GWAS of allometric body-shape indices in UK Biobank identifies loci suggesting associations with morphogenesis, organogenesis, adrenal cell renewal and cancer

Oxytocin receptor expression patterns in the human brain across development

Oxytocin plays a vital role in social behavior and homeostatic processes, with animal models indicating that oxytocin receptor (OXTR) expression patterns in the brain influence behavior and physiology. However, the developmental trajectory of OXTR gene expression is unclear. By analyzing gene expression data in human post-mortem brain samples, from the prenatal period to late adulthood, we demonstrate distinct patterns of OXTR gene expression in the developing brain, with increasing OXTR expression along the course of the prenatal period culminating in a peak during early childhood. This early life OXTR expression peak pattern appears slightly earlier in a comparative macaque sample, which is consistent with the relative immaturity of the human brain during early life compared to macaques. We also show that a network of genes with strong spatiotemporal couplings with OXTR is enriched in several psychiatric illness and body composition phenotypes. Taken together, these results demonstrate that oxytocin signaling plays an important role in a diverse set of psychological and somatic processes across the lifespan.

Comprehensive characterization of posttranscriptional impairment-related 3'-UTR mutations in 2413 whole genomes of cancer patients

The 3' untranslated region (3'-UTR) is the vital element regulating gene expression, but most studies have focused on variations in RNA-binding proteins (RBPs), miRNAs, alternative polyadenylation (APA) and RNA modifications. To explore the posttranscriptional function of 3'-UTR somatic mutations in tumorigenesis, we collected whole-genome data from 2413 patients across 18 cancer types. Our updated algorithm, PIVar, revealed 25,216 3'-UTR posttranscriptional impairment-related SNVs (3'-UTR piSNVs) spanning 2930 genes; 24 related RBPs were significantly enriched. The somatic 3'-UTR piSNV ratio was markedly increased across all 18 cancer types, which was associated with worse survival for four cancer types. Several cancer-related genes appeared to facilitate tumorigenesis at the protein and posttranscriptional regulation levels, whereas some 3'-UTR piSNV-affected genes functioned mainly via posttranscriptional mechanisms. Moreover, we assessed immune cell and checkpoint characteristics between the high/low 3'-UTR piSNV ratio groups and predicted 80 compounds associated with the 3'-UTR piSNV-affected gene expression signature. In summary, our study revealed the prevalence and clinical relevance of 3'-UTR piSNVs in cancers, and also demonstrates that in addition to affecting miRNAs, 3'-UTR piSNVs perturb RBPs binding, APA and m6A RNA modification, which emphasized the importance of considering 3'-UTR piSNVs in cancer biology.

Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium

Hispanic/Latinos have been underrepresented in genome-wide association studies (GWAS) for anthropometric traits despite their notable anthropometric variability, ancestry proportions, and high burden of growth stunting and overweight/obesity. To address this knowledge gap, we analyzed densely imputed genetic data in a sample of Hispanic/Latino adults to identify and fine-map genetic variants associated with body mass index (BMI), height, and BMI-adjusted waist-to-hip ratio (WHRadjBMI). We conducted a GWAS of 18 studies/consortia as part of the Hispanic/Latino Anthropometry (HISLA) Consortium (stage 1, n = 59,771) and generalized our findings in 9 additional studies (stage 2, n = 10,538). We conducted a trans-ancestral GWAS with summary statistics from HISLA stage 1 and existing consortia of European and African ancestries. In our HISLA stage 1 + 2 analyses, we discovered one BMI locus, as well as two BMI signals and another height signal each within established anthropometric loci. In our trans-ancestral meta-analysis, we discovered three BMI loci, one height locus, and one WHRadjBMI locus. We also identified 3 secondary signals for BMI, 28 for height, and 2 for WHRadjBMI in established loci. We show that 336 known BMI, 1,177 known height, and 143 known WHRadjBMI (combined) SNPs demonstrated suggestive transferability (nominal significance and effect estimate directional consistency) in Hispanic/Latino adults. Of these, 36 BMI, 124 height, and 11 WHRadjBMI SNPs were significant after trait-specific Bonferroni correction. Trans-ancestral meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our findings demonstrate that future studies may also benefit from leveraging diverse ancestries and differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification.

