Discovery and Mediation Analysis of Cross-Phenotype Associations Between Asthma and Body Mass Index in 12q13.2.

Twin studies suggest that shared genetics contributes to the comorbidity of asthma and obesity, but candidate-gene studies provide limited evidence of pleiotropy. We conducted genome-wide association analyses of asthma and body mass index (BMI; weight (kg)/height (m)2)) among 305,945 White British subjects recruited into the UK Biobank in 2006-2010. We searched for overlapping signals and conducted mediation analyses on genome-wide-significant cross-phenotype associations, assessing moderation by sex and age at asthma diagnosis, and adjusting for confounders of the asthma-BMI relationship. We identified a genome-wide-significant cross-phenotype association at rs705708 (asthma odds ratio = 1.05, 95% confidence interval: 1.03, 1.07; P = 7.20 × 10-9; and BMI ß = -0.065, 95% confidence interval: -0.087, -0.042; P = 1.30 × 10-8). rs705708 resides on 12q13.2, which harbors 9 other asthma- and BMI-associated variants (all P < 5 × 10-5 for asthma; all but one P < 5 × 10-5 for BMI). Follow-up analyses of rs705708 show that most of the BMI association occurred independently of asthma, with consistent magnitude between men and women and persons with and without asthma, irrespective of age at diagnosis; the asthma association was stronger for childhood versus adult asthma; and both associations remained after confounder adjustment. This suggests that 12q13.2 displays pleiotropy for asthma and BMI. Upon further characterization, 12q13.2 might provide a target for interventions that simultaneously prevent or treat asthma and obesity.

Examining the effect of obesity-associated gene variants on breast cancer survivors in a randomized weight loss intervention.

PURPOSE: Our study examined whether common variants of obesity-associated genes FTO, MC4R, BDNF, and CREB1 moderated the effects of a lifestyle intervention on weight change among breast cancer survivors. METHODS: 151 breast cancer survivors with a body mass index ≥ 25 kg/m2 were randomly assigned to a 6-month weight loss intervention or usual care group. Genotyping of FTO rs9939609, MC4R rs6567160, BDNF rs11030104, CREB1 rs17203016 was performed. Linear mixed models were used including the main effects of genotype (assuming a dominant genetic model), treatment arm on weight and percent body fat changes, and genotype by treatment interaction variable. All statistical tests were evaluated against a Bonferroni-corrected alpha of 0.0125. RESULTS: Women in the intervention group achieved significantly greater weight loss than the usual care group (5.9% vs 0.4%, p < 0.001), regardless of genotype. Changes in weight and percent body fat did not differ significantly between carriers of the FTO rs9939609, MC4R rs6567160, BDNF rs11030104, and CREB1 rs17203016 risk alleles compared to non-carriers (p-interaction > 0.0125 for each single-nucleotide polymorphisms). CONCLUSIONS: Women who are genetically predisposed to obesity and recently diagnosed with breast cancer may achieve significant and clinically meaningful weight loss through healthy eating and exercise. CLINICAL TRIAL REGISTRATION: NCT02863887 (Date of Registration: August 11, 2016); NCT02110641 (Date of Registration: April 10, 2014).

Risks of preterm birth among non-Hispanic black and non-Hispanic white women: Effect modification by maternal age.

