Elizabeth K. Speliotes

Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ∼ 2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10⁻⁸), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.

New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single-nucleotide polymorphisms (SNPs) in 1464 patients with T2D and 1467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D), we identified and confirmed three loci associated with T2D—in a noncoding region near CDKN2A and CDKN2B , in an intron of IGF2BP2 , and an intron of CDKAL1 —and replicated associations near HHEX and in SLC30A8 found by a recent whole-genome association study. We identified and confirmed association of a SNP in an intron of glucokinase regulatory protein (GCKR) with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues to the pathogenesis of common diseases.

A genome-wide association (GWA) study of more than 180,000 individuals has identified hundreds of genetic variants in at least 180 loci associated with adult human height. The loci are not clustered randomly but are enriched for genes involved in growth-related processes that influence adult height. This demonstrates that GWA studies of common human traits, and therefore of many diseases, can identify large numbers of loci that implicate potential causal genes. This very large genome-wide association study identifies hundreds of new genetic variants influencing adult height in at least 180 loci enriched for genes involved in skeletal growth defects. The results show that the likely causal gene is often located near the most strongly associated variant, that many loci have multiple independently associated variants and that associated variants are enriched for likely functional effects on genes. Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits1, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait2,3. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

To identify common variants influencing body mass index (BMI), we analyzed genome-wide association data from 16,876 individuals of European descent. After previously reported variants in FTO, the strongest association signal (rs17782313, P = 2.9 x 10(-6)) mapped 188 kb downstream of MC4R (melanocortin-4 receptor), mutations of which are the leading cause of monogenic severe childhood-onset obesity. We confirmed the BMI association in 60,352 adults (per-allele effect = 0.05 Z-score units; P = 2.8 x 10(-15)) and 5,988 children aged 7-11 (0.13 Z-score units; P = 1.5 x 10(-8)). In case-control analyses (n = 10,583), the odds for severe childhood obesity reached 1.30 (P = 8.0 x 10(-11)). Furthermore, we observed overtransmission of the risk allele to obese offspring in 660 families (P (pedigree disequilibrium test average; PDT-avg) = 2.4 x 10(-4)). The SNP location and patterns of phenotypic associations are consistent with effects mediated through altered MC4R function. Our findings establish that common variants near MC4R influence fat mass, weight and obesity risk at the population level and reinforce the need for large-scale data integration to identify variants influencing continuous biomedical traits.

Waist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association studies for WHR adjusted for body mass index (comprising up to 77,167 participants), following up 16 loci in an additional 29 studies (comprising up to 113,636 subjects). We identified 13 new loci in or near RSPO3, VEGFA, TBX15-WARS2, NFE2L3, GRB14, DNM3-PIGC, ITPR2-SSPN, LY86, HOXC13, ADAMTS9, ZNRF3-KREMEN1, NISCH-STAB1 and CPEB4 (P = 1.9 × 10⁻⁹ to P = 1.8 × 10⁻⁴⁰) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 × 10⁻³ to P = 1.2 × 10⁻¹³). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions.

Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable (∼26%-27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n = 880 to 3,070). By carrying out a fixed-effects meta-analysis of genome-wide association (GWA) results between CT hepatic steatosis and ∼2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome-wide significant levels (p<5×10(-8)) in or near PNPLA3, NCAN, and PPP1R3B. We genotype these and 42 other top CT hepatic steatosis-associated SNPs in 592 subjects with biopsy-proven NAFLD from the NASH Clinical Research Network (NASH CRN). In comparisons with 1,405 healthy controls from the Myocardial Genetics Consortium (MIGen), we observe significant associations with histologic NAFLD at variants in or near NCAN, GCKR, LYPLAL1, and PNPLA3, but not PPP1R3B. Variants at these five loci exhibit distinct patterns of association with serum lipids, as well as glycemic and anthropometric traits. We identify common genetic variants influencing CT-assessed steatosis and risk of NAFLD. Hepatic steatosis associated variants are not uniformly associated with NASH/fibrosis or result in abnormalities in serum lipids or glycemic and anthropometric traits, suggesting genetic heterogeneity in the pathways influencing these traits.

The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.

Concentrations of liver enzymes in plasma are widely used as indicators of liver disease. We carried out a genome-wide association study in 61,089 individuals, identifying 42 loci associated with concentrations of liver enzymes in plasma, of which 32 are new associations (P = 10(-8) to P = 10(-190)). We used functional genomic approaches including metabonomic profiling and gene expression analyses to identify probable candidate genes at these regions. We identified 69 candidate genes, including genes involved in biliary transport (ATP8B1 and ABCB11), glucose, carbohydrate and lipid metabolism (FADS1, FADS2, GCKR, JMJD1C, HNF1A, MLXIPL, PNPLA3, PPP1R3B, SLC2A2 and TRIB1), glycoprotein biosynthesis and cell surface glycobiology (ABO, ASGR1, FUT2, GPLD1 and ST3GAL4), inflammation and immunity (CD276, CDH6, GCKR, HNF1A, HPR, ITGA1, RORA and STAT4) and glutathione metabolism (GSTT1, GSTT2 and GGT), as well as several genes of uncertain or unknown function (including ABHD12, EFHD1, EFNA1, EPHA2, MICAL3 and ZNF827). Our results provide new insight into genetic mechanisms and pathways influencing markers of liver function.

Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.

To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11)) and MSRA (WC, P = 8.9x10(-9)). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8)). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.

A meta-analysis of genome-wide association studies of phenotypic variation for height and body mass index in human populations using 170,000 samples shows that one single nucleotide polymorphism at the FTO locus, which is associated with obesity, is also associated with phenotypic variation. Genome-wide association studies have successfully detected thousands of single nucleotide polymorphisms (SNPs) associated with complex traits in human populations. These studies tested the associations between SNPs and a phenotype — a disease or quantitative trait — expressed as a mean of the trait. This study is different, testing for associations between SNPs and variations of the phenotype, using more than 100,000 samples on height and body mass index in human populations. The authors find that one SNP at the FTO locus, which is known to be associated with obesity, is also associated with phenotypic variability. These results demonstrate that it is possible to find genetic variants that associate with variability and that between-person variability in obesity can partly be explained by genotype at the FTO locus. However, most genetic variants are not associated with phenotypic variance, or their effects on variability are very small. There is evidence across several species for genetic control of phenotypic variation of complex traits1,2,3,4, such that the variance among phenotypes is genotype dependent. Understanding genetic control of variability is important in evolutionary biology, agricultural selection programmes and human medicine, yet for complex traits, no individual genetic variants associated with variance, as opposed to the mean, have been identified. Here we perform a meta-analysis of genome-wide association studies of phenotypic variation using ∼170,000 samples on height and body mass index (BMI) in human populations. We report evidence that the single nucleotide polymorphism (SNP) rs7202116 at the FTO gene locus, which is known to be associated with obesity (as measured by mean BMI for each rs7202116 genotype)5,6,7, is also associated with phenotypic variability. We show that the results are not due to scale effects or other artefacts, and find no other experiment-wise significant evidence for effects on variability, either at loci other than FTO for BMI or at any locus for height. The difference in variance for BMI among individuals with opposite homozygous genotypes at the FTO locus is approximately 7%, corresponding to a difference of ∼0.5 kilograms in the standard deviation of weight. Our results indicate that genetic variants can be discovered that are associated with variability, and that between-person variability in obesity can partly be explained by the genotype at the FTO locus. The results are consistent with reported FTO by environment interactions for BMI8, possibly mediated by DNA methylation9,10. Our BMI results for other SNPs and our height results for all SNPs suggest that most genetic variants, including those that influence mean height or mean BMI, are not associated with phenotypic variance, or that their effects on variability are too small to detect even with samples sizes greater than 100,000.

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10−8), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits.

Obesity is not uniformly associated with the development of metabolic sequelae. Specific patterns of body fat distribution, in particular fatty liver, may preferentially predispose at-risk individuals to disease. In this study, we characterize the metabolic correlates of fat in the liver in a large community-based sample with and without respect to visceral fat. Fatty liver was measured by way of multidetector computed tomography of the abdomen in 2,589 individuals from the community-based Framingham Heart Study. Logistic and linear regression were used to determine the associations of fatty liver with cardio-metabolic risk factors adjusted for covariates with and without adjustment for other fat depots (body mass index, waist circumference, and visceral adipose tissue). The prevalence of fatty liver was 17%. Compared with participants without fatty liver, individuals with fatty liver had a higher adjusted odds ratio (OR) of diabetes (OR 2.98, 95% confidence interval [CI] 2.12-4.21), metabolic syndrome (OR 5.22, 95% CI 4.15-6.57), hypertension (OR 2.73, 95% CI 2.16-3.44), impaired fasting glucose (OR 2.95, 95% CI 2.32-3.75), insulin resistance (OR 6.16, 95% CI 4.90-7.76); higher triglycerides, systolic blood pressure (SBP), and diastolic blood pressure (DBP); and lower high-density lipoprotein (HDL) and adiponectin levels (P < 0.001 for all). After adjustment for other fat depots, fatty liver remained associated with diabetes, hypertension, impaired fasting glucose, metabolic syndrome, HDL, triglycerides, and adiponectin levels (all P < 0.001), whereas associations with SBP and DBP were attenuated (P > 0.05). Conclusion: Fatty liver is a prevalent condition and is characterized by dysglycemia and dyslipidemia independent of visceral adipose tissue and other obesity measures. This work begins to dissect the specific links between fat depots and metabolic disease. (HEPATOLOGY 2010;)

Single nucleotide polymorphisms (SNPs) near 7 loci have been associated with liver function tests or with liver steatosis by magnetic resonance spectroscopy. In this study we aim to test whether these SNPs influence the risk of histologically-confirmed nonalcoholic fatty liver disease (NAFLD). We tested the association of histologic NAFLD with SNPs at 7 loci in 592 cases of European ancestry from the Nonalcoholic Steatohepatitis Clinical Research Network and 1405 ancestry-matched controls. The G allele of rs738409 in PNPLA3 was associated with increased odds of histologic NAFLD (odds ratio [OR] = 3.26, 95% confidence intervals [CI] = 2.11-7.21; P = 3.6 x 10(-43)). In a case only analysis of G allele of rs738409 in PNPLA3 was associated with a decreased risk of zone 3 centered steatosis (OR = 0.46, 95% CI = 0.36-0.58; P = 5.15 x 10(-11)). We did not observe any association of this variant with body mass index, triglyceride levels, high- and low-density lipoprotein levels, or diabetes (P > 0.05). None of the variants at the other 6 loci were associated with NAFLD.Genetic variation at PNPLA3 confers a markedly increased risk of increasingly severe histological features of NAFLD, without a strong effect on metabolic syndrome component traits.

Matthew Robinson and colleagues report an analysis of population genetic differences in human height and body mass index (BMI) across 14 European populations. They estimate the proportion of additive genetic variance attributable to population genetic differences and find evidence for selection increasing height while reducing BMI in European nations. Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58).

