Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits.

Genetic effects on functionally related 'omic' traits often co-occur in relevant cellular contexts, such as tissues. Motivated by the multi-tissue methylation quantitative trait loci (mQTLs) and expression QTLs (eQTLs) analysis, we propose X-ING (Cross-INtegrative Genomics) for cross-omics and cross-context integrative analysis. X-ING takes as input multiple matrices of association statistics, each obtained from different omics data types across multiple cellular contexts. It models the latent binary association status of each statistic, captures the major association patterns among omics data types and contexts, and outputs the posterior mean and probability for each input statistic. X-ING enables the integration of effects from different omics data with varying effect distributions. In the multi-tissue cis-association analysis, X-ING shows improved detection and replication of mQTLs by integrating eQTL maps. In the trans-association analysis, X-ING reveals an enrichment of trans-associations in many disease/trait-relevant tissues.

An integrative multi-context Mendelian randomization method for identifying risk genes across human tissues.

Mendelian randomization (MR) provides valuable assessments of the causal effect of exposure on outcome, yet the application of conventional MR methods for mapping risk genes encounters new challenges. One of the issues is the limited availability of expression quantitative trait loci (eQTLs) as instrumental variables (IVs), hampering the estimation of sparse causal effects. Additionally, the often context/tissue-specific eQTL effects challenge the MR assumption of consistent IV effects across eQTL and GWAS data. To address these challenges, we propose a multi-context multivariable integrative MR framework, mintMR, for mapping expression and molecular traits as joint exposures. It models the effects of molecular exposures across multiple tissues in each gene region, while simultaneously estimating across multiple gene regions. It uses eQTLs with consistent effects across more than one tissue type as IVs, improving IV consistency. A major innovation of mintMR involves employing multi-view learning methods to collectively model latent indicators of disease relevance across multiple tissues, molecular traits, and gene regions. The multi-view learning captures the major patterns of disease-relevance and uses these patterns to update the estimated tissue relevance probabilities. The proposed mintMR iterates between performing a multi-tissue MR for each gene region and joint learning the disease-relevant tissue probabilities across gene regions, improving the estimation of sparse effects across genes. We apply mintMR to evaluate the causal effects of gene expression and DNA methylation for 35 complex traits using multi-tissue QTLs as IVs. The proposed mintMR controls genome-wide inflation and offers new insights into disease mechanisms.

Social Vulnerability and Risk of Suicide in US Adults, 2016-2020.

Importance: There were over 45 000 suicides in the US in 2020, making suicide the 12th leading cause of death. If social vulnerability is associated with suicide rates, targeted interventions for at-risk segments of the population may reduce US suicide rates. Objective: To determine the association between social vulnerability and suicide in adults. Design, Setting, and Participants: This cohort study analyzed 2 county-level social vulnerability measures (the Social Vulnerability Index [SVI] and the Social Vulnerability Metric [SVM]) and US Centers for Disease Control and Prevention-reported county-level suicides from 2016 to 2020. Data were analyzed November and December 2022. Exposures: County-level variability in social vulnerability. Main Outcomes and Measures: The primary outcome measure was number of county-level adult suicides from 2016 to 2020, offset by county adult population during those years. The association between social vulnerability (measured using the SVI and the newly created SVM for 2018) and suicide was modeled using a bayesian-censored Poisson regression model to account for the CDC's suppression of county-level suicide counts of less than 10, adjusted for age, racial and ethnic minority, and urban-rural county characteristics. Results: From 2016 to 2020, there were a total of 222 018 suicides in 3141 counties. Comparing the least socially vulnerable (0% to 10%) to the most socially vulnerable (90% to 100%) counties, there was a 56% increase in suicide rate (17.3 per 100 000 persons to 27.0 per 100 000 persons) as measured by the SVI (incidence rate ratio, 1.56; 95% credible interval, 1.51-1.60) and an 82% increase in suicide rate (13.8 per 100 000 persons to 25.1 per 100 000 persons) as measured by the SVM (incidence rate ratio, 1.82; 95% credible interval, 1.72-1.92). Conclusions and Relevance: This cohort study found that social vulnerability had a direct association with risk for adult suicide. Reducing social vulnerability may lead to life-saving reduction in the rate of suicide.

DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits.