BACKGROUND: Preterm birth (PTB) disproportionately affects African American compared with Caucasian women, although reasons for this disparity remain unclear. Some suggest that a differential effect of maternal age by race/ethnicity, especially at older maternal ages, may explain disparities. OBJECTIVE: To determine whether the relationship between maternal age and preterm birth varies by race/ethnicity among primiparae non-Hispanic blacks (NHB) and non-Hispanic whites (NHW). METHODS: A cross-sectional study of 367 081 singleton liveborn first births to NHB and NHW women in California from 2008 to 2012 was conducted. Rate ratios (RR) were estimated for PTB and its subtypes-spontaneous and clinician-initiated-after adjusting for confounders through Poisson regression. Universal age/race reference groups (NHW, 25-29 years) and race-specific reference groups (NHW or NHB, 25-29 years) were used for comparisons. RESULTS: Among all women, RR of PTB was highest at the extremes of age (<15 and ≥40 years). Among NHBs, the risk of PTB was higher than among NHWs at all maternal ages (adjusted RR of PTB 1.38-2.93 vs 0.98-2.38). However, using race-specific reference groups, the risk of PTB for NHB women (RR 0.91-1.88) vs NHW women (RR 0.98-2.39) was nearly identical at all maternal ages, with overlapping confidence intervals. Analyses did not demonstrate substantial divergence of risk with advancing maternal age. PTB, spontaneous PTB, and clinician-initiated PTB demonstrated similar risk patterns at younger but not older maternal ages, where risk of clinician-initiated PTB increased sharply for all women. CONCLUSIONS: Primiparae NHBs demonstrated increased risk of PTB, spontaneous PTB, and clinician-initiated PTB compared with NHWs at all maternal ages. However, RRs using race-specific reference groups converged across maternal ages, indicating a similar independent effect of maternal age on PTB by race/ethnicity. A differential effect of maternal age does not appear to explain disparities in preterm birth by race/ethnicity.

Statistical Analysis of Multiple Phenotypes in Genetic Epidemiologic Studies: From Cross-Phenotype Associations to Pleiotropy.

In the context of genetics, pleiotropy refers to the phenomenon in which a single genetic locus affects more than 1 trait or disease. Genetic epidemiologic studies have identified loci associated with multiple phenotypes, and these cross-phenotype associations are often incorrectly interpreted as examples of pleiotropy. Pleiotropy is only one possible explanation for cross-phenotype associations. Cross-phenotype associations may also arise due to issues related to study design, confounder bias, or nongenetic causal links between the phenotypes under analysis. Therefore, it is necessary to dissect cross-phenotype associations carefully to uncover true pleiotropic loci. In this review, we describe statistical methods that can be used to identify robust statistical evidence of pleiotropy. First, we provide an overview of univariate and multivariate methods for discovery of cross-phenotype associations and highlight important considerations for choosing among available methods. Then, we describe how to dissect cross-phenotype associations by using mediation analysis. Pleiotropic loci provide insights into the mechanistic underpinnings of disease comorbidity, and they may serve as novel targets for interventions that simultaneously treat multiple diseases. Discerning between different types of cross-phenotype associations is necessary to realize the public health potential of pleiotropic loci.

Multiethnic genome-wide association study identifies ethnic-specific associations with body mass index in Hispanics and African Americans.

BACKGROUND: Genome-wide association studies of obesity have typically assumed fixed genetic effects across ethnicities, rarely attempting to thoroughly compare and contrast findings across various ethnic groups. Therefore, our study aimed to identify novel genetic associations with body mass index (BMI), a common measure of obesity, and explore their cross-ethnic generalizability in a multiethnic population. To that end, we conducted â€‹ethnic-specific genome-wide association analyses among 1235 Hispanic, 706 Asian, 1549 African American, and 2395 European American subjects from the Multi-ethnic Study of Atherosclerosis (MESA). We compared findings â€‹across ethnicities and investigated single-nucleotide polymorphisms (SNPs) with suggestive BMI-association p-values among 3379 Hispanic and 6871 African American subjects from the Women's Health Initiative (WHI). RESULTS: We identified a genome-wide significant association in MESA Hispanics-rs12253976 in KLF6 (beta = 5.792 kg/m(2) per-allele, 95 % confidence interval (CI): 3.885, 7.698; p = 3.43 × 10(-9))-and suggestive SNPs with p < 5 × 10(-6) in MESA Hispanics, European Americans and African Americans that display ethnic-specific effects on BMI. Of these suggestive SNPs, Hispanic SNP rs12255372 and African American SNP rs6435678 had the most evidence of replication in WHI. rs12255372 (in TCF7L2) was associated with lower BMI in both MESA (beta = -1.111 kg/m(2), 95 % CI: -1.578, -0.645; p = 3.33 × 10(-6)) and WHI Hispanics (beta = -0.304 kg/m(2), 95 % CI: -0.613, 0.006; p = 0.054). This TCF7L2 intronic region contains several SNPs (rs7901695, rs4506565, rs4132670, and rs12243326) with low p-values (p < 10(-3)) in MESA and betas of similar magnitude and direction in MESA and WHI, but only rs12243326 is in strong linkage disequilibrium with rs12255372 in our Hispanic populations, suggesting independent signals in this region. rs6435678 (in ERBB4) was associated with greater BMI in both MESA (beta = 1.104 kg/m(2), 95 % CI: 0.643, 1.564; p = 2.85 × 10(-6)) and WHI African Americans (beta = 0.219 kg/m(2), 95 % CI: -0.021, 0.460; p = 0.074). CONCLUSIONS: Two BMI-association signals are present in the TCF7L2 intronic region of Hispanics, one of which is tagged by rs12255372. ERBB4 rs6435678 is a novel BMI-association signal in African Americans. Overall, our data suggest that ethnic-specific associations are involved in the genetic determination of BMI. Ethnic-specificity has potential implications for the development of gene-based therapies for obesity.

