The pathological and genomic impact of CTCF depletion in mammalian model systems

CCCTC-binding factor (CTCF) binds DNA, thereby helping to partition the mammalian genome into discrete structural and regulatory domains. In doing so, it insulates chromatin and fine-tunes gene activation, repression, and silencing. Complete removal of CTCF from mammalian cells causes catastrophic genomic dysregulation, most likely due to widespread collapse of 3D chromatin looping within the nucleus. In contrast, Ctcf hemizygous mice with lifelong reduction in CTCF expression are viable but have an increased incidence of spontaneous multi-lineage malignancies. In addition, CTCF is mutated in many human cancers and is thus implicated as a tumour suppressor gene. This study aimed to interrogate the genome-wide consequences of a reduced genomic concentration of Ctcf and its implications for carcinogenesis. In a genetically engineered mouse model, Ctcf hemizygous cells showed modest but robust changes in almost a thousand sites of genomic CTCF occupancy; these were enriched for lower affinity binding events with weaker evolutionary conservation across the mouse lineage. Furthermore, several hundred genes concentrated in cancer-related pathways were dysregulated due to changes in transcriptional regulation. Global chromatin structure was preserved but some loop interactions were destabilised, often around differentially expressed genes and their enhancers. Importantly, these transcriptional alterations were also seen in human cancers. These findings were then examined in a hepatocyte-specific mouse model of Ctcf hemizygosity with diethylnitrosamine-induced liver tumours. Ctcf hemizygous mice had a subtle liver-specific phenotype, although the overall tumour burden in Ctcf hemizygous and wild-type mice was the same. Using whole genome sequencing, the highly reproducible mutational signature caused by DEN exposure was characterised, revealing that Braf(V637E), orthologous to BRAF(V600E) in humans, was the predominant oncogenic driver in these liver tumours. Taken together, while Ctcf loss is partially physiologically compensated, chronic CTCF depletion dysregulates gene expression by subtly altering transcriptional regulation. This study also represents the first comprehensive genome-wide and histopathological characterisation of this commonly used liver cancer model.Wellcome Trust Programme for Clinicians Fellowship (106563/Z/14); EMBO|EuropaBio Fellowship (STF 7538); The Pathological Society of Great Britain & Ireland (SGS 2015/04/04); Cancer Research UK (core award 20412)

Who benefits and how? Public expectations of public benefits from data-intensive health research

The digitization of society and academic research endeavours have led to an explosion of interest in the potential uses of population data in research. Alongside this, increasing attention is focussing on the conditions necessary for maintaining a social license for research practices. Previous research has pointed to the importance of demonstrating “public benefits” from research for maintaining public support, yet there has been very little consideration of what the term “public benefits” means or what public expectations of “public benefits” are. In order to address this pressing issue a series of deliberative workshops with members of the public were held across Scotland in May and June 2017. The workshops aimed to engage a cross-section of the Scottish population in in-depth discussions of the ways that the public – or publics – might benefit from data-intensive health research. The findings reported here discuss workshop participants’ understandings and expectations of health research; who they considered to be “the public” that should benefit from health research and; in what ways they felt “the public” should benefit. Workshop participants’ preference was clearly for the widest possible public benefit to be felt by all, but they also acknowledged the value in research aiming to primarily benefit vulnerable groups within society. A key focus of discussions was the extent to which workshop participants were confident that potential public benefits would be realised. A crucial consideration then is the extent to which mechanisms and political support are in place to realise and maximise the public benefits of data-intensive health research

Public Preferences regarding Data Linkage for Health Research: A Discrete Choice Experiment

The potential for data collected in the public and private sector to be linked and used in research has led to increasing interest in public acceptability of data sharing and data linkage. The literature has identified a range of factors that are important for shaping public responses and in particular has noted that public support for research conducted through data linkage or data sharing is contingent on a number of conditions being met. In order to examine the relative importance of these conditions a Discrete Choice Experiment (DCE) was conducted via an online questionnaire among members of Ipsos MORI’s online panel in Scotland. The survey was completed by 1,004 respondents. Overall the two most influential factors shaping respondents’ preferences are: the type of data being linked; and, how profits are managed and shared. The type of data being linked is roughly twice as important as who the researchers are. There were slight differences across age groups and between genders and slight differences when comparing respondents with and without long term health conditions. The most notable differences between respondents were found when comparing respondents according to employment and working sector. This study provides much needed evidence regarding the relative importance of various conditions which may be essential for securing and sustaining public support for data-linkage in health research. This may be useful for indicating which factors to focus on in future public engagement and has important implications for the design and delivery of research and public engagement activities. The continuously evolving nature of the field means it will be necessary to revisit the key conditions for public support on an ongoing basis and to examine the contexts and circumstances in which these might change.

