Convergence of coronary artery disease genes onto endothelial cell programs

Linking variants from genome-wide association studies (GWAS) to underlying mechanisms of disease remains a challenge1-3. For some diseases, a successful strategy has been to look for cases in which multiple GWAS loci contain genes that act in the same biological pathway1-6. However, our knowledge of which genes act in which pathways is incomplete, particularly for cell-type-specific pathways or understudied genes. Here we introduce a method to connect GWAS variants to functions. This method links variants to genes using epigenomics data, links genes to pathways de novo using Perturb-seq and integrates these data to identify convergence of GWAS loci onto pathways. We apply this approach to study the role of endothelial cells in genetic risk for coronary artery disease (CAD), and discover 43 CAD GWAS signals that converge on the cerebral cavernous malformation (CCM) signalling pathway. Two regulators of this pathway, CCM2 and TLNRD1, are each linked to a CAD risk variant, regulate other CAD risk genes and affect atheroprotective processes in endothelial cells. These results suggest a model whereby CAD risk is driven in part by the convergence of causal genes onto a particular transcriptional pathway in endothelial cells. They highlight shared genes between common and rare vascular diseases (CAD and CCM), and identify TLNRD1 as a new, previously uncharacterized member of the CCM signalling pathway. This approach will be widely useful for linking variants to functions for other common polygenic diseases.

Variant Polycomb complexes in Drosophila consistent with ancient functional diversity

Polycomb group (PcG) mutants were first identified in Drosophila on the basis of their failure to maintain proper Hox gene repression during development. The proteins encoded by the corresponding fly genes mainly assemble into one of two discrete Polycomb repressive complexes: PRC1 or PRC2. However, biochemical analyses in mammals have revealed alternative forms of PRC2 and multiple distinct types of noncanonical or variant PRC1. Through a series of proteomic analyses, we identify analogous PRC2 and variant PRC1 complexes in Drosophila, as well as a broader repertoire of interactions implicated in early development. Our data provide strong support for the ancient diversity of PcG complexes and a framework for future analysis in a longstanding and versatile genetic system.

Identifying individuals with multiple non-communicable disease risk factors in Kenya: a latent class analysis

OBJECTIVES

Non-communicable diseases (NCDs) are the leading causes of death globally. In Kenya, the number of deaths resulting from NCDs is projected to surpass malaria and tuberculosis by 2030. Studies in Kenya show increasing NCDs; the aim of the present study is to examine the clustering of NCDs and risk factors in Kenya.

STUDY DESIGN

This is a cross-sectional study using data from the 2015 Kenya STEPwise Survey.

METHODS

This study examined relationships between NCDs (e.g. obesity, hypertension and diabetes) and health behaviours (e.g. sedentary activity, and fruit and vegetable consumption). Survey probability weights, which estimated the sampling design effect, were applied to consider the sampling units, and stratifications were used during sampling so that the results could be generalisable to the national adult Kenyan population. In total, 4350 adults were included in the study sample.

RESULTS

Overall, 24.43% of participants were classified as having hypertension, 1.88% as having type 2 diabetes, and 27.94% were classified as being overweight or obese. The best-fit model was a four-class solution. Class 1 is best described as 'young with high NCD risk' and had the highest sedentary activity. Class 2 is best described as 'poor rural with lower NCD risk' with a high chance of smoking and alcohol consumption. Class 3 is best described as 'rural with high NCD risk' and had the highest fruit and vegetable consumption. Class 4 is best described as 'wealthy young urban dwellers with high NCD risk' with a high chance of alcohol consumption and smoking. Individuals in Class 4 had the highest chance (40%) of being overweight/obese, a 2% chance of type 2 diabetes and a 23% chance of having hypertension.

CONCLUSIONS

NCDs are clustered in groups with high-risk behaviours. The group with the highest chance of having NCDs also had the highest chance of engaging in high-risk behaviours. The findings of this study suggest that smoking and alcohol consumption increase NCD risk in rural areas. Tailored and targeted interventions are needed to curb the increasing NCD prevalence in Kenya.