Gene-based analysis identified the gene ZNF248 is associated with late-onset asthma in African Americans.

BACKGROUND: Late-onset asthma (LOA) has distinct characteristics and its pathogenesis might rely on unique pathways. Although current studies are focused primarily on childhood asthma, more research is needed to show the mechanisms underlying LOA. OBJECTIVE: To conduct genomewide association analysis and gene-based analysis to identify single-nucleotide polymorphisms and genes associated with LOA. METHODS: The Women's Health Initiative (WHI) observational cohort and the Multi-Ethnic Study of Atherosclerosis (MESA) were used to identify subjects with LOA. The association between LOA and body mass index and smoking was evaluated. In the discovery stage of the genetic analysis, 1,218 African American subjects from WHI with genotype data (271 cases and 947 controls) were used for single-nucleotide polymorphism and gene-based association analyses. Significant or suggestive results were subsequently investigated in an independent African American population from MESA (38 cases and 806 controls). RESULTS: In WHI, the relative odds for LOA in obese vs normal-weight subjects was 2.55 (95% confidence interval 1.74-3.76). Ever smokers also had greater odds for LOA compared with never smokers (odds ratio 1.59, 95% confidence interval 1.21-2.09). The same trends were observed in MESA. In WHI, 6 single-nucleotide polymorphisms were associated with LOA at a genomewide-suggestive significance level (P < 1.0 × 10(-5)). The gene ZNF248 was associated with LOA and reached genomewide significance (P = 4.0 × 10(-7)). In MESA, the association between ZNF248 and LOA was successfully replicated (P = .015). CONCLUSION: Smoking and obesity are risk factors for LOA. ZNF248 confers increased susceptibility to LOA in African Americans.

Noncommunicable disease risk behaviors and protective factors among children in Samoa: Retrospective trend analysis of global school-based health surveys in 2011 and 2017.

Pacific Island countries experience a high prevalence of noncommunicable diseases (NCDs), which may be prevented by reducing risk behaviors and strengthening protective factors in childhood and adolescence. To better inform preventative interventions, our objective was to use publicly available data from the Global School-based Student Health Survey (GSHS), to provide cross-sectional and trend estimates for the prevalence of NCD risk and protective factors among school-aged children in 2011 and 2017 in Samoa. Two waves of cross-sectional data included 4,373 children (51.98% female), with a median age of 15 years, who were mainly in school years 9-10 in Samoa. Retrospective analyses were adjusted for the GSHS multistage stratified cluster sample design. Weighted prevalences of overweight/obesity, dietary behaviors, physical activity, and sedentary behavior, oral and hand hygiene, emotional and mental health, and community protective factors were reported by study year. Logistic regressions were fitted to assess differences in the prevalence of risk and protective factors, adjusted for age group, sex, and school year. In 2011 and 2017, the prevalence of overweight/obesity remained consistently high in females (59.12% and 64.29%, p = 0.428) and increased from 44.21% to 53.65% in males (p = 0.039). Time spent sitting for long periods, smoking cigarettes, using other tobacco products, and drinking alcohol were lower in 2017 compared to 2011 (all p<0.05). Many children reported experiencing bullying (33.27% for females and 59.30% for males in 2017), while physical fighting was common among males (73.72% in 2011 and 57.28% in 2017). The high prevalence of obesity and related NCD risk factors require urgent public health action in Samoa. Alongside the continued reduction of tobacco and alcohol use, emotional and mental wellness should be prioritized in interventions and programs to promote healthy behaviors and lifestyle changes starting in childhood.