Studies of DNA methylation (DNAm) in solid human tissues are relatively scarce; tissue-specific characterization of DNAm is needed to understand its role in gene regulation and its relevance to complex traits. We generated array-based DNAm profiles for 987 human samples from the Genotype-Tissue Expression (GTEx) project, representing 9 tissue types and 424 subjects. We characterized methylome and transcriptome correlations (eQTMs), genetic regulation in cis (mQTLs and eQTLs) across tissues and e/mQTLs links to complex traits. We identified mQTLs for 286,152 CpG sites, many of which (>5%) show tissue specificity, and mQTL colocalizations with 2,254 distinct GWAS hits across 83 traits. For 91% of these loci, a candidate gene link was identified by integration of functional maps, including eQTMs, and/or eQTL colocalization, but only 33% of loci involved an eQTL and mQTL present in the same tissue type. With this DNAm-focused integrative analysis, we contribute to the understanding of molecular regulatory mechanisms in human tissues and their impact on complex traits.

Car/Motorbike Drivers' Willingness to Use and to Pay for Alcohol Interlock in Taiwan.

This study explored the important factors affecting drunk car/motorbike drivers' willingness to use and pay for alcohol interlocks. Data were obtained through a survey upon choice-based sampling conducted in central Taiwan. Questionnaires were distributed to the participants of drunk driving and road safety education courses from 17 August to 26 October 2020. All drunk drivers whose driver's licenses are revoked for drunk driving are mandated to participate in this course. Prior to the survey, the researchers explained the questionnaires, instructed the participants to complete the questionnaires, and then collected all the questionnaires. The socioeconomic characteristics of drunk drivers, awareness of alcohol interlocks and drunk driving, drinking patterns and health self-assessment before and after drunk driving ban enforcement, and changes in the number of trips were investigated. This study applied the double-hurdle model for data analysis to estimate the variables affecting drunk car/motorbike drivers. Results indicate that the respondents who were classified by the Alcohol Use Disorders Identification Test as high-risk drinkers before and after drunk driving ban enforcement were more willing to use alcohol interlocks and to pay higher prices. Additionally, the respondents with declined health self-assessments were also more willing to use alcohol interlocks and pay higher prices. This study suggests offering subsidies for alcohol interlocks to families with financial difficulties, in order to increase the alcohol interlock installation rate. Moreover, since the current duration of license suspension and withdrawal is considerably long, drunk drivers avoid using and installing alcohol interlocks by reducing the number of trips. In other words, the willingness to install alcohol interlocks may be increased by reducing the duration of license suspension and withdrawal.

Severe COVID-19 infection is associated with aberrant cytokine production by infected lung epithelial cells rather than by systemic immune dysfunction.

The mechanisms explaining progression to severe COVID-19 remain poorly understood. It has been proposed that immune system dysregulation/over-stimulation may be implicated, but it is not clear how such processes would lead to respiratory failure. We performed comprehensive multiparameter immune monitoring in a tightly controlled cohort of 128 COVID-19 patients, and used the ratio of oxygen saturation to fraction of inspired oxygen (SpO2 / FiO2) as a physiologic measure of disease severity. Machine learning algorithms integrating 139 parameters identified IL-6 and CCL2 as two factors predictive of severe disease, consistent with the therapeutic benefit observed with anti-IL6-R antibody treatment. However, transcripts encoding these cytokines were not detected among circulating immune cells. Rather, in situ analysis of lung specimens using RNAscope and immunofluorescent staining revealed that elevated IL-6 and CCL2 were dominantly produced by infected lung type II pneumocytes. Severe disease was not associated with higher viral load, deficient antibody responses, or dysfunctional T cell responses. These results refine our understanding of severe COVID-19 pathophysiology, indicating that aberrant cytokine production by infected lung epithelial cells is a major driver of immunopathology. We propose that these factors cause local immune regulation towards the benefit of the virus.

[Observation on therapeutic effect of catgut implantation at acupoints on exercise fatigue and study on the mechanism].

OBJECTIVE: To probe into the therapeutic effect of catgut implantation at acupoint on exercise fatigue and to study on the mechanism. METHODS: Catgut implantation was given at main points Guanyuan (CV 4), Shen shu (BL 23), Mingmen (GV 4), Zusanli (ST 36), Sanyinjiao (SP 6) in 41 players during training for 2 courses. Training-related condition and changes of blood testosterone (T) and hemoglobin (Hb) before and after training were observed. RESULTS: After treatment, sleeping quality, the mental state at the time of getting out of bed in the morning, appetite, training wish, training stamina, training quality, training attention, etc. in the player significantly improved, and blood T and Hb levels significantly increased. CONCLUSION: Catgut implantation at acupoints can significantly improve exercise fatigue in the player and the mechanism is possibly related with increase of testosterone and hemoglobin levels.