Differential Genetic and Epigenetic Effects of the KLF14 Gene on Body Shape Indices and Metabolic Traits

The KLF14 gene is a key metabolic transcriptional transregulator with monoallelic maternal expression. KLF14 variants are only associated with adipose tissue gene expression, and KLF14 promoter methylation is strongly associated with age. This study investigated whether age, sex, and obesity mediate the effects of KLF14 variants and DNA methylation status on body shape indices and metabolic traits. In total, the data of 78,742 and 1636 participants from the Taiwan Biobank were included in the regional plot association analysis for KLF14 variants and KLF14 methylation, respectively. Regional plot association studies revealed that the KLF14 rs4731702 variant and the nearby strong linkage disequilibrium polymorphisms were the lead variants for lipid profiles, blood pressure status, insulin resistance surrogate markers, and metabolic syndrome mainly in female participants and for body shape indices mainly in obese women. Significant age-dependent associations between KLF14 promoter methylation levels and body shape indices, and metabolic traits were also noted predominantly in female participants. KLF14 variants and KLF14 hypermethylation status were associated with metabolically healthy and unhealthy phenotypes, respectively, in obese individuals, and only the KLF14 variants demonstrated a significant association with both higher adiposity and lower cardiometabolic risk in the same allele, revealing uncoupled excessive adiposity from its cardiometabolic comorbidities, especially in obese women. Variations of KLF14 are associated with body shape indices, metabolic traits, insulin resistance, and metabolically healthy status. Differential genetic and epigenetic effects of KLF14 are age-, sex- and obesity-dependent. These results provided a personalized reference for the management of cardiometabolic diseases in precision medicine.

Identification of genetic effects underlying type 2 diabetes in South Asian and European populations

South Asians are at high risk of developing type 2 diabetes (T2D). We carried out a genome-wide association meta-analysis with South Asian T2D cases (n = 16,677) and controls (n = 33,856), followed by combined analyses with Europeans (neff = 231,420). We identify 21 novel genetic loci for significant association with T2D (P = 4.7 × 10-8 to 5.2 × 10-12), to the best of our knowledge at the point of analysis. The loci are enriched for regulatory features, including DNA methylation and gene expression in relevant tissues, and highlight CHMP4B, PDHB, LRIG1 and other genes linked to adiposity and glucose metabolism. A polygenic risk score based on South Asian-derived summary statistics shows ~4-fold higher risk for T2D between the top and bottom quartile. Our results provide further insights into the genetic mechanisms underlying T2D, and highlight the opportunities for discovery from joint analysis of data from across ancestral populations.

Genomic correlation, shared loci, and causal relationship between obesity and polycystic ovary syndrome: a large-scale genome-wide cross-trait analysis

BACKGROUND

The comorbidity between polycystic ovary syndrome (PCOS) and obesity has long been observed in clinical settings, but their shared genetic basis remains unclear.

METHODS

Leveraging summary statistics of large-scale GWAS(s) conducted in European-ancestry populations on body mass index (adult BMI, Nfemale=434,794; childhood BMI, N=39,620), waist-to-hip ratio (WHR, Nfemale=381,152), WHR adjusted for BMI (WHRadjBMI, Nfemale=379,501), and PCOS (Ncase=10,074, Ncontrol=103,164), we performed a large-scale genome-wide cross-trait analysis to quantify overall and local genetic correlation, to identify shared loci, and to infer causal relationship.

RESULTS

We found positive genetic correlations between PCOS and adult BMI (rg=0.47, P=2.19×10-16), childhood BMI (rg=0.31, P=6.72×10-5), and WHR (rg=0.32, P=1.34×10-10), all withstanding Bonferroni correction. A suggestive significant genetic correlation was found between PCOS and WHRadjBMI (rg=0.09, P=0.04). Partitioning the whole genome into 1703 nearly independent regions, we observed a significant local genetic correlation for adult BMI and PCOS at chromosome 18: 57630483-59020751. We identified 16 shared loci underlying PCOS and obesity-related traits via cross-trait meta-analysis including 9 loci shared between BMI and PCOS (adult BMI and PCOS: 5 loci; childhood BMI and PCOS: 4 loci), 6 loci shared between WHR and PCOS, and 5 loci shared between WHRadjBMI and PCOS. Mendelian randomization (MR) supported the causal roles of both adult BMI (OR=2.92, 95% CI=2.33-3.67) and childhood BMI (OR=2.76, 95% CI=2.09-3.66) in PCOS, but not WHR (OR=1.19, 95% CI=0.93-1.52) or WHRadjBMI (OR=1.03, 95% CI=0.87-1.22). Genetic predisposition to PCOS did not seem to influence the risk of obesity-related traits.