Nonalcoholic fatty liver disease (NAFLD) is a common cause of chronic liver disease. A single‐nucleotide polymorphism (SNP), rs6834314, was associated with serum liver enzymes in the general population, presumably reflecting liver fat or injury. We studied rs6834314 and its nearest gene, 17‐beta hydroxysteroid dehydrogenase 13 ( HSD17B13 ), to identify associations with histological features of NAFLD and to characterize the functional role of HSD17B13 in NAFLD pathogenesis. The minor allele of rs6834314 was significantly associated with increased steatosis but decreased inflammation, ballooning, Mallory‐Denk bodies, and liver enzyme levels in 768 adult Caucasians with biopsy‐proven NAFLD and with cirrhosis in the general population. We found two plausible causative variants in the HSD17B1 3 gene. rs72613567, a splice‐site SNP in high linkage with rs6834314 ( r 2 = 0.94) generates splice variants and shows a similar pattern of association with NAFLD histology. Its minor allele generates simultaneous expression of exon 6‐skipping and G‐nucleotide insertion variants. Another SNP, rs62305723 (encoding a P260S mutation), is significantly associated with decreased ballooning and inflammation. Hepatic expression of HSD17B13 is 5.9‐fold higher ( P = 0.003) in patients with NAFLD. HSD17B13 is targeted to lipid droplets, requiring the conserved amino acid 22‐28 sequence and amino acid 71‐106 region. The protein has retinol dehydrogenase (RDH) activity, with enzymatic activity dependent on lipid droplet targeting and cofactor binding site. The exon 6 deletion, G insertion, and naturally occurring P260S mutation all confer loss of enzymatic activity. Conclusion: We demonstrate the association of variants in HSD17B13 with specific features of NAFLD histology and identify the enzyme as a lipid droplet–associated RDH; our data suggest that HSD17B13 plays a role in NAFLD through its enzymatic activity.

The mechanisms that predispose to hypertension, coronary artery disease (CAD), and type 2 diabetes (T2D) in individuals of normal weight are poorly understood. In contrast, in monogenic primary lipodystrophy-a reduction in subcutaneous adipose tissue-it is clear that it is adipose dysfunction that causes severe insulin resistance (IR), hypertension, CAD, and T2D. We aimed to test the hypothesis that common alleles associated with IR also influence the wider clinical and biochemical profile of monogenic IR. We selected 19 common genetic variants associated with fasting insulin-based measures of IR. We used hierarchical clustering and results from genome-wide association studies of eight nondisease outcomes of monogenic IR to group these variants. We analyzed genetic risk scores against disease outcomes, including 12,171 T2D cases, 40,365 CAD cases, and 69,828 individuals with blood pressure measurements. Hierarchical clustering identified 11 variants associated with a metabolic profile consistent with a common, subtle form of lipodystrophy. A genetic risk score consisting of these 11 IR risk alleles was associated with higher triglycerides (β = 0.018; P = 4 × 10(-29)), lower HDL cholesterol (β = -0.020; P = 7 × 10(-37)), greater hepatic steatosis (β = 0.021; P = 3 × 10(-4)), higher alanine transaminase (β = 0.002; P = 3 × 10(-5)), lower sex-hormone-binding globulin (β = -0.010; P = 9 × 10(-13)), and lower adiponectin (β = -0.015; P = 2 × 10(-26)). The same risk alleles were associated with lower BMI (per-allele β = -0.008; P = 7 × 10(-8)) and increased visceral-to-subcutaneous adipose tissue ratio (β = -0.015; P = 6 × 10(-7)). Individuals carrying ≥17 fasting insulin-raising alleles (5.5% population) were slimmer (0.30 kg/m(2)) but at increased risk of T2D (odds ratio [OR] 1.46; per-allele P = 5 × 10(-13)), CAD (OR 1.12; per-allele P = 1 × 10(-5)), and increased blood pressure (systolic and diastolic blood pressure of 1.21 mmHg [per-allele P = 2 × 10(-5)] and 0.67 mmHg [per-allele P = 2 × 10(-4)], respectively) compared with individuals carrying ≤9 risk alleles (5.5% population). Our results provide genetic evidence for a link between the three diseases of the "metabolic syndrome" and point to reduced subcutaneous adiposity as a central mechanism.

Non-alcoholic fatty liver disease affects ∼30% of US adults, yet the role of sugar-sweetened beverages and diet soda on these diseases remains unknown. We examined the cross-sectional association between intake of sugar-sweetened beverages or diet soda and fatty liver disease in participants of the Framingham Offspring and Third Generation cohorts.Fatty liver disease was defined using liver attenuation measurements generated from computed tomography in 2634 participants. Alanine transaminase concentration, a crude marker of fatty liver disease, was measured in 5908 participants. Sugar-sweetened beverage and diet soda intake were estimated using a food frequency questionnaire. Participants were categorized as either non-consumers or consumers (3 categories: 1 serving/month to <1 serving/week, 1 serving/week to <1 serving/day, and ⩾1 serving/day) of sugar-sweetened beverages or diet soda.After adjustment for age, sex, smoking status, Framingham cohort, energy intake, alcohol, dietary fiber, fat (% energy), protein (% energy), diet soda intake, and body mass index, the odds ratios of fatty liver disease were 1, 1.16 (0.88, 1.54), 1.32 (0.93, 1.86), and 1.61 (1.04, 2.49) across sugar-sweetened beverage consumption categories (p trend=0.04). Sugar-sweetened beverage consumption was also positively associated with alanine transaminase levels (p trend=0.007). We observed no significant association between diet soda intake and measures of fatty liver disease.In conclusion, we observed that regular sugar-sweetened beverage consumption was associated with greater risk of fatty liver disease, particularly in overweight and obese individuals, whereas diet soda intake was not associated with measures of fatty liver disease.

Non-alcoholic fatty liver disease (NAFLD) is highly prevalent and is associated with development of metabolic disease including atherosclerotic cardiovascular disease (CVD). Our aim is to examine the association of hepatic steatosis with prevalent clinical and subclinical CVD outcomes in a large community-based sample, the Framingham Heart Study.Hepatic steatosis was measured in 3529 participants using multidetector computed tomography scanning. Multivariable logistic regression was used to determine whether hepatic steatosis is associated with prevalent CVD adjusted for covariates. We also tested whether associations were independent of other metabolic diseases/traits. The primary clinical outcome was composite prevalent clinical CVD defined by prior non-fatal myocardial infarction, stroke, transient ischemic attack, heart failure, or peripheral arterial disease. Subclinical cardiovascular outcomes were coronary artery calcium (CAC) and abdominal artery calcium (AAC).3014 participants were included (50.5% women). There was a non-significant association of hepatic steatosis with clinical CVD (OR 1.14 [p=0.07]). Hepatic steatosis was associated with both CAC and AAC (OR 1.20 [p<0.001] and OR 1.16 [p<0.001], respectively). Associations persisted for CAC even when controlling for other risk factors/metabolic diseases, but for AAC, the associations became non-significant after adjustment for visceral adipose tissue. The association between hepatic steatosis and AAC was stronger in men than in women (p sex interaction=0.022).There was a significant association of hepatic steatosis with subclinical CVD outcomes independent of many metabolic diseases/traits with a trend towards association between hepatic steatosis and clinical CVD outcomes. The association with AAC was stronger in men than in women.

A common genetic variant near MBOAT7 (rs641738C>T) has been previously associated with hepatic fat and advanced histology in NAFLD; however, these findings have not been consistently replicated in the literature. We aimed to establish whether rs641738C>T is a risk factor across the spectrum of NAFLD and to characterise its role in the regulation of related metabolic phenotypes through a meta-analysis.We performed a meta-analysis of studies with data on the association between rs641738C>T genotype and liver fat, NAFLD histology, and serum alanine aminotransferase (ALT), lipids or insulin. These included directly genotyped studies and population-level data from genome-wide association studies (GWAS). We performed a random effects meta-analysis using recessive, additive and dominant genetic models.Data from 1,066,175 participants (9,688 with liver biopsies) across 42 studies were included in the meta-analysis. rs641738C>T was associated with higher liver fat on CT/MRI (+0.03 standard deviations [95% CI 0.02-0.05], pz = 4.8×10-5) and diagnosis of NAFLD (odds ratio [OR] 1.17 [95% CI 1.05-1.3], pz = 0.003) in Caucasian adults. The variant was also positively associated with presence of advanced fibrosis (OR 1.22 [95% CI 1.03-1.45], pz = 0.021) in Caucasian adults using a recessive model of inheritance (CC + CT vs. TT). Meta-analysis of data from previous GWAS found the variant to be associated with higher ALT (pz = 0.002) and lower serum triglycerides (pz = 1.5×10-4). rs641738C>T was not associated with fasting insulin and no effect was observed in children with NAFLD.Our study validates rs641738C>T near MBOAT7 as a risk factor for the presence and severity of NAFLD in individuals of European descent.Fatty liver disease is a common condition where fat builds up in the liver, which can cause liver inflammation and scarring (including 'cirrhosis'). It is closely linked to obesity and diabetes, but some genes are also thought to be important. We did this study to see whether one specific change ('variant') in one gene ('MBOAT7') was linked to fatty liver disease. We took data from over 40 published studies and found that this variant near MBOAT7 is linked to more severe fatty liver disease. This means that drugs designed to work on MBOAT7 could be useful for treating fatty liver disease.

Serum liver enzyme concentrations are the most frequently-used laboratory markers of liver disease, a major cause of mortality. We conduct a meta-analysis of genome-wide association studies of liver enzymes from UK BioBank and BioBank Japan. We identified 160 previously-unreported independent alanine aminotransferase, 190 aspartate aminotransferase, and 199 alkaline phosphatase genome-wide significant associations, with some affecting multiple different enzymes. Associated variants implicate genes that demonstrate diverse liver cell type expression and promote a range of metabolic and liver diseases. These findings provide insight into the pathophysiology of liver and other metabolic diseases that are associated with serum liver enzyme concentrations.

Non-alcoholic fatty liver disease (NAFLD) can progress to cirrhosis and hepatic decompensation, but whether genetic variants influence the rate of progression to cirrhosis or are useful in risk stratification among patients with NAFLD is uncertain.We included participants from 2 independent cohorts, they Michigan Genomics Initiative (MGI) and UK Biobank (UKBB), who had NAFLD defined by elevated alanine aminotransferase (ALT) levels in the absence of alternative chronic liver disease. The primary predictors were genetic variants and metabolic comorbidities associated with cirrhosis. We conducted time-to-event analyses using Fine-Gray competing risk models.We included 7893 and 46,880 participants from MGI and UKBB, respectively. In univariable analysis, PNPLA3-rs738409-GG genotype, diabetes, obesity, and ALT of ≥2× upper limit of normal were associated with higher incidence rate of cirrhosis in both MGI and UKBB. PNPLA3-rs738409-GG had additive effects with clinical risk factors including diabetes, obesity, and ALT elevations. Among patients with indeterminate fibrosis-4 (FIB4) scores (1.3-2.67), those with diabetes and PNPLA3-rs738409-GG genotype had an incidence rate of cirrhosis comparable to that of patients with high-risk FIB4 scores (>2.67) and 2.9-4.8 times that of patients with diabetes but CC/CG genotypes. In contrast, FIB4 <1.3 was associated with an incidence rate of cirrhosis significantly lower than that of FIB4 of >2.67, even in the presence of clinical risk factors and high-risk PNPLA3 genotype.PNPLA3-rs738409 genotype and diabetes identified patients with NAFLD currently considered indeterminate risk (FIB4 1.3-2.67) who had a similar risk of cirrhosis as those considered high-risk (FIB4 >2.67). PNPLA3 genotyping may improve prognostication and allow for prioritization of intensive intervention.

