Homogeneity and Heterogeneity as Situational Properties: Producing – and Moving Beyond? – Race in Post-Genomic Science

In this article, we explore current thinking and practices around the logics of difference in gene–environment interaction research in the post-genomic era. We find that scientists conducting gene–environment interaction research continue to invoke well-worn notions of racial difference and diversity, but use them strategically to try to examine other kinds of etiologically significant differences among populations. Scientists do this by seeing populations not as inherently homogeneous or heterogeneous, but rather by actively working to produce homogeneity along some dimensions and heterogeneity along others in their study populations. Thus we argue that homogeneity and heterogeneity are situational properties – properties that scientists seek to achieve in their study populations, the available data, and other aspects of the research situation they are confronting, and then leverage to advance post-genomic science. Pointing to the situatedness of homogeneity and heterogeneity in gene–environment interaction research underscores the work that these properties do and the contingencies that shape decisions about research procedures. Through a focus on the situational production of homogeneity and heterogeneity more broadly, we find that gene–environment interaction research attempts to shift the logic of difference from solely racial terms as explanatory ends unto themselves, to racial and other dimensions of difference that may be important clues to the causes of complex diseases

Research priorities in children and adults with congenital heart disease: a James Lind Alliance Priority Setting Partnership

Objective To bring together patients, parents, charities and clinicians in a Priority Setting Partnership to establish national clinical priorities for research in children and adults with congenital heart disease. Methods The established James Lind Alliance methodology was used to identify and prioritise research on the management of congenital heart disease, focusing on diagnosis, treatment and outcomes. An initial open survey was used to gather potential uncertainties which were filtered, categorised, converted into summary questions and checked against current evidence. In a second survey, respondents identified the unanswered questions most important to them. At two final workshops, patients, parents, charities and healthcare professionals agreed the top 10 lists of priorities for child/antenatal and adult congenital heart disease research. Results 524 respondents submitted 1373 individual questions, from which 313 out of scope or duplicate questions were removed. The remaining 1060 questions were distilled into summary questions and checked against existing literature, with only three questions deemed entirely answered and removed. 250 respondents completed the child/antenatal survey (56 uncertainties) and 252 completed the adult survey (47 uncertainties). The questions ranked the highest by clinicians and non-clinicians were taken forward to consensus workshops, where two sets of top 10 research priorities were agreed. Conclusions Through an established and equitable process, we determined national clinical priorities for congenital heart disease research. These will be taken forward by specific working groups, a national patient and public involvement group, and through the establishment of a UK and Ireland network for collaborative, multicentre clinical trials in congenital heart disease

Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting

Objectives: Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi. Methods: Ninety-four E. coli isolates from patients admitted to Queen’s Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics. Results: Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was blaCTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates]. Conclusions: This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance

Functional cardiac fibroblasts derived from human pluripotent stem cells via second heart field progenitors

Cardiac fibroblasts (CFs) play critical roles in heart development, homeostasis, and disease. The limited availability of human CFs from native heart impedes investigations of CF biology and their role in disease. Human pluripotent stem cells (hPSCs) provide a highly renewable and genetically defined cell source, but efficient methods to generate CFs from hPSCs have not been described. Here, we show differentiation of hPSCs using sequential modulation of Wnt and FGF signaling to generate second heart field progenitors that efficiently give rise to hPSC-CFs. The hPSC-CFs resemble native heart CFs in cell morphology, proliferation, gene expression, fibroblast marker expression, production of extracellular matrix and myofibroblast transformation induced by TGFβ1 and angiotensin II. Furthermore, hPSC-CFs exhibit a more embryonic phenotype when compared to fetal and adult primary human CFs. Co-culture of hPSC-CFs with hPSC-derived cardiomyocytes distinctly alters the electrophysiological properties of the cardiomyocytes compared to co-culture with dermal fibroblasts. The hPSC-CFs provide a powerful cell source for research, drug discovery, precision medicine, and therapeutic applications in cardiac regeneration.J.L.C. received funding from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior and Fundação de Amparo à Pesquisa do Distrito Federal. The work was funded by NIH R01 HL129798 (T.J.K.); NIH U01 HL134764 (T.J.K.); S10RR025644 (T.J.K.); and the UW Institute for Clinical and Translational Research, grant UL1TR000427, from the Clinical and Translational Science Award of the NCATS/NIH.S