CONCLUSIONS

Our cross-trait analysis suggests a shared genetic basis underlying obesity and PCOS and provides novel insights into the biological mechanisms underlying these complex traits. Our work informs public health intervention by confirming the important role of weight management in PCOS prevention.

Weighted single-step GWAS for body mass index and scans for recent signatures of selection in Yorkshire pigs

Controlling extra fat deposition is economically favorable in modern swine industry. Understanding the genetic architecture of fat deposition traits such as body mass index (BMI) can help in improving genomic selection for such traits. We utilized a weighted single-step genome-wide association study (WssGWAS) to detect genetic regions and candidate genes associated with BMI in a Yorkshire pig population. Three extended haplotype homozygosity (EHH)-related statistics were also incorporated within a de-correlated composite of multiple signals (DCMS) framework to detect recent selection signatures signals. Overall, the full pedigree consisted of 7,016 pigs, of which 5,561 had BMI records and 598 pigs were genotyped with an 80 K single nucleotide polymorphism (SNP) array. Results showed that the most significant windows (top 15) explained 9.35% of BMI genetic variance. Several genes were detected in regions previously associated with pig fat deposition traits and treated as potential candidate genes for BMI in Yorkshire pigs: FTMT, SRFBP1, KHDRBS3, FOXG1, SOD3, LRRC32, TSKU, ACER3, B3GNT6, CCDC201, ADCY1, RAMP3, TBRG4, CCM2. Signature of selection analysis revealed multiple candidate genes previously associated with various economic traits. However, BMI genetic variance explained by regions under selection pressure was minimal (1.31%). In conclusion, candidate genes associated with Yorkshire pigs’ BMI trait were identified using WssGWAS. Gene enrichment analysis indicated that the identified candidate genes were enriched in the insulin secretion pathway. We anticipate that these results further advance our understanding of the genetic architecture of BMI in Yorkshire pigs and provide information for genomic selection for fat deposition in this breed.

The Effect of Alzheimer's Disease-Associated Genetic Variants on Longevity

Human longevity is influenced by the genetic risk of age-related diseases. As Alzheimer’s disease (AD) represents a common condition at old age, an interplay between genetic factors affecting AD and longevity is expected. We explored this interplay by studying the prevalence of AD-associated single-nucleotide-polymorphisms (SNPs) in cognitively healthy centenarians, and replicated findings in a parental-longevity GWAS. We found that 28/38 SNPs that increased AD-risk also associated with lower odds of longevity. For each SNP, we express the imbalance between AD- and longevity-risk as an effect-size distribution. Based on these distributions, we grouped the SNPs in three groups: 17 SNPs increased AD-risk more than they decreased longevity-risk, and were enriched for β-amyloid metabolism and immune signaling; 11 variants reported a larger longevity-effect compared to their AD-effect, were enriched for endocytosis/immune-signaling, and were previously associated with other age-related diseases. Unexpectedly, 10 variants associated with an increased risk of AD and higher odds of longevity. Altogether, we show that different AD-associated SNPs have different effects on longevity, including SNPs that may confer general neuro-protective functions against AD and other age-related diseases.

Correlation between gene expression and MRI STIR signals in patients with chronic low back pain and Modic changes indicates immune involvement

Disability and distress caused by chronic low back pain (LBP) lacking clear pathoanatomical explanations cause huge problems both for patients and society. A subgroup of patients has Modic changes (MC), identifiable by MRI as vertebral bone marrow lesions. The cause of such changes and their relationship to pain are not yet understood. We explored the pathobiology of these lesions using profiling of gene expression in blood, coupled with an edema-sensitive MRI technique known as short tau inversion recovery (STIR) imaging. STIR images and total RNA from blood were collected from 96 patients with chronic LBP and MC type I, the most inflammatory MC state. We found the expression of 37 genes significantly associated with STIR signal volume, ten genes with edema abundancy (a constructed combination of STIR signal volume, height, and intensity), and one gene with expression levels significantly associated with maximum STIR signal intensity. Gene sets related to interferon signaling, mitochondrial metabolism and defense response to virus were identified as significantly enriched among the upregulated genes in all three analyses. Our results point to inflammation and immunological defense as important players in MC biology in patients with chronic LBP.