Baculoviral IAP repeat proteins (BIRPs) may affect cell death, cell division, and tumorigenesis. The C. elegans BIRP BIR-1 was localized to chromosomes and to the spindle midzone. Embryos and fertilized oocytes lacking BIR-1 had defects in chromosome behavior, spindle midzone formation, and cytokinesis. We observed indistinguishable defects in fertilized oocytes and embryos lacking the Aurora-like kinase AIR-2. AIR-2 was not present on chromosomes in the absence of BIR-1. Histone H3 phosphorylation and HCP-1 staining, which marks kinetochores, were reduced in the absence of either BIR-1 or AIR-2. We propose that BIR-1 localizes AIR-2 to chromosomes and perhaps to the spindle midzone, where AIR-2 phosphorylates proteins that affect chromosome behavior and spindle midzone organization. The human BIRP survivin, which is upregulated in tumors, could partially substitute for BIR-1 in C. elegans. Deregulation of bir-1 promotes changes in ploidy, suggesting that similar deregulation of mammalian BIRPs may contribute to tumorigenesis.

Nonalcoholic fatty liver disease (NAFLD) is an obesity-related condition affecting over 50% of individuals in some populations and is expected to become the number one cause of liver disease worldwide by 2020. Common, robustly associated genetic variants in/near five genes were identified for hepatic steatosis, a quantifiable component of NAFLD, in European ancestry individuals. Here we tested whether these variants were associated with hepatic steatosis in African- and/or Hispanic-Americans and fine-mapped the observed association signals. We measured hepatic steatosis using computed tomography in five African American (n = 3,124) and one Hispanic American (n = 849) cohorts. All analyses controlled for variation in age, age(2) , gender, alcoholic drinks, and population substructure. Heritability of hepatic steatosis was estimated in three cohorts. Variants in/near PNPLA3, NCAN, LYPLAL1, GCKR, and PPP1R3B were tested for association with hepatic steatosis using a regression framework in each cohort and meta-analyzed. Fine-mapping across African American cohorts was conducted using meta-analysis. African- and Hispanic-American cohorts were 33.9/37.5% male, with average age of 58.6/42.6 years and body mass index of 31.8/28.9 kg/m(2) , respectively. Hepatic steatosis was 0.20-0.34 heritable in African- and Hispanic-American families (P < 0.02 in each cohort). Variants in or near PNPLA3, NCAN, GCKR, PPP1R3B in African Americans and PNPLA3 and PPP1R3B in Hispanic Americans were significantly associated with hepatic steatosis; however, allele frequency and effect size varied across ancestries. Fine-mapping in African Americans highlighted missense variants at PNPLA3 and GCKR and redefined the association region at LYPLAL1.Multiple genetic variants are associated with hepatic steatosis across ancestries. This explains a substantial proportion of the genetic predisposition in African- and Hispanic-Americans. Missense variants in PNPLA3 and GCKR are likely functional across multiple ancestries.

A genome-wide association study associated 5 genetic variants with hepatic steatosis (identified by computerized tomography) in individuals of European ancestry. We investigated whether these variants were associated with measures of hepatic steatosis (HS) in non-Hispanic white (NHW), non-Hispanic black, and Mexican American (MA) participants in the US population-based National Health and Nutrition Examination Survey III, phase 2.We analyzed data from 4804 adults (1825 NHW, 1442 non-Hispanic black, and 1537 MA; 51.7% women; mean age at examination, 42.5 y); the weighted prevalence of HS was 37.3%. We investigated whether ultrasound-measured HS, with and without increased levels of alanine aminotransferase (ALT), or level of ALT alone, was associated with rs738409 (patatin-like phospholipase domain-containing protein 3 [PNPLA3]), rs2228603 (neurocan [NCAN]), rs12137855 (lysophospholipase-like 1), rs780094 (glucokinase regulatory protein [GCKR]), and rs4240624 (protein phosphatase 1, regulatory subunit 3b [PPP1R3B]) using regression modeling in an additive genetic model, controlling for age, age-squared, sex, and alcohol consumption.The G allele of rs738409 (PNPLA3) and the T allele of rs780094 (GCKR) were associated with HS with a high level of ALT (odds ratio [OR], 1.36; P = .01; and OR, 1.30; P = .03, respectively). The A allele of rs4240624 (PPP1R3B) and the T allele of rs2228603 (NCAN) were associated with HS (OR, 1.28; P = .03; and OR, 1.40; P = .04, respectively). Variants of PNPLA3 and NCAN were associated with ALT level among all 3 ancestries. Some single-nucleotide polymorphisms were associated with particular races or ethnicities: variants in PNPLA3, NCAN, GCKR, and PPP1R3B were associated with NHW and variants in PNPLA3 were associated with MA. No variants were associated with NHB.We used data from the National Health and Nutrition Examination Survey III to validate the association between rs738409 (PNPLA3), rs780094 (GCKR), and rs4240624 (PPP1R3B) with HS, with or without increased levels of ALT, among 3 different ancestries. Some, but not all, associations between variants in NCAN, lysophospholipase-like 1, GCKR, and PPP1R3B with HS (with and without increased ALT level) were significant within subpopulations.

Central obesity, measured by waist circumference (WC) or waist-hip ratio (WHR), is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS) of fat distribution among those of predominantly African ancestry (AA). We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1). Overall, 25 SNPs with single genomic control (GC)-corrected p-values<5.0 × 10(-6) were followed-up (stage 2) in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA) WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10(-8) for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10(-8) for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5 × 10(-8); RREB1: p = 5.7 × 10(-8)). Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region) in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN). Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02). In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce the concept that there are fat distribution loci that are independent of generalized adiposity.

Nonalcoholic fatty liver disease (NAFLD) is a common condition that is most often asymptomatic. It is associated with metabolic syndrome, incident diabetes, carotid atherosclerosis, and endothelial dysfunction, conditions that in turn are strongly linked with brain damage and cognitive impairment. However, it is not known whether NAFLD is associated with structural brain measures in humans.To assess the association between prevalent NAFLD and brain magnetic resonance imaging (MRI) measures.The cross-sectional association between NAFLD and brain MRI measures was assessed from November 6, 2002, to March 16, 2011, in 766 individuals from the Offspring cohort of the Framingham Study. Participants were included if they did not have excessive alcohol intake and were free of stroke and dementia. Data analysis was conducted from December 30, 2015, to June 15, 2016.Nonalcoholic fatty liver disease was assessed by multidetector computed tomographic scans of the abdomen.Linear or logistic regression models were used to evaluate the cross-sectional association between NAFLD and brain MRI measures, adjusting for age, sex, alcohol consumption, visceral adipose tissue, body mass index, menopausal status, systolic blood pressure, hypertension, current smoking, high-density lipoprotein and low-density lipoprotein cholesterol levels, lipid treatment, type 2 diabetes, cardiovascular disease, physical activity, insulin resistance, C-reactive protein levels, and plasma homocysteine values. Brain MRI measures included total cerebral brain volume, hippocampal and white matter hyperintensity volumes, and presence or absence of covert brain infarcts.Of the 766 individuals in the study sample (410 women and 356 men; mean [SD] age at the time of brain MRI, 67 [9] years), 137 (17.9%) had NAFLD. Nonalcoholic fatty liver disease was significantly associated with smaller total cerebral brain volume even after adjustment for all the covariates included in the study (β [SE], -0.26 [0.11]; P = .02). Differences in total cerebral brain volume between those with and without NAFLD corresponded to 4.2 years of brain aging in the general sample and to 7.3 years in individuals younger than 60 years of age. No statistically significant associations were observed between NAFLD and hippocampal or white matter hyperintensity volumes or covert brain infarcts.Nonalcoholic fatty liver disease is associated with a smaller total cerebral brain volume, independent of visceral adipose tissue and cardiometabolic risk factors, pointing to a possible link between hepatic steatosis and brain aging.

Intramuscular fat accumulates between muscle fibers or within muscle cells. We investigated the association of intramuscular fat with other ectopic fat deposits and metabolic risk factors.Participants (n=2945; 50.2% women; mean age 50.8 years) from the Framingham Heart Study underwent multidetector computed tomography scanning of the abdomen. Regions of interest were placed on the left and right paraspinous muscle, and the muscle attenuation (MA) in Hounsfield units was averaged. We examined the association between MA and metabolic risk factors in multivariable models, and additionally adjusted for body mass index (BMI) and visceral adipose tissue (VAT) in separate models. MA was associated with dysglycemia, dyslipidemia, and hypertension in both sexes. In women, per standard deviation decrease in MA, there was a 1.34 (95% confidence interval, 1.10-1.64) increase in the odds of diabetes mellitus, a 1.40 (95% confidence interval, 1.22-1.61) increase in the odds of high triglycerides, and a 1.29 (95% confidence interval, 1.12-1.48) increase in the odds of hypertension. However, none of these associations persisted after adjustment for BMI or VAT. In men, we observed similar patterns for most risk factors. The exception was metabolic syndrome, which retained association in women even after adjustment for BMI and VAT, and low high density lipoprotein and high triglycerides in men, whose associations also persisted after adjustment for BMI and VAT.MA was associated with metabolic risk factors, but most of these associations were lost after adjustment for BMI or VAT. However, a unique association remained for metabolic syndrome in women and lipids in men.

Diverticular disease is common and has a high morbidity. Treatments are limited owing to the poor understanding of its pathophysiology. Here, to elucidate its etiology, we performed a genome-wide association study of diverticular disease (27,444 cases; 382,284 controls) from the UK Biobank and tested for replication in the Michigan Genomics Initiative (2,572 cases; 28,649 controls). We identified 42 loci associated with diverticular disease; 39 of these loci are novel. Using data-driven expression-prioritized integration for complex traits (DEPICT), we show that genes in these associated regions are significantly enriched for expression in mesenchymal stem cells and multiple connective tissue cell types and are co-expressed with genes that have a role in vascular and mesenchymal biology. Genes in these associated loci have roles in immunity, extracellular matrix biology, cell adhesion, membrane transport and intestinal motility. Phenome-wide association analysis of the 42 variants shows a common etiology of diverticular disease with obesity and hernia. These analyses shed light on the genomic landscape of diverticular disease.