Moving from Trust to Trustworthiness: Experiences of public engagement in the Scottish Health Informatics Programme

The Scottish Health Informatics Programme (SHIP) was a Scotland-wide research programme exploring ways of collecting, managing and analysing electronic patient records for health research. As part of the SHIP public engagement work stream, a series of eight focus groups and a stakeholder workshop were conducted to explore perceptions of the role, relevance and functions of trust (or trustworthiness) in relation to research practices. The findings demonstrate that the public’s relationships of trust and/or mistrust in science and research are not straightforward. This paper aims to move beyond simple descriptions of whether publics trust researchers, or in whom members of the public place their trust, and to explore more fully the bases of public trust/mistrust in science, what trust implies and equally what it means for research/researchers to be trustworthy. This has important implications for public engagement in interdisciplinary projects

DNA lesion bypass and the stochastic dynamics of transcription coupled repair

DNA base damage is a major source of oncogenic mutations and disruption to gene expression. The stalling of RNA polymerase II (RNAP) at sites of DNA damage and the subsequent triggering of repair processes have major roles in shaping the genome-wide distribution of mutations, clearing barriers to transcription, and minimizing the production of miscoded gene products. Despite its importance for genetic integrity, key mechanistic features of this transcription-coupled repair (TCR) process are controversial or unknown. Here, we exploited a well-powered in vivo mammalian model system to explore the mechanistic properties and parameters of TCR for alkylation damage at fine spatial resolution and with discrimination of the damaged DNA strand. For rigorous interpretation, a generalizable mathematical model of DNA damage and TCR was developed. Fitting experimental data to the model and simulation revealed that RNA polymerases frequently bypass lesions without triggering repair, indicating that small alkylation adducts are unlikely to be an efficient barrier to gene expression. Following a burst of damage, the efficiency of transcription-coupled repair gradually decays through gene bodies with implications for the occurrence and accurate inference of driver mutations in cancer. The reinitation of transcription from the repair site is not a general feature of transcription-coupled repair, and the observed data is consistent with reinitiation never taking place. Collectively, these results reveal how the directional but stochastic activity of TCR shapes the distribution of mutations following DNA damage

Short report: Evaluation of wider community support for a neurodiversity teaching programme designed using participatory methods

Children with diagnoses such as autism, attention-deficit/hyperactivity disorder (ADHD), dyslexia and so on often experience bullying at school. This group can be described as neurodivergent, meaning they think and process information differently from most people. Previous research suggests that increasing people's knowledge can be an effective way to reduce stigma and bullying. Therefore, we decided to create a primary school resource to teach about neurodiversity - the concept that all humans vary in how our brains work. Working with educators, our research team - which included neurodivergent people - developed plans for a teaching programme called Learning About Neurodiversity at School (LEANS). Next, we wanted to know whether these plans, developed by our small neurodiverse team, would be endorsed by the wider community. To find out, we conducted an online feedback survey about our plans for the resource. We analysed feedback from 111 people who participated. Most of them identified as neurodivergent (70%) and reported being familiar with neurodiversity (98%), meaning they could provide an informed opinion on our plans. Over 90% of people expressed support for the planned programme content described in the survey, and 73% of them approved our intended definition of the resource's core concept, neurodiversity. From these results, we concluded that there was a high level of support for the planned LEANS programme content across those from the wider community who completed the survey. Consequently, we continued developing the LEANS programme in line with the initial plans from our neurodiverse team. The completed resource is now available as a free download

Cell-penetrating peptides, targeting the regulation of store-operated channels, slow decay of the progesterone-induced [Ca 2+ ] i signal in human sperm

© 2015 The Authors. Published by Oxford University Press. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1093/molehr/gav019Previous work has provided evidence for involvement of store-operated channels (SOCs) in [Ca(2+)]i signalling of human sperm, including a contribution to the transient [Ca(2+)]i elevation that occurs upon activation of CatSper, a sperm-specific cation channel localized to the flagellum, by progesterone. To further investigate the potential involvement of SOCs in the generation of [Ca(2+)]i signals in human sperm, we have used cell-penetrating peptides containing the important basic sequence KIKKK, part of the STIM-Orai activating region/CRAC activating domain (SOAR/CAD) of the regulatory protein stromal interaction molecule 1. SOAR/CAD plays a key role in controlling the opening of SOCs, which occurs upon mobilization of stored Ca(2+). Resting [Ca(2+)]i temporarily decreased upon application of KIKKK peptide (3-4 min), but scrambled KIKKK peptide had a similar effect, indicating that this action was not sequence-specific. However, in cells pretreated with KIKKK, the transient [Ca(2+)]i elevation induced by stimulation with progesterone decayed significantly more slowly than in parallel controls and in cells pretreated with scrambled KIKKK peptide. Examination of single-cell responses showed that this effect was due, at least in part, to an increase in the proportion of cells in which the initial transient was maintained for an extended period, lasting up to 10 min in a subpopulation of cells. We hypothesize that SOCs contribute to the progesterone-induced [Ca(2+)]i transient, and that interference with the regulatory mechanisms of SOC delays their closure, causing a prolongation of the [Ca(2+)]i transient.L.L. was supported by theWellcome Trust (Grant #086470). J.M. was supported by a University of Birmingham Teaching Assistantship. Funding to pay the Open Access publication charges for this article was provided by . .