Obesity measures, metabolic health and their association with 15-year all-cause and cardiovascular mortality in the SAMINOR 1 Survey: a population-based cohort study

Background

The mortality of metabolic-obesity phenotypes has been thoroughly studied, but it is not known if or how the association between mortality and body mass index (BMI), waist circumference or a body shape index (ABSI) differ in strata of cardiometabolic health status.

Methods

We linked data on 12,815 men and women aged 36–79 years from the SAMINOR 1 Survey with mortality data from the Norwegian Cause of Death Registry. We defined metabolically healthy and unhealthy as having zero and ≥ 1, respectively, of the following: MetS, pre-existing diabetes or cardiovascular disease (CVD), or prescribed drugs for high blood pressure, hyperglycaemia or dyslipidaemia. We defined general and abdominal obesity as BMI ≥ 30 kg/m² and waist circumference ≥ 88 cm (women) or 102 cm (men), respectively, and cross-classified these categories with metabolic status to create metabolically healthy non-obese and obese (MHNO and MHO) and metabolically unhealthy non-obese and obese (MUNO and MUO) phenotypes. We used Cox regression to estimate the hazard ratio (HR) for all-cause and CVD mortality for 1) the four phenotypes and 2) BMI, waist circumference and ABSI fitted with restricted cubic splines. We adjusted for age and lifestyle, and tested for interactions with sex and metabolic status (only continuous measures).

Results

The MHO phenotype was present in 7.8% of women and 5.8% of men. During a median follow-up of 15.3/15.2 years, 596/938 women/men had died, respectively. The MUNO and MUO groups had higher mortality than the MHNO group. Sex and phenotypes interacted with respect to CVD mortality: relative to the MHNO group, the MHO group had an adjusted HR (95% confidence interval) for CVD mortality of 1.05 (0.38–2.88) in women and 2.92 (1.71–5.01) in men. We found curvilinear associations between BMI/waist circumference and all-cause mortality irrespective of metabolic status. Corresponding relationships with CVD mortality were linear and the slope differed by sex and metabolic status. ABSI was linearly and positively associated with all-cause and CVD mortality in men.

Conclusion

The relationships between BMI, waist circumference or ABSI and mortality differed by sex, metabolic status and cause of death. Poor metabolic health substantially increases mortality regardless of obesity status.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12872-021-02288-9.

Association of body-shape phenotypes with imaging measures of body composition in the UK Biobank cohort: relevance to colon cancer risk

Background

Body mass index (BMI), waist and hip circumference are strongly correlated and do not reflect body composition. A Body Shape Index (ABSI) and Hip Index (HI) define waist and hip size among individuals with the same weight and height and would thus reflect body density. We examined differences in body composition between body-shape phenotypes defined with ABSI and HI and used this information to propose explanations for associations between body-shape phenotypes and colon cancer risk.

Methods

We used data from the UK Biobank Resource for 15,520 men, 16,548 women with dual-emission X-ray absorptiometry (DXA) measurements; 3997 men, 4402 women with magnetic resonance imaging (MRI) measurements; 200,289 men, 230,326 women followed-up for colon cancer. We defined body-shape phenotypes as: large-ABSI-small-HI (“apple”), small-ABSI-large-HI (“pear”), small-ABSI-small-HI (“slim”), large-ABSI-large-HI (“wide”). We evaluated differences in body composition in linear models and associations with colon cancer risk in Cox proportional hazards models adjusted for confounders and explored heterogeneity by BMI.

Results

Among individuals with the same height and weight, visceral adipose tissue (VAT) was lowest for “pear” and highest for “apple”, while abdominal subcutaneous adipose tissue (ASAT) was lowest for “slim” and highest for “wide” phenotype. In the gynoid region, differences between “apple” and “pear” phenotypes were accounted for mainly by fat mass in women but by lean mass in men. In men, lean mass was inversely associated with waist size, while the pattern of gynoid fat resembled ASAT in women. Lean and fat mass were higher for higher BMI, but not hand grip strength. Compared to normal weight “pear”, the risk of colon cancer in men (1029 cases) was higher for “apple” phenotype for normal weight (hazard ratio HR = 1.77; 95% confidence interval: 1.16–2.69) and comparably for overweight and obese, higher for “wide” phenotype for overweight (HR = 1.60; 1.14–2.24) and comparably for obese, but higher for “slim” phenotype only for obese (HR = 1.98; 1.35–2.88). Associations with colon cancer risk in women (889 cases) were weaker.