Nonalcoholic fatty liver disease (NAFLD) is rapidly becoming the most common cause of chronic liver disease worldwide.1Dietrich P. Hellerbrand C. Non-alcoholic fatty liver disease, obesity and the metabolic syndrome.Best Pract Res Clin Gastroenterol. 2014; 28: 637-653Crossref PubMed Scopus (258) Google Scholar, 2Anstee Q.M. Targher G. Day C.P. Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis.Nat Rev Gastroenterol Hepatol. 2013; 10: 330-344Crossref PubMed Scopus (1017) Google Scholar NAFLD includes a spectrum of disease ranging from the accumulation of fat in the liver (steatosis) to histologic evidence of necroinflammation (nonalcoholic steatohepatitis [NASH]), then fibrosis and cirrhosis, in the absence of excessive alcohol ingestion.2Anstee Q.M. Targher G. Day C.P. Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis.Nat Rev Gastroenterol Hepatol. 2013; 10: 330-344Crossref PubMed Scopus (1017) Google Scholar, 3Clark J.M. The epidemiology of nonalcoholic fatty liver disease in adults.J Clin Gastroenterol. 2006; 40: S5-S10PubMed Google Scholar Approximately one-third of the US population has radiologic evidence of NAFLD. Although the majority (70%–90%) will have relatively benign simple steatosis,4Hernaez R. McLean J. Lazo M. et al.Association between variants in or near PNPLA3, GCKR, and PPP1R3B with ultrasound-defined steatosis based on data from the third National Health and Nutrition Examination Survey.Clin Gastroenterol Hepatol. 2013; 11: 1183-1190 e2Abstract Full Text Full Text PDF PubMed Scopus (93) Google Scholar, 5Speliotes E.K. Massaro J.M. Hoffmann U. et al.Fatty liver is associated with dyslipidemia and dysglycemia independent of visceral fat: the Framingham Heart Study.Hepatology. 2010; 51: 1979-1987Crossref PubMed Scopus (281) Google Scholar, 6Browning J.D. Szczepaniak L.S. Dobbins R. et al.Prevalence of hepatic steatosis in an urban population in the United States: impact of ethnicity.Hepatology. 2004; 40: 1387-1395Crossref PubMed Scopus (2859) Google Scholar NAFLD may progress to cirrhosis or hepatocellular carcinoma, and can lead to liver failure in the absence of lifestyle change or effective pharmacological treatments.2Anstee Q.M. Targher G. Day C.P. Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis.Nat Rev Gastroenterol Hepatol. 2013; 10: 330-344Crossref PubMed Scopus (1017) Google Scholar, 7Harrison S.A. Neuschwander-Tetri B.A. Nonalcoholic fatty liver disease and nonalcoholic steatohepatitis.Clin Liver Dis. 2004; 8: 861-879Abstract Full Text Full Text PDF PubMed Scopus (99) Google Scholar Although morbidity and mortality from liver disease are increased greatly in patients with NAFLD, morbidity and mortality from cardiovascular disease is even more prevalent in this population.8Review T. LaBrecque D.R. Abbas Z. et al.World Gastroenterology Organisation global guidelines: Nonalcoholic fatty liver disease and nonalcoholic steatohepatitis.J Clin Gastroenterol. 2014; 48: 467-473Crossref PubMed Scopus (248) Google Scholar NAFLD, a complex trait influenced by interpatient genetic variations and environmental influences, is widely considered to be the hepatic manifestation of the metabolic syndrome.1Dietrich P. Hellerbrand C. Non-alcoholic fatty liver disease, obesity and the metabolic syndrome.Best Pract Res Clin Gastroenterol. 2014; 28: 637-653Crossref PubMed Scopus (258) Google Scholar, 2Anstee Q.M. Targher G. Day C.P. Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis.Nat Rev Gastroenterol Hepatol. 2013; 10: 330-344Crossref PubMed Scopus (1017) Google Scholar It correlates epidemiologically with the presence of features of the metabolic syndrome, which consists of having ≥3 of the following: impaired fasting glucose, central obesity, dyslipidemia (low high-density lipoprotein cholesterol, high low-density lipoprotein [LDL], or both) and hypertension.8Review T. LaBrecque D.R. Abbas Z. et al.World Gastroenterology Organisation global guidelines: Nonalcoholic fatty liver disease and nonalcoholic steatohepatitis.J Clin Gastroenterol. 2014; 48: 467-473Crossref PubMed Scopus (248) Google Scholar There is substantial interpatient variation in which features of the metabolic syndrome are exhibited, and which clinical sequelae an individual may develop. In some cases the metabolic syndrome predisposes to NAFLD9Hamaguchi M. Kojima T. Takeda N. et al.The metabolic syndrome as a predictor of nonalcoholic fatty liver disease.Ann Intern Med. 2005; 143: 722-728Crossref PubMed Scopus (827) Google Scholar and in others to cardiovascular disease.10Wang J. Ruotsalainen S. Moilanen L. et al.The metabolic syndrome predicts cardiovascular mortality: a 13-year follow-up study in elderly non-diabetic Finns.Eur Heart J. 2007; 28: 857-864Crossref PubMed Scopus (252) Google Scholar Determining why this occurs is critical to making clinical recommendations based on personal rather than population risk. Although the exact cause of NAFLD or NASH has not been elucidated, we are now able to begin to understand the genetic basis for the disease. NAFLD clusters in families,11Schwimmer J.B. Celedon M.A. Lavine J.E. et al.Heritability of nonalcoholic fatty liver disease.Gastroenterology. 2009; 136: 1585-1592Abstract Full Text Full Text PDF PubMed Scopus (321) Google Scholar and its heritability is estimated to be 26%–27% for CT-measured hepatic steatosis.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar Genome-wide association studies (GWAS) and candidate gene studies have provided important insights into the genetic contribution to NAFLD.13Anstee Q.M. Day C.P. The genetics of NAFLD.Nat Rev Gastroenterol Hepatol. 2013; 10: 645-655Crossref PubMed Scopus (230) Google Scholar The nonsynonymous single nucleotide polymorphism (SNP), rs738409 (c.444 C>G, I148M) in patatin-like phospholipase domain-containing 3 (PNPLA3) was associated significantly with 1H-magnetic resonance spectroscopy measured hepatic triglyceride (TG) content14Romeo S. Kozlitina J. Xing C. et al.Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2008; 40: 1461-1465Crossref PubMed Scopus (2096) Google Scholar and has subsequently been validated globally as a major genetic determinant of not only steatosis, but also severity of NASH, stage of hepatic fibrosis/cirrhosis, and occurrence of NAFLD-associated HCC.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar, 15Liu Y.L. Patman G.L. Leathart J.B. et al.Carriage of the PNPLA3 rs738409 C >G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinoma.J Hepatol. 2014; 61: 75-81Abstract Full Text Full Text PDF PubMed Scopus (304) Google Scholar, 16Valenti L. Al-Serri A. Daly A.K. et al.Homozygosity for the patatin-like phospholipase-3/adiponutrin I148M polymorphism influences liver fibrosis in patients with nonalcoholic fatty liver disease.Hepatology. 2010; 51: 1209-1217Crossref PubMed Scopus (479) Google Scholar The largest GWAS meta-analysis for NAFLD to date, using 2.4 million SNPs imputed to HapMap in 7176 individuals of European ancestry, identified common variants at 5 loci. These variants are in or near the genes PNPLA3, GCKR, LYPLAL1, and PPP1R3B, and a region on chromosome 19 (19p13.11) that contains multiple genes and has variously been called NCAN/TM6SF2/CILP2/PBX4 in the literature.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar The variants at most of these loci are also associated with NASH/fibrosis (all but those at PPP1R3B).12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar Variants at the PNPLA3 locus conferred the strongest effect, predisposing to advanced liver disease with an odds ratio (OR) of 3.26 (95% CI, 2.11–7.21), with the variants at the 19p13.11 locus being the second strongest at 1.65 (95% CI, 1.15–2.65) per mutant allele.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar The PNPLA3 and chromosome 19p13.11 locus also associated with histologic NASH/fibrosis in an independent sample of bariatric surgery patients.17Gorden A. Yang R. Yerges-Armstrong L.M. et al.Genetic variation at NCAN locus is associated with inflammation and fibrosis in non-alcoholic fatty liver disease in morbid obesity.Hum Hered. 2013; 75: 34-43Crossref PubMed Scopus (66) Google Scholar Interestingly, NAFLD-associated variants did not result in uniform abnormalities of serum lipids or glycemic and anthropometric traits.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar In particular, variants at the chromosome 19p13.11 locus associated with increased hepatic steatosis/NASH/fibrosis were also associated with decreased serum LDL cholesterol and lower serum TGs,12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar, 18Teslovich T.M. Musunuru K. Smith A.V. et al.Biological, clinical and population relevance of 95 loci for blood lipids.Nature. 2010; 466: 707-713Crossref PubMed Scopus (2703) Google Scholar, 19Willer C.J. Schmidt E.M. Sengupta S. et al.Global Lipids Genetics ConsortiumDiscovery and refinement of loci associated with lipid levels.Nat Genet. 2013; 45: 1274-1283Crossref PubMed Scopus (1769) Google Scholar which was contrary to the usually observed epidemiologic pattern of these traits. Variants at 19p13.11 were not associated significantly with serum glucose or measures of insulin resistance in the best powered analyses at the time.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar, 18Teslovich T.M. Musunuru K. Smith A.V. et al.Biological, clinical and population relevance of 95 loci for blood lipids.Nature. 2010; 466: 707-713Crossref PubMed Scopus (2703) Google Scholar, 19Willer C.J. Schmidt E.M. Sengupta S. et al.Global Lipids Genetics ConsortiumDiscovery and refinement of loci associated with lipid levels.Nat Genet. 2013; 45: 1274-1283Crossref PubMed Scopus (1769) Google Scholar Variants at PNPLA3 and LYPLAL1 did not affect serum lipid or glycemic traits, whereas those at GCKR and PPP1R3B were associated with increased serum LDL cholesterol and lower serum glucose levels.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar These results suggested a heterogeneous etiology to NAFLD and the existence of multiple genetic metabolic disease “subtypes” that may require more precision treatment in the future.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar Work from several groups has now extended these findings. It has recently been reported that a nonsynonymous genetic variant within a gene of unknown function called TM6SF2, transmembrane 6 superfamily member 2, (rs58542926 c.449 C>T) at the 19p13.11 locus was associated with hepatic steatosis in 2,736 individuals genotyped using a human exome chip.20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar This variant is in strong linkage disequilibrium (r2 = 0.798) with variants in the chromosome 19p13.11 locus previously reported to be NAFLD risk factors,12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar making it likely that the new and old signals are the same. Indeed, conditional analyses indicate that TM6SF2 rs58542926 may be the causal variant driving the association at this locus.20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar, 21Liu Y.L. Reeves H.L. Burt A.D. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (384) Google Scholar The TM6SF2 rs58542926 variant has subsequently been associated with severity of NAFLD-associated hepatic fibrosis/cirrhosis (OR, 1.88 [95% CI, 1.41–2.5] for advanced fibrosis per each copy of the minor allele carried), independent of confounding factors including age, diabetes, obesity, or PNPLA3 genotype, in a cohort of >1000 histologically characterized patients,21Liu Y.L. Reeves H.L. Burt A.D. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (384) Google Scholar consistent with previous associations at this locus.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar This association has itself been validated independently21Liu Y.L. Reeves H.L. Burt A.D. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (384) Google Scholar, 22Dongiovanni P. Petta S. Maglio C. et al.Transmembrane 6 superfamily member 2 gene variant disentangles nonalcoholic steatohepatitis from cardiovascular disease.Hepatology. 2015; 61: 506-514Crossref PubMed Scopus (337) Google Scholar and other studies have also associated the TM6SF2 variant with decreased levels of serum LDL cholesterol and TG20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar, 23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar (consistent with the earlier reports12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar). Studies have also described associations of the minor allele at this locus with increased serum alanine transaminase, aspartate transaminase,20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar and increased risk of diabetes,24Morris A.P. Voight B.F. Teslovich T.M. et al.Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.Nat Genet. 2012; 44: 981-990Crossref PubMed Scopus (1377) Google Scholar with decreased serum alkaline phosphatase and lower risk of myocardial infarction,23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar atherosclerosis, and cardiovascular disease22Dongiovanni P. Petta S. Maglio C. et al.Transmembrane 6 superfamily member 2 gene variant disentangles nonalcoholic steatohepatitis from cardiovascular disease.Hepatology. 2015; 61: 506-514Crossref PubMed Scopus (337) Google Scholar (Table 1).Table1Association of Variants at chr 19p13.11 Locus With Manifestations of the Metabolic SyndromeSNP (Minor Allele, MAF)SNP Annotation Gene: Protein ChangeLD (r2) With rs58542926Association With Other TraitsT2DCAD/MIDBPSBPFasting GlucoseHOMA-IRLDL-CTGTCFatty liverALP/ALT/ASTNASH/Fibrosisrs222860312Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar(T, 0.07)exonic: NCAN:P92S0.798NANANANANSaBased on P value after correcting for multiple tests.NSaBased on P value after correcting for multiple tests.↓↓NA↑NA/NA/NA↑rs1040196919Willer C.J. Schmidt E.M. Sengupta S. et al.Global Lipids Genetics ConsortiumDiscovery and refinement of loci associated with lipid levels.Nat Genet. 2013; 45: 1274-1283Crossref PubMed Scopus (1769) Google Scholar(C, 0.09)intronic: SUGP10.97↑↓NSaBased on P value after correcting for multiple tests.NSaBased on P value after correcting for multiple tests.NSaBased on P value after correcting for multiple tests.NA↓↓↓NANA/NA/NANArs1040196924Morris A.P. Voight B.F. Teslovich T.M. et al.Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.Nat Genet. 2012; 44: 981-990Crossref PubMed Scopus (1377) Google Scholar(C, 0.08)intronic: SUGP10.98↑NANANANSaBased on P value after correcting for multiple tests.NSaBased on P value after correcting for multiple tests.↓↓↓NANA/NA/NANArs5854292623Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar(T, 0.084)exonic:TM6SF2:E167KSame SNPNA↓NANANANA↓↓↓NANA/↑/NANArs5854292620Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar(T, 0.07)exonic:TM6SF2:E167KSame SNPNANANANANANA↓↓NA↑↓/↑/↑↑rs5854292621Liu Y.L. Reeves H.L. Burt A.D. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (384) Google Scholar(T, 0.12)exonic:TM6SF2:E167KSame SNPNANANANANANANANANA↑NA/NA/NA↑ALP, alkaline phosphatase; ALT, alanine aminotransferase; AST, aspartate transaminase; CAD/MI, coronary artery disease/myocardial infarction; DBP, diastolic blood pressure; HOMA-IR, homeostatic model assessment for insulin resistance; LDL-C, low-density lipoprotein cholesterol; MAF, minor allele frequency in Europeans; NA, not assessed in the study referenced; NASH, nonalcoholic steatohepatitis; SBP, systolic blood pressure; T2D, type 2 diabetes; TC, total cholesterol; TG, triglycerides; ↑, significant increase; ↓, significant decrease.a Based on P value after correcting for multiple tests. Open table in a new tab ALP, alkaline phosphatase; ALT, alanine aminotransferase; AST, aspartate transaminase; CAD/MI, coronary artery disease/myocardial infarction; DBP, diastolic blood pressure; HOMA-IR, homeostatic model assessment for insulin resistance; LDL-C, low-density lipoprotein cholesterol; MAF, minor allele frequency in Europeans; NA, not assessed in the study referenced; NASH, nonalcoholic steatohepatitis; SBP, systolic blood pressure; T2D, type 2 diabetes; TC, total cholesterol; TG, triglycerides; ↑, significant increase; ↓, significant decrease. Because the association signal in the chromosome 19p13.11 region covers >20 genes and the SNPs across this region are in high LD with one another (highly correlated) and include both known (in TM6SF2, NCAN, CILP2) and yet to be discovered nonsynonymous SNPs, it remains to be proven whether all of these phenotypes are owing to 1 or possibly multiple correlated functional variants/genes in the region. Toward this end, several groups have started to carry out functional experiments with the genes under the GWAS signal and their variants to narrow down the causal gene(s) and variant(s). TM6SF2 rs58542926 c.449 C>T heterozygous variant is a nonsynonymous change producing a glutamate to lysine amino acid substitution at residue 167 (E167K), with the glutamate being highly conserved across mammals.20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar In mice, overexpression of human wild-type TM6SF2 in liver resulted in higher total cholesterol, LDL cholesterol, TGs and lower high-density lipoprotein cholesterol, whereas knockdown of mouse Tm6sf2 in liver resulted in decreased serum total cholesterol.23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar Because the E167K allele results in lower total cholesterol in humans, these data suggest that the E167K mutation in TM6SF2 was a loss of function allele.23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar Kozlitina et al20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar showed that expression of TM6SF2 (E167K) protein is lower than wild type, consistent with this being a loss of function allele, and showed that knockdown of mouse Tm6sf2 resulted in increased liver lipid accumulation and decreased serum TG and LDL. They also found that knockdown of mouse Tm6sf2 resulted in decreased very low-density lipoprotein (VLDL) cholesterol secretion.20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar In other independent work25Mahdessian H. Taxiarchis A. Popov S. et al.TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content.Proc Natl Acad Sci U S A. 2014; 111: 8913-8918Crossref PubMed Scopus (207) Google Scholar using confocal microscopy, investigators observed localization of green fluorescent protein–tagged TM6SF2 to the endoplasmic reticulum in 2 human hepatoma cell lines. Additionally, knockdown of TM6SF2 in both cell lines resulted in reduced secretion of TG-rich lipoproteins, apolipoprotein B, and increased cellular TG levels. At the subcellular level, a marked increase in lipid droplet area, which could be attributed to increases in both the number and average size of lipid droplets, was reported. Conversely, overexpression of TM6SF2 caused a decrease in the number and average size of lipid droplets.25Mahdessian H. Taxiarchis A. Popov S. et al.TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content.Proc Natl Acad Sci U S A. 2014; 111: 8913-8918Crossref PubMed Scopus (207) Google Scholar In parallel experiments, Kozlitina et al20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar also observed an increase in the size and number of lipid droplets in the livers of mice after knockdown of Tm6sf2. These results suggest a role for TM6SF2 in regulating the supply of lipids for the synthesis of TG-rich lipoproteins. Finally, RNAi knockdown of both TM6SF2 and NCAN in HeLa cells resulted in increased free cholesterol,26Blattmann P. Schuberth C. Pepperkok R. et al.RNAi-based functional profiling of loci from blood lipid genome-wide association studies identifies genes with cholesterol-regulatory function.PLoS Genet. 2013; 9: e1003338Crossref PubMed Scopus (40) Google Scholar suggesting that the product of >1 gene in this region may be involved in hepatic lipid handling. Not all the studies have unequivocal findings. Neither Kozlitina et al20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar nor Holmen et al23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar observed changes with serum alkaline phosphatase in the mouse experiments described, contrary to the results observed in humans. Kozlitina et al20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar reported increased accumulation of hepatic TGs in Tm6sf2 knockdown mice, whereas Holmen et al23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar found no evidence of TG accumulation in the livers of Tm6sf2 knockdown mice. Kozlitina et al used adeno-associated virus knockdown, whereas Holmen used adenovirus knockdown of TM6SF2 in liver in C57BL/6J mice. These differences in hepatic steatosis may be owing to differences between humans and mice, to the short duration of gene-altering studies in mouse livers, or to species- or tissue-specific effects of TM6SF2. Targeting just the liver for knockdown/overexpression in mice, for example, may result in phenotypes related to just this organ, whereas TM6SF2, which is expressed more widely, may exert some of its effects via its role in extrahepatic organs. TM6SF2 has highest expression levels in the intestine, where alkaline phosphatase is also expressed (in addition to the liver) and thus TM6SF2 may influence on serum alkaline phosphatase via intestinal effects. The association between TM6SF2 rs58542926 and the NAFLD phenotype spectrum from steatosis to advanced fibrosis/cirrhosis has now been robustly demonstrated in several large independent cohorts12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar, 20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar, 21Liu Y.L. Reeves H.L. Burt A.D. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (384) Google Scholar, 22Dongiovanni P. Petta S. Maglio C. et al.Transmembrane 6 superfamily member 2 gene variant disentangles nonalcoholic steatohepatitis from cardiovascular disease.Hepatology. 2015; 61: 506-514Crossref PubMed Scopus (337) Google Scholar, 25Mahdessian H. Taxiarchis A. Popov S. et al.TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content.Proc Natl Acad Sci U S A. 2014; 111: 8913-8918Crossref PubMed Scopus (207) Google Scholar; however, 2 studies—1 from China27Wong V.W. Wong G.L. Tse C.H. et al.Prevalence of the TM6SF2 variant and non-alcoholic fatty liver disease in Chinese.J Hepatol. 2014; 61: 708-709Abstract Full Text Full Text PDF PubMed Scopus (55) Google Scholar and 1 from South America28Sookoian S. Castano G.O. Scian R. et al.Genetic variation in TM6SF2 and the risk of nonalcoholic fatty liver disease and histological disease severity.Hepatology. 2015; 61: 515-525Crossref PubMed Scopus (149) Google Scholar—have been unable to replicate these associations. This may, in part, be owing to the generally low minor allele frequency of NAFLD associating variants in the 19p13.11 locus and interethnic variations in their frequency of carriage. Specifically, the minor allele at rs58542926 (T), has a frequency of 0.07 in Europeans, 0.04 in Hispanics, and 0.02 in African Americans.29Palmer N.D. Musani S.K. Yerges-Armstrong L.M. et al.Characterization of European ancestry nonalcoholic fatty liver disease-associated variants in individuals of African and Hispanic descent.Hepatology. 2013; 58: 966-975Crossref PubMed Scopus (96) Google Scholar Thus, the liver disease promoting allele at TM6SF2 will affect more individuals of European ancestry than Hispanic or African ancestry. Inadequate statistical power to detect an effect on histologic markers of disease progression is a particular issue in the South American study,28Sookoian S. Castano G.O. Scian R. et al.Genetic variation in TM6SF2 and the risk of nonalcoholic fatty liver disease and histological disease severity.Hepatology. 2015; 61: 515-525Crossref PubMed Scopus (149) Google Scholar where only 226 NAFLD cases with histologically mild disease were included. Of these cases, only 130 had anything more than bland steatosis, but these cases exhibited a mean fibrosis stage of only 1.4 out of 4, further degrading the sensitivity of the study. It is, therefore, not surprising that the authors were unable to detect an association with features of steatohepatitis or fibrosis, whereas groups with larger cohorts have been successful.12Speliotes E.K. Yerges-Armstrong L.M. Wu J. et al.Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.PLoS Genet. 2011; 7: e1001324Crossref PubMed Scopus (662) Google Scholar, 21Liu Y.L. Reeves H.L. Burt A.D. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (384) Google Scholar, 22Dongiovanni P. Petta S. Maglio C. et al.Transmembrane 6 superfamily member 2 gene variant disentangles nonalcoholic steatohepatitis from cardiovascular disease.Hepatology. 2015; 61: 506-514Crossref PubMed Scopus (337) Google Scholar The above functional studies in vivo20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar, 23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar and in vitro20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar, 23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar, 25Mahdessian H. Taxiarchis A. Popov S. et al.TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content.Proc Natl Acad Sci U S A. 2014; 111: 8913-8918Crossref PubMed Scopus (207) Google Scholar suggest that the TM6SF2 gene affects hepatic lipid efflux, with its deletion or mutation resulting in a reduction of lipoprotein secretion (VLDL, TG, and apolipoprotein B) coincident with increased hepatocellular lipid droplet size and TG content. The 19p13.11 locus overall, and the TM6SF2 rs58542926 variant in particular, provide new insights into the mechanistic basis of progressive NAFLD, and the association between NAFLD and cardiovascular disease. They suggest that TM6SF2 is an important determinant of clinical outcome across metabolic syndrome related end-organ damage. Indeed, current evidence suggests that TM6SF2 may act as a ‘switch’ with TM6SF2 rs58542926 T-allele mediating hepatic retention of TG and cholesterol predisposing to NAFLD-fibrosis, whereas C-allele carriage promotes VLDL excretion, protecting the liver at the expense of increased risk of atherosclerosis and cardiovascular disease (Figure 1). Thus, although in the general population, NAFLD is associated with an increased risk of cardiovascular disease, these can become dissociated: individuals carrying the minor (T) allele of TM6SF2 rs58542926 (167K) may be prone to experience liver-related rather than cardiovascular morbidity and mortality.2Anstee Q.M. Targher G. Day C.P. Progression of NAFLD to diabetes mellitus, cardiovascular disease or cirrhosis.Nat Rev Gastroenterol Hepatol. 2013; 10: 330-344Crossref PubMed Scopus (1017) Google Scholar, 30Ekstedt M. Franzen L.E. Mathiesen U.L. et al.Long-term follow-up of patients with NAFLD and elevated liver enzymes.Hepatology. 2006; 44: 865-873Crossref PubMed Scopus (1728) Google Scholar, 31Zhou Y. Llauradó G. Oresic M. et al.Circulating triacylglycerol signatures and insulin sensitivity in NAFLD associated with the E167K variant in TM6SF2.J Hepatol. 2015; 62: 657-663Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar Corroborating this finding, even though only about 0.5% of individuals of European ancestry in the population are homozygous for the minor allele of TM6SF2, 1.5% of individuals selected for having histologic NASH/fibrosis have this genotype, suggesting that carrying 2 copies of the T allele predisposes to developing advanced liver disease.21Liu Y.L. Reeves H.L. Burt A.D. et al.TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.Nat Commun. 2014; 5: 4309Crossref PubMed Scopus (384) Google Scholar In contrast, carriage of the C-allele is associated with multiple classic characteristics of the metabolic syndrome, including dyslipidemia and cardiovascular disease.23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar Thus, carrying the T allele protects against development of dyslipidemia and cardiovascular disease.23Holmen O.L. Zhang H. Fan Y. et al.Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.Nat Genet. 2014; 46: 345-351Crossref PubMed Scopus (202) Google Scholar Whether the effects of variants at the 167 position will be strong enough to overshadow the effects of many other environmental or genetic variants on the risk of liver and cardiovascular disease at an individual level, and so merit distinct medical recommendations for patients carrying this allele, remains to be determined. Nevertheless, studying the effects of NAFLD-associated human genetic variants on related metabolic traits promises to teach us much about how these traits interrelate to one another pathophysiologically. Although we have learned many things already from these discoveries, some interesting questions remain. The T allele of TM6SF2 rs58542926 has been associated with decreased alkaline phosphatase levels, but how the E167K change in TM6SF2 actually results in this biochemical effect remains to be determined. Interestingly, knocking down hepatic TM6SF2 expression did not result in changes in serum alkaline phosphatase.20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar Because TM6SF2 is expressed not only in liver but also in intestine where alkaline phosphatase is also present at high levels, the authors suggest that intestine may be where the E167K change may exert its effect to cause lower levels of alkaline phosphatase.20Kozlitina J. Smagris E. Stender S. et al.Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2014; 46: 352-356Crossref PubMed Scopus (701) Google Scholar This theory remains to be tested. Another unresolved question relates to the role of TM6SF2 in the development of type 2 diabetes mellitus. Although one large meta-analysis suggests that TM6SF2 T-allele carriage is associated with an increased risk of type 2 diabetes,24Morris A.P. Voight B.F. Teslovich T.M. et al.Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.Nat Genet. 2012; 44: 981-990Crossref PubMed Scopus (1377) Google Scholar its effect on serum glucose and on insulin resistance is not significant24Morris A.P. Voight B.F. Teslovich T.M. et al.Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.Nat Genet. 2012; 44: 981-990Crossref PubMed Scopus (1377) Google Scholar and direct evidence of an effect on insulin sensitivity is currently lacking, with clamp studies finding no reduction in whole body, hepatic, or adipose tissue insulin sensitivity.31Zhou Y. Llauradó G. Oresic M. et al.Circulating triacylglycerol signatures and insulin sensitivity in NAFLD associated with the E167K variant in TM6SF2.J Hepatol. 2015; 62: 657-663Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar Further research, perhaps utilizing stable global and tissue-specific knockouts of TM6SF2 in mice, may help to clarify these questions. Even though there is evidence that the E167K mutation of TM6SF2 results in less VLDL in serum, the exact mechanism by which this occurs is not known. Because VLDL formation requires a multistep process where TGs are combined with apolipoproteins that are then secreted, altered, and eventually taken up again by the liver as VLDL remnants, how if at all this cycle is disrupted by the E167K variant at TM6SF2 remains to be tested. Because chylomicron assembly and circulation in intestine parallels VLDL assembly and circulation in liver and because TM6SF2 is also expressed in intestine, it remains to be determined whether chylomicron biology is also affected by the E167K TM6SF2 change in humans and mice. Through further study of TM6SF2 and other NAFLD-related loci, we will be able to better understand the mechanisms by which metabolic disease develops so that we can hopefully better tailor clinical recommendations for disease treatment in the future. Indeed, although genetic testing for common diseases is currently limited, this may change with a better understanding of how this information can be used to inform patient care.