A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.

Magnocellular neurons (MCNs) in the hypothalamo-neurohypophysial system (HNS) are highly specialized to release large amounts of arginine vasopressin (Avp) or oxytocin (Oxt) into the blood stream and play critical roles in the regulation of body fluid homeostasis. The MCNs are osmosensory neurons and are excited by exposure to hypertonic solutions and inhibited by hypotonic solutions. The MCNs respond to systemic hypertonic and hypotonic stimulation with large changes in the expression of their Avp and Oxt genes, and microarray studies have shown that these osmotic perturbations also cause large changes in global gene expression in the HNS. In this paper, we examine gene expression in the rat supraoptic nucleus (SON) under normosmotic and chronic salt-loading SL) conditions by the first time using "new-generation", RNA sequencing (RNA-Seq) methods. We reliably detect 9,709 genes as present in the SON by RNA-Seq, and 552 of these genes were changed in expression as a result of chronic SL. These genes reflect diverse functions, and 42 of these are involved in either transcriptional or translational processes. In addition, we compare the SON transcriptomes resolved by RNA-Seq methods with the SON transcriptomes determined by Affymetrix microarray methods in rats under the same osmotic conditions, and find that there are 6,466 genes present in the SON that are represented in both data sets, although 1,040 of the expressed genes were found only in the microarray data, and 2,762 of the expressed genes are selectively found in the RNA-Seq data and not the microarray data. These data provide the research community a comprehensive view of the transcriptome in the SON under normosmotic conditions and the changes in specific gene expression evoked by salt loading.

Analysis of transcription factor mRNAs in identified oxytocin and vasopressin magnocellular neurons isolated by laser capture microdissection.

The oxytocin (Oxt) and vasopressin (Avp) magnocellular neurons (MCNs) in the hypothalamus are the only neuronal phenotypes that are present in the supraoptic nucleus (SON), and are characterized by their robust and selective expression of either the Oxt or Avp genes. In this paper, we take advantage of the differential expression of these neuropeptide genes to identify and isolate these two individual phenotypes from the rat SON by laser capture microdissection (LCM), and to analyze the differential expression of several of their transcription factor mRNAs by qRT-PCR. We identify these neuronal phenotypes by stereotaxically injecting recombinant Adeno-Associated Viral (rAAV) vectors which contain cell-type specific Oxt or Avp promoters that drive expression of EGFP selectively in either the Oxt or Avp MCNs into the SON. The fluorescent MCNs are then dissected by LCM using a novel Cap Road Map protocol described in this paper, and the purified MCNs are extracted for their RNAs. qRT-PCR of these RNAs show that some transcription factors (RORA and c-jun) are differentially expressed in the Oxt and Avp MCNs.

Cell-type specific expression of the vasopressin gene analyzed by AAV mediated gene delivery of promoter deletion constructs into the rat SON in vivo.

The magnocellular neurons (MCNs) in the supraoptic nucleus (SON) of the hypothalamus selectively express either oxytocin (Oxt) or vasopressin (Avp) neuropeptide genes. In this paper we examine the cis-regulatory domains in the Avp gene promoter that are responsible for its cell-type specific expression. AAV vectors that contain various Avp gene promoter deletion constructs using EGFP as the reporter were stereotaxically injected into the rat SON. Two weeks following the injection immunohistochemical assays of EGFP expression from these constructs were done to determine whether the expressed EGFP reporter co-localizes with either the Oxt- or Avp-immunoreactivity in the MCNs. The results identify three major enhancer domains located at -2.0 to -1.5 kbp, -1.5 to -950 bp, and -950 to -543 bp in the Avp gene promoter that regulate the expression in Avp MCNs. The results also show that cell-type specific expression in Avp MCNs is maintained in constructs containing at least 288 bp of the promoter region upstream of the transcription start site, but this specificity is lost at 116 bp and below. Based on these data, we hypothesize that the -288 bp to -116 bp domain contains an Avp MCN specific activator and a possible repressor that inhibits expression in Oxt-MCNs, thereby leading to the cell-type specific expression of the Avp gene only in the Avp-MCNs.