Conclusions

ABSI-by-HI body-shape phenotypes provide information for body composition. Colon cancer risk in men appears related to ASAT quantity for “slim” and “wide” but to factors determining VAT accumulation for “apple” phenotype.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08820-6.

A Body Shape Index (ABSI), hip index, and risk of cancer in the UK Biobank cohort

Abdominal size is associated positively with the risk of some cancers but the influence of body mass index (BMI) and gluteofemoral size is unclear because waist and hip circumference are strongly correlated with BMI. We examined associations of 33 cancers with A Body Shape Index (ABSI) and hip index (HI), which are independent of BMI by design, and compared these with waist and hip circumference, using multivariable Cox proportional hazards models in UK Biobank. During a mean follow-up of 7 years, 14,682 incident cancers were ascertained in 200,289 men and 12,965 cancers in 230,326 women. In men, ABSI was associated positively with cancers of the head and neck (hazard ratio HR = 1.14; 95% confidence interval 1.03-1.26 per one standard deviation increment), esophagus (adenocarcinoma, HR = 1.27; 1.12-1.44), gastric cardia (HR = 1.31; 1.07-1.61), colon (HR = 1.18; 1.10-1.26), rectum (HR = 1.13; 1.04-1.22), lung (adenocarcinoma, HR = 1.16; 1.03-1.30; squamous cell carcinoma [SCC], HR = 1.33; 1.17-1.52), and bladder (HR = 1.15; 1.04-1.27), while HI was associated inversely with cancers of the esophagus (adenocarcinoma, HR = 0.89; 0.79-1.00), gastric cardia (HR = 0.79; 0.65-0.96), colon (HR = 0.92; 0.86-0.98), liver (HR = 0.86; 0.75-0.98), and multiple myeloma (HR = 0.86; 0.75-1.00). In women, ABSI was associated positively with cancers of the head and neck (HR = 1.27; 1.10-1.48), esophagus (SCC, HR = 1.37; 1.07-1.76), colon (HR = 1.08; 1.01-1.16), lung (adenocarcinoma, HR = 1.17; 1.06-1.29; SCC, HR = 1.40; 1.20-1.63; small cell, HR = 1.39; 1.14-1.69), kidney (clear-cell, HR = 1.25; 1.03-1.50), and post-menopausal endometrium (HR = 1.11; 1.02-1.20), while HI was associated inversely with skin SCC (HR = 0.91; 0.83-0.99), post-menopausal kidney cancer (HR = 0.77; 0.67-0.88), and post-menopausal melanoma (HR = 0.90; 0.83-0.98). Unusually, ABSI was associated inversely with melanoma in men (HR = 0.89; 0.82-0.96) and pre-menopausal women (HR = 0.77; 0.65-0.91). Waist and hip circumference reflected associations with BMI, when examined individually, and provided biased risk estimates, when combined with BMI. In conclusion, preferential positive associations of ABSI or inverse of HI with several major cancers indicate an important role of factors determining body shape in cancer development.

Association of X-ray Absorptiometry Body Composition Measurements with Basic Anthropometrics and Mortality Hazard

Dual-energy X-ray absorptiometry (DEXA) is a non-invasive imaging modality that can estimate whole-body and regional composition in terms of fat, lean, and bone mass. We examined the ability of DEXA body composition measures (whole-body, trunk, and limb fat mass and fat-free mass) to predict mortality in conjunction with basic body measures (anthropometrics), expressed using body mass index (BMI) and a body shape index (ABSI). We used data from the 1999-2006 United States National Health and Nutrition Examination Survey (NHANES), with mortality follow-up to 2015. We found that all DEXA-measured masses were highly correlated with each other and with ABSI and that adjustment for BMI and ABSI reduced these dependencies. Whole-body composition did not substantially improve mortality prediction compared to basic anthropometrics alone, but regional composition did, with high trunk fat-free mass and low limb fat-free mass both associated with elevated mortality risk. These findings illustrate how DEXA body composition could guide health assessment in conjunction with the more widely employed simple anthropometrics.