Fatty liver is the hepatic manifestation of obesity, but community-based assessment of fatty liver among unselected patients is limited. We sought to determine the feasibility of and optimal protocol for quantifying fat content in the liver in the Framingham Heart Study using multidetector computed tomography (MDCT) scanning.Participants (n = 100, 49% women, mean age 59.4 years, mean body mass index 27.8 kg/m(2)) were drawn from the Framingham Heart Study cohort. Two readers measured the attenuation of the liver, spleen, paraspinal muscles, and an external standard from MDCT scans using multiple slices in chest and abdominal scans.The mean measurement variation was larger within a single axial computed tomography (CT) slice than between multiple axial CT slices for the liver and spleen, whereas it was similar for the paraspinal muscles. Measurement variation in the liver, spleen, and paraspinal muscles was smaller in the abdomen than in the chest. Three versus six measures of attenuation in the liver and two versus three measures in the spleen gave reproducible measurements of tissue attenuation (intraclass correlation coefficient [ICCC] of 1 in the abdomen). Intra reader and interreader reproducibility (ICCC) of the liver-to-spleen ratio was 0.98 and 0.99, the liver-to-phantom ratio was 0.99 and 0.99, and the liver-to-muscle ratio was 0.93 and 0.86, respectively.One cross-sectional slice is adequate to capture the majority of variance of fat content in the liver per individual. Abdominal scan measures as compared to chest scan measures of fat content in the liver are more precise. The measurement of fat content in the liver on MDCT scans is feasible and reproducible.

