Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of on-going abnormal mutational processes, consistent with field-effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissue or between different ERG-lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.
Changes in gene dosage are a major driver of cancer, engineered from a finite, but increasingly well annotated, repertoire of mutational mechanisms1. This can potentially generate correlated copy number alterations across hundreds of linked genes, as exemplified by the 2% of childhood acute lymphoblastic leukemia (ALL) with recurrent amplification of megabase regions of chromosome 21 (iAMP21)2,3. We used genomic, cytogenetic and transcriptional analysis, coupled with novel bioinformatic approaches, to reconstruct the evolution of iAMP21 ALL. We find that individuals born with the rare constitutional Robertsonian translocation between chromosomes 15 and 21, rob(15;21)(q10;q10)c, have ~2700-fold increased risk of developing iAMP21 ALL compared to the general population. In such cases, amplification is initiated by a chromothripsis event involving both sister chromatids of the Robertsonian chromosome, a novel mechanism for cancer predisposition. In sporadic iAMP21, breakage-fusion-bridge cycles are typically the initiating event, often followed by chromothripsis. In both sporadic and rob(15;21)c-associated iAMP21, the final stages frequently involve duplications of the entire abnormal chromosome. The end-product is a derivative of chromosome 21 or the rob(15;21)c chromosome with gene dosage optimised for leukemic potential, showing constrained copy number levels over multiple linked genes. Thus, dicentric chromosomes may be an important precipitant of chromothripsis, as we show rob(15;21)c to be constitutionally dicentric and breakage-fusion-bridge cycles generate dicentric chromosomes somatically. Furthermore, our data illustrate that several cancer-specific mutational processes, applied sequentially, can co-ordinate to fashion copy number profiles over large genomic scales, incrementally refining the fitness benefits of aggregated gene dosage changes.
Angiosarcoma is an aggressive malignancy that arises spontaneously or secondarily to ionising radiation or chronic lymphoedema1. Previous work has identified aberrant angiogenesis, including occasional somatic mutations in angiogenesis signalling genes, as a key driver of angiosarcoma1. Here, we employed whole genome, exome, and targeted sequencing to study the somatic changes underpinning primary and secondary angiosarcoma. We identified recurrent mutations in two genes, PTPRB and PLCG1, which are intimately linked to angiogenesis. The endothelial phosphatase PTPRB, a negative regulator of vascular growth factor tyrosine kinases, harboured predominantly truncating mutations in 10/39 (26%) tumours. PLCG1, a signal transducer of tyrosine kinases, presented with a recurrent, likely activating R707Q missense variant in 3/34 cases (9%). Overall, 15/39 (38%) tumours harboured at least one driver mutation in angiogenesis signalling genes. Our findings inform and reinforce current therapeutic efforts to target angiogenesis signalling in angiosarcoma.
Background Patient and public involvement and engagement is an important and expected component of health-related research activity in the UK. Specifically within the health research sphere, public engagement (usually defined as raising awareness of research) and patient involvement (usually defined as actively involving people in research) have traditionally been seen as separate but have much to gain from working together towards a common goal of better health outcomes for all. Methods This paper describes a unique approach taken by the Public Programmes Team: a small interdisciplinary team of public engagement specialists, with backgrounds in science, community development, public engagement and involvement, policy, ethics, communications, industry, museums and creative practice, embedded within translational research infrastructure and delivery in Manchester in the North West of England. We propose a new model of professional practice – a 'cycle' of engagement and involvement – innovating across the complementary fields of public engagement and patient involvement, and working inclusively and in partnership with people in health research. Further, our approach capitalises on strategic collaboration offering economies of scale and a joined up way of working. Our ambition is to boldly experiment, learn and reflect, responsibly and based on evidence and partnerships, using methods of engagement that address issues of social justice. Results Here, we report on preliminary case studies exemplifying the impact of our approach, and data relating to achievements and learning between April 2017 and March 2018. Informed by our findings, we propose that our approach has the potential to be replicated elsewhere. Conclusions Our practice and the beginning of its evaluation lead us to believe that our way of working and model of professional practice – the ‘cycle’ of engagement and involvement – is effective in: addressing our vision of making health research relevant and inclusive for everyone; and embedding and joining up public involvement in a busy and fertile translational health research ecosystem.
Background Public involvement in clinical translational research is increasingly recognised as essential for relevant and reliable research. Public involvement must be diverse and inclusive to enable research that has the potential to reach those that stand to benefit from it the most, and thus address issues of health equity. Several recent reports, however, indicate that public involvement is exclusive, including in its interactions with ethnic groups. This paper outlines a novel community-led methodology – a community sandpit – to address the inclusion of ethnic groups in public involvement in research, reports on its evaluation, findings, legacy and impact. Methods Through detailed planning – thinking through and taking into account all stakeholders perspectives in the planning and design of the sandpit, relationship-building, co-design and co-delivery between the Public Programmes team based at Manchester University NHS Foundation Trust and the Greater Manchester Black and Minority Ethnic Network - the community sandpit was held in July 2018. Results Fifteen community organisations took part in the two-day event, as well as six researchers, and six creative practitioners. Six community-based partnership projects were seed-funded; four of these received additional funding from other sources also. Conclusions Evaluation of the sandpit showed the format to be well-received by all: it levelled power relationships between community organisations, health researchers and research infrastructure; it developed capacity amongst researchers about the accessibility, role and potential of community organisations. Described as “not another community seed fund” by community partners, the sandpit offered community partners, equitable avenues for collaboration within Greater Manchester translational research and led to the formation of the Black, Asian and Minority Ethnic Research Advisory Group (BRAG Vocal Website information, - https://www.wearevocal.org/opportunities/black-asian-and-minority-ethnic-research-advisory-group-brag/, 2021). The method has the potential to be replicated elsewhere to support inclusive public involvement in research and inclusive research.
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