Improving the use of research evidence in guideline development: 12. Incorporating considerations of equity

BACKGROUND: The World Health Organization (WHO), like many other organisations around the world, has recognised the need to use more rigorous processes to ensure that health care recommendations are informed by the best available research evidence. This is the 12(th )of a series of 16 reviews that have been prepared as background for advice from the WHO Advisory Committee on Health Research to WHO on how to achieve this. OBJECTIVES: We reviewed the literature on incorporating considerations of equity in guidelines and recommendations. METHODS: We searched PubMed and three databases of methodological studies for existing systematic reviews and relevant methodological research. We did not conduct systematic reviews ourselves. Our conclusions are based on the available evidence, consideration of what WHO and other organisations are doing and logical arguments. KEY QUESTIONS AND ANSWERS: We found few directly relevant empirical methodological studies. These answers are based largely on logical arguments. When and how should inequities be addressed in systematic reviews that are used as background documents for recommendations? • The following question should routinely be considered: Are there plausible reasons for anticipating differential relative effects across disadvantaged and advantaged populations? • If there are plausible reasons for anticipating differential effects, additional evidence should be included in a review to inform judgments about the likelihood of differential effects. What questions about equity should routinely be addressed by those making recommendations on behalf of WHO? • The following additional questions should routinely be considered: • How likely is it that the results of available research are applicable to disadvantaged populations and settings? • How likely are differences in baseline risk that would result in differential absolute effects across disadvantaged and advantaged populations? • How likely is it that there are important differences in trade-offs between the expected benefits and harms across disadvantaged and advantaged populations? • Are there different implications for disadvantaged and advantaged populations, or implications for addressing inequities? What context specific information is needed to inform adaptation and decision making in a specific setting with regard to impacts on equity? • Those making recommendations on behalf of WHO should routinely consider and offer advice about the importance of the following types of context specific data that might be needed to inform adaptation and decision making in a specific setting: • Effect modifiers for disadvantaged populations and for the likelihood of differential effects • Baseline risk in relationship to social and economic status • Utilization and access to care in relationship to social and economic status • Costs in relationship to social and economic status • Ethics and laws that may impact on strategies for addressing inequities • Availability of resources to address inequities What implementation strategies are likely be needed to ensure that recommendations are implemented equitably? • Organisational changes are likely to be important to address inequities. While it may only be possible to consider these in relationship to specific settings, consideration should be given to how best to provide support for identifying and addressing needs for organisational changes. In countries with pervasive inequities institutional, cultural and political changes may first be needed. • Appropriate indicators of social and economic status should be used to monitor the effects of implementing recommendations on disadvantaged populations and on changes in social and economic status

Epidemiologic and Genomic Reidentification of Yaws, Liberia

We confirmed endemicity and autochthonous transmission of yaws in Liberia after a population-based, community-led burden estimation (56,825 participants). Serologically confirmed yaws was rare and focal at population level (24 cases; 2.6 [95% CI 1.4-3.9] cases/10,000 population) with similar clinical epidemiology to other endemic countries in West Africa. Unsupervised classification of spatially referenced case finding data indicated that yaws was more likely to occur in hard-to-reach communities; healthcare-seeking was low among communities, and clinical awareness of yaws was low among healthcare workers. We recovered whole bacterial genomes from 12 cases and describe a monophyletic clade of Treponema pallidum subspecies pertenue, phylogenetically distinct from known TPE lineages, including those affecting neighboring nonhuman primate populations (Taï Forest, Côte d'Ivoire). Yaws is endemic in Liberia but exhibits low focal population prevalence with evidence of a historical genetic bottleneck and subsequent local expansion. Reporting gaps appear attributable to challenging epidemiology and low disease awareness

'They never pass me the ball’: exposing ableism through the leisure experiences of disabled children, young people and their families.