To investigate the genetic architecture of severe obesity, we performed a genome-wide association study of 775 cases and 3197 unascertained controls at ∼550 000 markers across the autosomal genome. We found convincing association to the previously described locus including the FTO gene. We also found evidence of association at a further six of 12 other loci previously reported to influence body mass index (BMI) in the general population and one of three associations to severe childhood and adult obesity and that cases have a higher proportion of risk-conferring alleles than controls. We found no evidence of homozygosity at any locus due to identity-by-descent associating with phenotype which would be indicative of rare, penetrant alleles, nor was there excess genome-wide homozygosity in cases relative to controls. Our results suggest that variants influencing BMI also contribute to severe obesity, a condition at the extreme of the phenotypic spectrum rather than a distinct condition.

Obesity-associated non-alcoholic fatty liver disease (NAFLD) may cause liver dysfunction and failure. In a previously reported genome-wide association meta-analysis, single nucleotide polymorphisms (SNPs) near PNPLA3, NCAN, GCKR, LYPLAL1 and PPP1R3B were associated with NAFLD and with distinctive serum lipid profiles. The present study examined the relevance of these variants to NAFLD in extreme obesity.In 1,092 bariatric surgery patients, the candidate SNPs were genotyped and association analyses with liver histology and serum lipids were performed.We replicated the association of hepatosteatosis with PNPLA3 rs738409[G] and with NCAN rs2228603[T]. We also replicated the association of rs2228603[T] with hepatic inflammation and fibrosis. rs2228603[T] was associated with lower serum low-density lipoprotein, total cholesterol and triglycerides. After stratification by the presence or absence of NAFLD, these associations were present predominantly in the subgroup with NAFLD.NCAN rs2228603[T] is a risk factor for liver inflammation and fibrosis, suggesting that this locus is responsible for progression from steatosis to steatohepatitis. In this bariatric cohort, rs2228603[T] was associated with low serum lipids only in patients with NAFLD. This supports a NAFLD model in which the liver may sequester triglycerides as a result of either increased triglyceride uptake and/or decreased lipolysis.

Patients with nonalcoholic fatty liver disease (NAFLD) have an increased risk of cardiovascular disease; however, it is not known whether NAFLD contributes to cardiovascular disease independent of established risk factors. We examined the association between NAFLD and vascular function.We conducted a cross-sectional study of 2284 Framingham Heart Study participants without overt cardiovascular disease who had liver fat attenuation measured on computed tomography and who had measurements of vascular function and covariates. We evaluated the association between NAFLD and vascular function using multivariable partial correlations adjusting for age, sex, cohort, smoking, diabetes mellitus, hyperlipidemia, hypertension, body mass index, and visceral adipose tissue. The prevalence of NAFLD in our sample (mean age, 52±12 years; 51.4% women) was 15.3%. In age-, sex-, and cohort-adjusted analyses, greater liver fat was modestly associated with lower flow-mediated dilation (r=-0.05; P=0.02), lower peripheral arterial tonometry ratio (r=-0.20; P<0.0001), higher carotid-femoral pulse wave velocity (r=0.13; P<0.0001), and higher mean arterial pressure (r=0.11; P<0.0001). In multivariable-adjusted models, NAFLD remained associated with higher mean arterial pressure (r=0.06; P=0.005) and lower peripheral arterial tonometry ratio (r=-0.12; P<0.0001). The association between NAFLD and peripheral arterial tonometry ratio persisted after further adjustment for body mass index and visceral adipose tissue.For multiple measures of vascular function, the relationship with NAFLD appeared largely determined by shared cardiometabolic risk factors. The persistent relationship with reduced peripheral arterial tonometry response beyond established risk factors suggests that NAFLD may contribute to microvascular dysfunction.