Binge drinking, HIV/HPV co-infection risk, and HIV testing: Factors associated with HPV vaccination among young adults in the United States

Human papillomavirus (HPV) is a common sexually transmitted infection. Binge drinkers often engage in HIV/HPV co-infection high-risk behaviors. We examined the association between binge drinking, HIV/HPV co-infection risk, HIV testing and HPV vaccination among young adults. Data from the 2017 Behavioral Risk Factor Surveillance System survey were examined. Participants (N = 430/450,016; 0.11%) were HPV vaccine-eligible young adults ages 18-26 years. Multivariable logistic regression examined the association between binge drinking in the past 30 days, HIV/HPV co-infection high-risk risk behaviors, HIV testing, and HPV vaccination (initiated/completed, unvaccinated) among young adults. Respondents were primarily cisgender (99.8%), non-Hispanic White (41.4%), employed (46.2%) or student (35.4%), and insured (68.2%). Most did not binge drink (55.2%). The majority did not engage in HIV/HPV co-infection high-risk risk behaviors (78.2%). More than one-half had never been tested for HIV (59%) nor vaccinated against HPV (60.6%). Although binge drinkers (44.8%) were significantly more likely to engage in HIV/HPV co-infection high-risk behaviors (OR = 2.1; 95% CI: 1.0-4.5), binge drinking was not positively associated with HIV testing (OR = 0.98; 95% CI: 0.63-1.53). After adjusting for demographics and HIV/HPV co-infection high-risk behaviors, one (aOR = 2.71; 95% CI: 1.11-6.65) and two episodes (aOR = 3.05; 95% CI: 1.26-7.41) of binge drinking in the past 30 days were significantly associated with HPV vaccination uptake. Positive associations between HPV vaccination and participants having an HIV test in 2017 (aOR = 3.86; 95% CI: 1.42-10.55) and before 2017 (aOR = 2.62; 95% CI: 1.23-5.56) were also statistically significant. Because young adult binge drinkers are more likely to engage in HIV/HPV co-infection high-risk behaviors, promoting HPV vaccination and HIV testing are important public health objectives.

Covariates of alcohol consumption among career firefighters

BACKGROUND

Little is known about rates of alcohol consumption in career firefighters.

AIMS

To assess the quantity and frequency of alcohol consumption among career firefighters and the covariates that influence consumption levels.

METHODS

A convenience sample of career firefighters completed an online, self-administered, health assessment survey. Hierarchical binary logistic regression assessed the ability of several covariates to predict binge drinking status.

RESULTS

The majority of the sample (n = 160) consumed alcohol (89%), with approximately one-third (34%) having a drinking binge in the past 30 days. The regression model explained 13-18% of the variance in binge drinking status and correctly classified 71% of cases. Race (P < 0.05) and time of service (P < 0.01) were the only covariates that made a statistically significant contribution to the model. After controlling for other factors in the model, white respondents were ~4.5 times more likely to binge drink than non-white respondents (95% CI: 1.15-17.4). For each additional year of service, firefighters were 1.08 times less likely to binge drink (95% CI: 0.87-0.97).

CONCLUSIONS

Drinking levels observed in this study exceed those of the general adult population, including college students. Thus, it appears that firefighters represent an at-risk drinking group. Further investigations addressing reasons for alcohol use and abuse among firefighters are warranted. This study and subsequent research will provide information necessary for the development and testing of tailored interventions aimed at reducing firefighter alcohol consumption.

Recent origin of Plasmodium falciparum from a single progenitor

Genetic variability of Plasmodium falciparum underlies its transmission success and thwarts efforts to control disease caused by this parasite. Genetic variation in antigenic, drug resistance, and pathogenesis determinants is abundant, consistent with an ancient origin of P. falciparum, whereas DNA variation at silent (synonymous) sites in coding sequences appears virtually absent, consistent with a recent origin of the parasite. To resolve this paradox, we analyzed introns and demonstrated that these are deficient in single-nucleotide polymorphisms, as are synonymous sites in coding regions. These data establish the recent origin of P. falciparum and further provide an explanation for the abundant diversity observed in antigen and other selected genes.

The 10q25 neocentromere and its inactive progenitor have identical primary nucleotide sequence: further evidence for epigenetic modification

We have previously localized the core centromere protein-binding domain of a 10q25.2-derived neocentromere to an 80-kb genomic region. Detailed analysis has indicated that the 80-kb neocentromere (NC) DNA has a similar overall organization to the corresponding region on a normal chromosome 10 (HC) DNA, derived from a genetically unrelated CEPH individual. Here we report sequencing of the HC DNA and its comparison to the NC sequence. Single-base differences were observed at a maximum rate of 4.6 per kb; however, no deletions, insertions, or other structural rearrangements were detected. To investigate whether the observed changes, or subsets of these, might be de novo mutations involved in neocentromerization (i.e., in committing a region of a chromosome to neocentromere formation), the progenitor DNA (PnC) from which the NC DNA descended, was cloned and sequenced. Direct comparison of the PnC and NC sequences revealed 100% identity, suggesting that the differences between NC and HC DNA are single nucleotide polymorphisms (SNPs) and that formation of the 10q25.2 NC did not involve a change in DNA sequence in the core centromere protein-binding NC region. This is the first study in which a cloned NC DNA has been compared directly with its inactive progenitor DNA at the primary sequence level. The results form the basis for future sequence comparison outside the core protein-binding domain, and provide direct support for the involvement of an epigenetic mechanism in neocentromerization.