In this paper, we explore the participation of disabled children, young people and their families in leisure activities. Drawing on the accounts of disabled children, young people and their parents and carers, we reflect on the leisure spaces that they access and record some of their experiences within them. Using the concept of ‘ableism’ (Campbell 2009) we interrogate the data gathered as part a two-year project funded by the Economic and Social Research Council (RES – 062-23-1138) (http//www.rihsc.mmu.ac.uk/postblairproject/):‘Does every child matter, Post-Blair: the interconnections of disabled childhoods'. By doing so we identify some of the inherent and embedded discriminations in favour of those children and young people who are perceived to be ‘able’ that simultaneously work to exclude the young 'kinds of people' (Hacking 2007), categorised as 'disabled', and their families from leisure facilities and opportunities. We suggest that currently, disabled families and children occupy a mix of ‘mainstream', ‘segregated’ and ‘separate’ leisure spaces. We discuss the impact of occupying these spaces and ask: What do the experiences of accessing leisure by disabled children, young people and their families reveal about the processes and practices of ableism? To what extent are children and families required to 'pass'as'normal enough' to gain access to leisure spaces? To what extent are ‘segregated’ leisure opportunities regulated and produced by a kind of ‘diagnostic apartheid’ (Campbell 2008a: 155)? What is the role and value of 'separate' leisure activities? </p

hMMS2 serves a redundant role in human PCNA polyubiquitination

<p>Abstract</p> <p>Background</p> <p>In yeast, DNA damage leads to the mono and polyubiquitination of the sliding clamp PCNA. Monoubiquitination of PCNA is controlled by RAD18 (E3 ligase) and RAD6 (E2 conjugating enzyme), while the extension of the monoubiquitinated PCNA into a polyubiquitinated substrate is governed by RAD5, and the heterodimer of UBC13/MMS2. Each modification directs a different branch of the DNA damage tolerance pathway (DDT). While PCNA monoubiquitination leads to error-prone bypass via TLS, biochemical studies have identified MMS2 along with its heteromeric partner UBC13 to govern the error-free repair of DNA lesions by catalyzing the formation of lysine 63-linked polyubiquitin chains (K63-polyUb). Recently, it was shown that PCNA polyubiquitination is conserved in human cells and that this modification is dependent on RAD18, UBC13 and SHPRH. However, the role of hMMS2 in this process was not specifically addressed.</p> <p>Results</p> <p>In this report we show that mammalian cells in which MMS2 was reduced by siRNA-mediated knockdown maintains PCNA polyubiquitination while a knockdown of RAD18 or UBC13 abrogates PCNA ubiquitination. Moreover, the additional knockdown of a UEV1A (MMS2 homolog) does not deplete PCNA polyubiquitination. Finally, mouse embryonic stem cells null for MMS2 with or without the additional depletion of mUEV1A continue to polyubiquitinated PCNA with normal kinetics.</p> <p>Conclusion</p> <p>Our results point to a high level of redundancy in the DDT pathway and suggest the existence of another hMMS2 variant (hMMSv) or complex that can compensate for its loss.</p

Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis

Genome-wide association studies (GWAS) conducted using commercial single nucleotide polymorphisms (SNP) arrays have proven to be a powerful tool for the detection of common disease susceptibility variants. However, their utility for the detection of lower frequency variants is yet to be practically investigated. Here we describe the application of a rare variant collapsing method to a large genome-wide SNP dataset, the Wellcome Trust Case Control Consortium rheumatoid arthritis (RA) GWAS. We partitioned the data into gene-centric bins and collapsed genotypes of low frequency variants (defined here as MAF ≤0.05) into a single count coupled with univariate analysis. We then prioritised gene regions for further investigation in an independent cohort of 3,355 cases and 2,427 controls based on rare variant signal p value and prior evidence to support involvement in RA. A total of 14,536 gene bins were investigated in the primary analysis and signals mapping to the TNFAIP3 and chr17q24 loci were selected for further investigation. We detected replicating association to low frequency variants in the TNFAIP3 gene (combined p = 6.6 × 10−6). Even though rare variants are not well-represented and can be difficult to genotype in GWAS, our study supports the application of low frequency variant collapsing methods to genome-wide SNP datasets as a means of exploiting data that are routinely ignored