To date, genome-wide association studies (GWASs) have identified >100 loci with single variants associated with body mass index (BMI). This approach may miss loci with high allelic heterogeneity; therefore, the aim of the present study was to use gene-based meta-analysis to identify regions with high allelic heterogeneity to discover additional obesity susceptibility loci. We included GWAS data from 123 865 individuals of European descent from 46 cohorts in Stage 1 and Metabochip data from additional 103 046 individuals from 43 cohorts in Stage 2, all within the Genetic Investigation of ANthropometric Traits (GIANT) consortium. Each cohort was tested for association between ∼2.4 million (Stage 1) or ∼200 000 (Stage 2) imputed or genotyped single variants and BMI, and summary statistics were subsequently meta-analyzed in 17 941 genes. We used the 'VErsatile Gene-based Association Study' (VEGAS) approach to assign variants to genes and to calculate gene-based P-values based on simulations. The VEGAS method was applied to each cohort separately before a gene-based meta-analysis was performed. In Stage 1, two known (FTO and TMEM18) and six novel (PEX2, MTFR2, SSFA2, IARS2, CEP295 and TXNDC12) loci were associated with BMI (P < 2.8 × 10(-6) for 17 941 gene tests). We confirmed all loci, and six of them were gene-wide significant in Stage 2 alone. We provide biological support for the loci by pathway, expression and methylation analyses. Our results indicate that gene-based meta-analysis of GWAS provides a useful strategy to find loci of interest that were not identified in standard single-marker analyses due to high allelic heterogeneity.

Cirrhosis is characterized by extensive fibrosis of the liver and is a major cause of liver-related mortality. Cirrhosis is partially heritable but genetic contributions to cirrhosis have not been systemically explored. Here, we carry out association analyses with cirrhosis in two large biobanks and determine the effects of cirrhosis associated variants on multiple human disease/traits.We carried out a genome-wide association analysis of cirrhosis as a diagnosis in UK BioBank (UKBB; 1088 cases vs. 407 873 controls) and then tested top-associating loci for replication with cirrhosis in a hospital-based cohort from the Michigan Genomics Initiative (MGI; 875 cases of cirrhosis vs. 30 346 controls). For replicating variants or variants previously associated with cirrhosis that also affected cirrhosis in UKBB or MGI, we determined single nucleotide polymorphism effects on all other diagnoses in UKBB (PheWAS), common metabolic traits/diseases and serum/plasma metabolites.Unbiased genome-wide association study identified variants in/near PNPLA3 and HFE, and candidate variant analysis identified variants in/near TM6SF2, MBOAT7, SERPINA1, HSD17B13, STAT4 and IFNL4 that reproducibly affected cirrhosis. Most affected liver enzyme concentrations and/or aspartate transaminase-to-platelet ratio index. PheWAS, metabolic trait and serum/plasma metabolite association analyses revealed effects of these variants on lipid, inflammatory and other processes including new effects on many human diseases and traits.We identified eight loci that reproducibly associate with population-based cirrhosis and define their diverse effects on human diseases and traits.

A glutamate-to-lysine variant (rs58542926-T) in transmembrane 6 superfamily member 2 (<i>TM6SF2</i>) is associated with increased fatty liver disease and diabetes in conjunction with decreased cardiovascular disease risk. To identify mediators of the effects of <i>TM6SF2</i>, we tested for associations between rs58542926-T and serum lipoprotein/metabolite measures in cross-sectional data from nondiabetic statin-naïve participants. We identified independent associations between rs58542926-T and apoB-100 particles (β = −0.057 g/l, <i>P</i> = 1.99 × 10⁻¹⁴) and tyrosine levels (β = 0.0020 mmol/l, <i>P</i> = 1.10 × 10⁻⁸), controlling for potential confounders, in 6,929 Finnish men. The association between rs58542926-T and apoB-100 was confirmed in an independent sample of 2,196 Finnish individuals from the FINRISK study (β_replication = −0.029, <i>P</i>_replication = 0.029). Secondary analyses demonstrated an rs58542926-T dose-dependent decrease in particle concentration, cholesterol, and triglyceride (TG) content for VLDL and LDL particles (<i>P</i> < 0.001 for all). No significant associations between rs58542926-T and HDL measures were observed. <i>TM6SF2</i> SNP rs58542926-T and tyrosine levels were associated with increased incident T2D risk in both METSIM and FINRISK. Decreased liver production/secretion of VLDL, decreased cholesterol and TGs in VLDL/LDL particles in serum, and increased tyrosine levels identify possible mechanisms by which rs58542926-T exerts its effects on increasing risk of fatty liver disease, decreasing cardiovascular disease, and increasing diabetes risk, respectively.

Nonalcoholic fatty liver disease (NAFLD) is caused by hepatic steatosis, which can progress to nonalcoholic steatohepatitis, fibrosis/cirrhosis, and hepatocellular carcinoma in the absence of excessive alcohol consumption. Nonalcoholic fatty liver disease will become the number one cause of liver disease worldwide by 2020. Nonalcoholic fatty liver disease is correlated albeit imperfectly with obesity and other metabolic diseases such as diabetes, hyperlipidemia, and cardiovascular disease, but exactly how having one of these diseases contributes to the development of other metabolic diseases is only now being elucidated. Development of NAFLD and related metabolic diseases is genetically influenced in the population, and recent genome-wide association studies (GWASs) have discovered genetic variants that associate with these diseases. These GWAS-associated variants cannot only help us to identify individuals at high risk of developing NAFLD, but also to better understand its pathophysiology so that we can develop more effective treatments for this disease and related metabolic diseases in the future.

The accumulation of excess fat in the liver (hepatic steatosis) in the absence of heavy alcohol consumption causes nonalcoholic fatty liver disease (NAFLD), which has become a global epidemic. Identifying metabolic risk factors that interact with the genetic risk of NAFLD is important for reducing disease burden. We tested whether serum glucose, insulin, insulin resistance, triglyceride (TG), low‐density lipoprotein cholesterol, high‐density lipoprotein cholesterol, body mass index (BMI), and waist‐to‐hip ratio adjusted for BMI interact with genetic variants in or near the patatin‐like phospholipase domain containing 3 ( PNPLA3 ) gene, the glucokinase regulatory protein ( GCKR ) gene, the neurocan/transmembrane 6 superfamily member 2 ( NCAN/TM6SF2 ) gene , and the lysophospholipase‐like 1 ( LYPLAL1 ) gene to exacerbate hepatic steatosis, estimated by liver attenuation. We performed association analyses in 10 population‐based cohorts separately and then meta‐analyzed results in up to 14,751 individuals (11,870 of European ancestry and 2,881 of African ancestry). We found that PNPLA3‐ rs738409 significantly interacted with insulin, insulin resistance, BMI, glucose, and TG to increase hepatic steatosis in nondiabetic individuals carrying the G allele. Additionally, GCKR‐ rs780094 significantly interacted with insulin, insulin resistance, and TG. Conditional analyses using the two largest European ancestry cohorts in the study showed that insulin levels accounted for most of the interaction of PNPLA3‐ rs738409 with BMI, glucose, and TG in nondiabetic individuals. Insulin, PNPLA3 ‐rs738409, and their interaction accounted for at least 8% of the variance in hepatic steatosis in these two cohorts. Conclusion: Insulin resistance, either directly or through the resultant elevated insulin levels, more than other metabolic traits, appears to amplify the PNPLA3 ‐rs738409‐G genetic risk for hepatic steatosis. Improving insulin resistance in nondiabetic individuals carrying PNPLA3‐ rs738409‐G may preferentially decrease hepatic steatosis.

Nonalcoholic fatty liver disease (NAFLD) is a risk factor for type 2 diabetes (T2D). We aimed to identify the peripheral blood DNA methylation signature of hepatic fat. We conducted epigenome-wide association studies of hepatic fat in 3,400 European ancestry (EA) participants and in 401 Hispanic ancestry and 724 African ancestry participants from four population-based cohort studies. Hepatic fat was measured using computed tomography or ultrasound imaging and DNA methylation was assessed at &amp;gt;400,000 cytosine-guanine dinucleotides (CpGs) in whole blood or CD14+ monocytes using a commercial array. We identified 22 CpGs associated with hepatic fat in EA participants at a false discovery rate &amp;lt;0.05 (corresponding P = 6.9 × 10−6) with replication at Bonferroni-corrected P &amp;lt; 8.6 × 10−4. Mendelian randomization analyses supported the association of hypomethylation of cg08309687 (LINC00649) with NAFLD (P = 2.5 × 10−4). Hypomethylation of the same CpG was also associated with risk for new-onset T2D (P = 0.005). Our study demonstrates that a peripheral blood–derived DNA methylation signature is robustly associated with hepatic fat accumulation. The hepatic fat–associated CpGs may represent attractive biomarkers for T2D. Future studies are warranted to explore mechanisms and to examine DNA methylation signatures of NAFLD across racial/ethnic groups.

Steatotic liver disease (SLD), characterized by elevated liver fat content (LFC), is influenced by genetics and diet. However, whether diet has differential effect based on genetic risk is not well-characterized. We aimed to determine how genetic factors interact with diet to affect SLD in a large national biobank.We included UK Biobank participants with dietary intake measured by 24-hour recall and genotyping. The primary predictors were dietary pattern, PNPLA3-rs738409-G, TM6SF2-rs58542926-T, a 16-variant hepatic steatosis polygenic risk score (PRS), and gene-environment interactions. The primary outcome was LFC, and secondary outcomes were iron-controlled T1 time (cT1, a measure of liver inflammation and fibrosis) and liver-related events/mortality.21,619 participants met inclusion criteria. In non-interaction models, Mediterranean diet and intake of fruit/vegetables/legumes and fish associated with lower LFC, while higher red/processed meat intake and all genetic predictors associated with higher LFC. In interaction models, all genetic predictors interacted with Mediterranean diet and fruit/vegetable/legume intake; the steatosis PRS interacted with fish intake; and TM6SF2 genotype interacted with red/processed meat intake, to affect LFC. Dietary effects on LFC were up to 3.8 times as high in PNPLA3-rs738409-GG vs. -CC individuals, and 1.4-3.0 times as high in the top vs. bottom quartile of the steatosis PRS. Gene-diet interactions were stronger in participants with vs. without overweight. The steatosis PRS interacted with Mediterranean diet and fruit/vegetable/legume intake to affect cT1 and most dietary and genetic predictors associated with risk of liver-related events or mortality by age 70.Effects of diet on LFC and cT1 were markedly accentuated in patients at increased genetic risk for SLD, implying dietary interventions may be more impactful in these populations.

Basic fibroblast growth factor (bFGF) is a polypeptide with potent trophic effects on brain neurons, glia, and endothelial cells. In the current study, we used Northern blotting, in situ hybridization, and immunohistochemical techniques to examine bFGF expression in brain following focal infarction due to permanent occlusion of the proximal middle cerebral artery in mature Sprague-Dawley rats. We found a four-fold increase in bFGF mRNA in tissue surrounding focal infarcts at 1 day after ischemia. In situ hybridization showed that this increase was found throughout several structures in the ipsilateral hemisphere, including frontoparietal, temporal, and cingulate cortex, as well as in caudoputamen, globus pallidus, septal nuclei, nucleus accumbens, and olfactory tubercle. Increased bFGF mRNA expression was associated with cells having the distinct morphological appearance of astroglia in these structures. Immunohistochemistry showed an increase in the size and number of bFGF-immunoreactive (IR) nuclei in these same structures, as well as a shift from nuclear to nuclear plus cytoplasmic localization of immunoreactivity, beginning at 1 day, and peaking at 3 days after ischemia. Double immunostaining identified bFGF-IR cells as astroglia in these structures. (An exception was the piriform cortex, in which both increased bFGF mRNA levels and increased bFGF-IR was found in neurons at 1 day after ischemia). Overall, the peak of increased bFGF expression preceded the peak in expression of the astroglial marker GFAP within the ipsilateral hemisphere. Increased bFGF expression may play an important role in the glial, neuronal, and vascular changes occurring after focal infarction.

