.34) years for Black patients, 5.62 (95% CI, 5.11-6.67) years for Hispanic patients, 4.11 (95% CI, 3.96-4.25) years for White patients, and 3.59 (95% CI, 3.23-3.97) years for other patients. Median unadjusted overall survival was 6.26 (95% CI, 6.03-6.46) years among all patients, 8.36 (95% CI, 8.0-8.8) years for Black patients, 8.56 (95% CI, 7.3-9.7) years for Hispanic patients, 5.48 (95% CI, 5.2-5.7) years for White patients, and 4.48 (95% CI, 4.1-5.0) years for other patients.

Conclusions and Relevance

The findings of this cohort study of patients with nmCRPC suggest that differences in outcomes by race and ethnicity exist; in addition, Black and Hispanic men may have considerably improved outcomes when treated in an equal-access setting.

Addressing cancer care in low- to middle-income countries: a call for sustainable innovations and impactful research

Most new cancer cases are currently arising in low- and middle-income countries, where their outcomes are significantly poorer compared to high-income countries. Innovative solutions are imperiously needed to prevent, detect early, and manage cancer in low- and middle-income countries, aiming to improve the chances of survival.

CRISPR screening reveals gleason score and castration resistance related oncodriver ring finger protein 19 A (RNF19A) in prostate cancer

Prostate cancer (PCa) is one of the most lethal causes of cancer-related death in male. It is characterized by chromosomal instability and disturbed signaling transduction. E3 ubiquitin ligases are well-recognized as mediators leading to genomic alterations and malignant phenotypes. There is a lack of systematic study on novel oncodrivers with genomic and clinical significance in PCa. In this study we used clustered regularly interspaced short palindromic repeats (CRISPR) system to screen 656 E3 ubiquitin ligases as oncodrivers or tumor repressors in PCa cells. We identified 51 significantly changed genes, and conducted genomic and clinical analysis on these genes. It was found that the Ring Finger Protein 19 A (RNF19A) was a novel oncodriver in PCa. RNF19A was frequently amplified and highly expressed in PCa and other cancer types. Clinically, higher RNF19A expression correlated with advanced Gleason Score and predicted castration resistance. Mechanistically, transcriptomics, quantitative and ubiquitination proteomic analysis showed that RNF19A ubiquitylated Thyroid Hormone Receptor Interactor 13 (TRIP13) and was transcriptionally activated by androgen receptor (AR) and Hypoxia Inducible Factor 1 Subunit Alpha (HIF1A). This study uncovers the genomic and clinical significance of a oncodriver RNF19A in PCa. The results of this study indicate that targeting AR/HIF1A-RNF19A-TRIP13 signaling axis could be an alternative option for PCa diagnosis and therapy.

Systematic assays and resources for the functional annotation of non-coding variants

Identification of genetic variation in individual genomes is now a routine procedure in human genetic research and diagnostics. For many variants, however, insufficient evidence is available to establish a pathogenic effect, particularly for variants in non-coding regions. Furthermore, the sheer number of candidate variants renders testing in individual assays virtually impossible. While scalable approaches are being developed, the selection of methods and resources and the application of a given framework to a particular disease or trait remain major challenges. This limits the translation of results from both genome-wide association studies and genome sequencing. Here, we discuss computational and experimental approaches available for functional annotation of non-coding variation.

Ancestry-defined molecular taxonomy of prostate cancer

Recent studies by Gong et al. and Jaratlerdsiri et al. re-evaluate the mutational landscape of prostate cancer (PCa) in a global context based on ancestry. These two studies revealed African-specific PCa taxonomy, including novel oncogenic drivers with promising therapeutic targets and the opportunity to predict patient outcomes using a unified pipeline.