The Movember Global Action Plan 1 (GAP1): Unique Prostate Cancer Tissue Microarray Resource

BackgroundThe need to better understand the molecular underpinnings of the heterogeneous outcomes of patients with prostate cancer is a pressing global problem and a key research priority for Movember. To address this, the Movember Global Action Plan 1 Unique tissue microarray (GAP1-UTMA) project constructed a set of unique and richly annotated tissue microarrays (TMA) from prostate cancer samples obtained from multiple institutions across several global locations.MethodsThree separate TMA sets were built that differ by purpose and disease state.ResultsThe intended use of TMA1 (Primary Matched LN) is to validate biomarkers that help determine which clinically localized prostate cancers with associated lymph node metastasis have a high risk of progression to lethal castration-resistant metastatic disease, and to compare molecular properties of high-risk index lesions within the prostate to regional lymph node metastases resected at the time of prostatectomy. TMA2 (Pre vs. Post ADT) was designed to address questions regarding risk of castration-resistant prostate cancer (CRPC) and response to suppression of the androgen receptor/androgen axis, and characterization of the castration-resistant phenotype. TMA3 (CRPC Met Heterogeneity)'s intended use is to assess the heterogeneity of molecular markers across different anatomic sites in lethal prostate cancer metastases.ConclusionsThe GAP1-UTMA project has succeeded in combining a large set of tissue specimens from 501 patients with prostate cancer with rich clinical annotation.ImpactThis resource is now available to the prostate cancer community as a tool for biomarker validation to address important unanswered clinical questions around disease progression and response to treatment.</p

Assessment of fishing guide knowledge, attitudes, and behaviours in global recreational fisheries

Fishing guides are held in high esteem by recreational fishing clients whom they likely influence (for better or worse) through role-modelling. This, coupled with consensus that angler behaviour is a key determinant of ecological outcomes in the catch-and-release (C&R) process suggests exploring the state of fishing guide knowledge, attitudes and behaviour on trips is critical for effective intervention in the global fish crisis. Fishing guides were recruited for an online survey using collaborator networks and social media (n = 342; 47 countries). The survey assessed the guides’ knowledge of C&R best practices, attitudes towards environmental behaviours, attitudes towards environmental responsibility and their current practices on guided-angling trips. While most fishing guides were deemed “knowledgeable” (69.0%) having answered most (≥4/7) of the best practice questions correctly, many had poor knowledge of key C&R processes such as oesophageal unhooking. Most fishing guides were untrained (64.0%), and only 8.8% had accredited training. Fishing guides generally had positive environmental attitudes towards C&R behaviour (50.9 – 96.2%), suggesting pro-environmental behavioural intentions. Fishing guides deemed “knowledgeable” had significantly more pro-environmental attitudes towards angling behaviours (p = 0.003), which suggests that best practice training may improve their C&R behaviours. Most fishing guides had pro-environmental attitudes towards their environmental responsibilities (87.1 – 89.5%), but these broad attitudes may have little bearing on actual behaviours when faced with a significant trade-off between client satisfaction and ecological integrity. Despite some fishing guides’ good knowledge of appropriate behaviours, positive attitudes towards the environment and towards C&R practices, there is room for improvement to meet sustainability goals for C&R fisheries, which may be facilitated through opportunities for best practice training

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Long interspersed nuclear element–1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3′ transduction. Because 3′ transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3′ transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3′ transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3′ transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation; analyses timings and patterns of tumour evolution; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity; and evaluates a range of more-specialized features of cancer genomes