Sequence analysis of an 80 kb human neocentromere

We previously described the cloning of an 80 kb DNA corresponding to the core protein-binding domain of a human chromosome 10-derived neocentromere. Here we report the complete sequence of this DNA (designated NC DNA) and its detailed structural analysis. The sequence is devoid of human centromeric alpha-satellite DNA and the pericentric beta- and gamma-satellites, the ATRS and 48 bp repeat DNA. One copy of a sequence that is related to the CENPB box motif is present, and a number of copies of other pericentric sequences including pJalpha and classical satellites I and III are present but both their relative sparsity and non-tandem organization suggest that each sequence, on its own, is unlikely to mimic any role the sequence may have in the normal centromere. The DNA-binding motifs of the architectural and regulatory proteins HMGI and topoII have a normal abundance and random distribution, implying that these sequences are not key functional elements. The total A + T content of the sequence is not notably different from that of the human genome, but an abundance of AT-rich islands and a biased distribution of these islands within the NC sequence are clearlydiscernible and may be functionally significant. Substantial amounts of transposable elements and low copy number tandem repeats, including several that are highly AT- and purine-rich, are also present and may act as functional elements. One of the AT-rich tandemrepeats (AT28) may form interesting structures and is described in detail. The defined features show only a loose resemblance to the structures of known centromeres, highlighting the possibility that, rather than a conserved primary sequence, it is the overallcomposition and distribution patterns of various unknown functional elements, or any 'ordinary' DNA under appropriate epigenetic influences, that determine centromere formation and function. This is the firstdetailed analysis of a neocentromere DNA and provides a basis for comparison against future sequences.

Direct cloning of human 10q25 neocentromere DNA using transformation-associated recombination (TAR) in yeast

The transformation-associated recombination (TAR) procedure allows rapid, site-directed cloning of specific human chromosomal regions as yeast artificial chromosomes (YACs). The procedure requires knowledge of only a single, relatively small genomic sequence that resides adjacent to the chromosomal region of interest. We applied this approach to the cloning of the neocentromere DNA of a marker chromosome that we have previously shown to have originated through the activation of a latent centromere at human chromosome 10q25. Using a unique 1.4-kb DNA fragment as a "hook" in TAR experiments, we achieved single-step isolation of the critical neocentromere DNA region as two stable, 110- and 80-kb circular YACs. For obtaining large quantities of highly purified DNA, these YACs were retrofitted with the yeast-bacteria-mammalian-cells shuttle vector BRV1, electroporated into Escherichia coli DH10B, and isolated as bacterial artificial chromosomes (BACs). Extensive characterization of these YACs and BACs by PCR and restriction analyses revealed that they are identical to the corresponding regions of the normal chromosome 10 and provided further support for the formation of the neocentromere within the marker chromosome through epigenetic activation.

A functional neo-centromere formed through activation of a latent human centromere and consisting of non-alpha-satellite DNA

We recently described a human marker chromosome containing a functional neo-centromere that binds anti-centromere antibodies, but is devoid of centromeric alpha-satellite repeats and derived from a hitherto non-centromeric region of chromosome 10q25. Chromosome walking using cloned single-copy DNA from this region enabled us to identify the antibody-binding domain of this centromere. Extensive restriction mapping indicates that this domain has an identical genomic organization to the corresponding normal chromosomal region, suggesting a mechanism for the origin of this centromere through the activation of a latent centromere that exists within 10q25.

Cleaning of anaesthesia breathing circuits and tubings: a Canadian survey

A cross-Canada survey of 38 university-affiliated hospitals with over 250 beds was undertaken to examine the procedures for cleaning anaesthetic tubings and circuits. Twenty-eight (74 per cent) hospitals responded. Gluteraldehyde was the most commonly used method (13/28), and pasteurization was the second most used method (9/28). These two methods are described and recommendations are made for basic requirements for disinfection.