Non-alcoholic fatty liver disease is an epidemic. Identifying modifiable risk factors for non-alcoholic fatty liver disease development is essential to design effective prevention programmes. We tested whether 25-year patterns of body mass index change are associated with midlife non-alcoholic fatty liver disease.In all, 4423 participants from Coronary Artery Risk Development in Young Adults, a prospective population-based biracial cohort (age 18-30), underwent body mass index measurement at baseline (1985-1986) and 3 or more times over 25 years. At Year 25, 3115 had liver fat assessed by non-contrast computed tomography. Non-alcoholic fatty liver disease was defined as liver attenuation ≤40 Hounsfield Units after exclusions. Latent mixture modelling identified 25-year trajectories in body mass index per cent change (%Δ) from baseline.We identified four distinct trajectories of BMI%Δ: stable (26.2% of cohort, 25-year BMI %Δ = 3.1%), moderate increase (46.0%, BMI%Δ = 21.7%), high increase (20.9%, BMI%Δ = 41.9%) and extreme increase (6.9%, BMI%Δ = 65.9%). Y25 non-alcoholic fatty liver disease prevalence was higher in groups with greater BMI %Δ: 4.1%, 9.3%, 13.0%, and 17.6%, respectively (P-trend <.0001). In multivariable analyses, participants with increasing BMI%Δ had increasingly greater odds of non-alcoholic fatty liver disease compared to the stable group: OR: 3.35 (95% CI: 2.07-5.42), 7.80 (4.60-13.23) and 12.68 (6.68-24.09) for moderate, high and extreme body mass index increase, respectively. Associations were only moderately attenuated when adjusted for baseline or Y25 body mass index.Trajectories of weight gain during young adulthood are associated with greater non-alcoholic fatty liver disease prevalence in midlife independent of metabolic covariates and baseline or concurrent body mass index highlighting the importance of weight maintenance throughout adulthood as a target for primary non-alcoholic fatty liver disease prevention.

Obesity is a heritable trait that contributes to substantial global morbidity and mortality. Here, we summarize findings from the past decade of genetic and epigenetic research focused on unravelling the underpinnings of adiposity. More than 140 genetic regions now are known to influence adiposity traits. The genetics of general adiposity, as measured by body mass index, and that of abdominal obesity, as measured by waist-to-hip ratio, have distinct biological backgrounds. Gene expression associated with general adiposity is enriched in the nervous system. In contrast, genes associated with abdominal adiposity function in adipose tissue. Recent population-based epigenetic analyses have highlighted additional distinct loci. We discuss how associated genetic variants can lead to understanding causal mechanisms, and to disentangling reverse causation in epigenetic analyses. Discoveries emerging from population genomics are identifying new disease markers and potential novel drug targets to better define and combat obesity and related diseases. Obesity is a heritable trait that contributes to substantial global morbidity and mortality. Here, we summarize findings from the past decade of genetic and epigenetic research focused on unravelling the underpinnings of adiposity. More than 140 genetic regions now are known to influence adiposity traits. The genetics of general adiposity, as measured by body mass index, and that of abdominal obesity, as measured by waist-to-hip ratio, have distinct biological backgrounds. Gene expression associated with general adiposity is enriched in the nervous system. In contrast, genes associated with abdominal adiposity function in adipose tissue. Recent population-based epigenetic analyses have highlighted additional distinct loci. We discuss how associated genetic variants can lead to understanding causal mechanisms, and to disentangling reverse causation in epigenetic analyses. Discoveries emerging from population genomics are identifying new disease markers and potential novel drug targets to better define and combat obesity and related diseases. Michael MendelsonView Large Image Figure ViewerDownload Hi-res image Download (PPT)Elizabeth K. SpeliotesView Large Image Figure ViewerDownload Hi-res image Download (PPT) Obesity is a global epidemic and its subsequent health conditions, including nonalcoholic fatty liver disease, type 2 diabetes, and cardiovascular disease, result in extensive morbidity, mortality, and health care expenditures (Figure 1).1Lette M. Bemelmans W.J. Breda J. et al.Health care costs attributable to overweight calculated in a standardized way for three European countries.Eur J Health Econ. 2016; 17: 61-69Crossref PubMed Scopus (26) Google Scholar Few effective treatments exist for obesity, in part owing to a limited understanding of its complex and multifactorial etiology. Discoveries emerging from population genomics are identifying biomarkers and relevant causal mechanisms, which enable the development of better preventive, diagnostic, and therapeutic approaches. Measures of adiposity are heritable across generations, in part owing to inherited variations in the genetic code.2Nan C. Guo B. Warner C. et al.Heritability of body mass index in pre-adolescence, young adulthood and late adulthood.Eur J Epidemiol. 2012; 27: 247-253Crossref PubMed Scopus (72) Google Scholar In addition to genetic contributions, obesity is the result of a complex interplay of environmental, behavioral, and social factors, which can be relayed from parent to offspring independent of genetic sequence variation. At the molecular level, exposures may influence obesity through lasting epigenetic modifications of DNA. With advances in genomic technologies we can integrate genetic, epigenetic, and environment factors among thousands of individuals to gain insight into the biology of obesity and related traits. Although the vast majority of the human DNA code is nonvariable, a typical genome is reported to differ from a reference human genome at 4.1–5.0 million sites.3Auton A. Brooks L.D. et al.1000 Genomes Project ConsortiumA global reference for human genetic variation.Nature. 2015; 526: 68-74Crossref PubMed Scopus (8429) Google Scholar The majority of these variations (>99.9%) consist of single-nucleotide polymorphisms (SNPs) (Figure 2) and short insertions or deletions; however, larger structural changes occur and in total affect more base pairs.3Auton A. Brooks L.D. et al.1000 Genomes Project ConsortiumA global reference for human genetic variation.Nature. 2015; 526: 68-74Crossref PubMed Scopus (8429) Google Scholar Genetic sequence variants can influence the overall function and the quantity of a gene product. The expression of genes, which varies across tissues and time points, also can be influenced by DNA methylation, an epigenetic modification, through alterations of transcription factor binding and chromatin structure (Figure 2). Modifications to histones, proteins to which DNA coils around to form condensed structures, also are correlated to gene expression. It is not clear whether these modifications have a direct regulatory function or play a stabilizing role after gene expression changes occur.4Benveniste D. Sonntag H.J. Sanguinetti G. et al.Transcription factor binding predicts histone modifications in human cell lines.Proc Natl Acad Sci U S A. 2014; 111: 13367-13372Crossref PubMed Scopus (79) Google Scholar Segments of RNA, present in various lengths, which do not code proteins (micro RNAs or long noncoding RNAs), also can influence the quantity and structure of messenger RNA and subsequent protein production. In summary, genetic and epigenetic changes may be silent or alter the quantity, structure, and function of RNA and proteins, which ultimately can influence fat mass and distribution. Both genetic and epigenetic variations across individuals thus can alter adiposity phenotypes and lead to variation in traits across individuals. Up to the end of the past century, identification of genetic variants associated with obesity relied heavily on linkage studies in rodents with obesity caused by a mutation in a single gene (monogenic obesity) and candidate-gene–based approaches in severely obese human beings. During this time period, several loss-of-function mutations causing monogenic obesity were identified in the appetite-regulating leptin-melanocortin pathway, including leptin,5Montague C.T. Farooqi I.S. Whitehead J.P. et al.Congenital leptin deficiency is associated with severe early-onset obesity in humans.Nature. 1997; 387: 903-908Crossref PubMed Scopus (2441) Google Scholar leptin receptor,6Clement K. Vaisse C. Lahlou N. et al.A mutation in the human leptin receptor gene causes obesity and pituitary dysfunction.Nature. 1998; 392: 398-401Crossref PubMed Scopus (1920) Google Scholar pro-opiomelanocortin (POMC), and melanocortin 4 receptor (MC4R).7Vaisse C. Clement K. Guy-Grand B. et al.A frameshift mutation in human MC4R is associated with a dominant form of obesity.Nat Genet. 1998; 20: 113-114Crossref PubMed Scopus (858) Google Scholar, 8Yeo G.S. Farooqi I.S. Aminian S. et al.A frameshift mutation in MC4R associated with dominantly inherited human obesity.Nat Genet. 1998; 20: 111-112Crossref PubMed Scopus (896) Google Scholar Children with MC4R mutations experience mealtime hyperphagia and more frequent snacking compared with other obese children.9Valette M. Bellisle F. Carette C. et al.Eating behaviour in obese patients with melanocortin-4 receptor mutations: a literature review.Int J Obes (Lond). 2013; 37: 1027-1035Crossref PubMed Scopus (39) Google Scholar In addition, children with leptin deficiency have intense hyperphagia with food-seeking behavior and show aggressive behavior when food is denied.10Farooqi I.S. O'Rahilly S. 20 years of leptin: human disorders of leptin action.J Endocrinol. 2014; 223: T63-T70Crossref PubMed Scopus (179) Google Scholar This behavior can be normalized with leptin supplementation. Such disrupting mutations, however, explain only a small part of the etiology of early onset severe obesity and very little of the etiology of adiposity in the general population. Although these early studies suggested that appetite regulation was important in genetic susceptibility to obesity, hypothesis-free unbiased approaches in recent years have implicated a wide range of obesogenic mechanisms. In the past 15 years, technical advancements in molecular biology and genomics have enabled researchers to study variation at millions of sites in the human genome in relation to adiposity. These genome-wide association studies (GWAS) require large numbers of individuals to distinguish real associations from background variation, combining individuals from many smaller studies to increase sample sizes. With the availability of larger biobanks such as the UK Biobank,11Ganna A. Ingelsson E. 5 year mortality predictors in 498,103 UK Biobank participants: a prospective population-based study.Lancet. 2015; 386: 533-540Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar the US Million Veterans Program,12Gaziano J.M. Concato J. Brophy M. et al.Million Veteran Program: a mega-biobank to study genetic influences on health and disease.J Clin Epidemiol. 2016; 70: 214-223Abstract Full Text Full Text PDF PubMed Scopus (403) Google Scholar and the Kadooire Biobank,13Chen Z. Chen J. Collins R. et al.China Kadoorie Biobank of 0.5 million people: survey methods, baseline characteristics and long-term follow-up.Int J Epidemiol. 2011; 40: 1652-1666Crossref PubMed Scopus (529) Google Scholar comprising approximately half a million to a million participants each, there likely will be larger single-study reports and massive meta-analyses in the near future. DNA methylation is the most frequently studied epigenetic modification in population-based studies, largely because of its relative stability and ease of measurement in high-throughput, array-based assays. Methylation of DNA involves the addition of a methyl group to the 5’ position of a cytosine residue of the DNA, specifically at cytosine-phosphate-guanine dinucleotides (CpG) (Figure 2). DNA methylation modulates gene expression and may influence an individual’s susceptibility to obesity or its downstream consequences. Unlike genotype, DNA methylation is cell- and tissue-specific,14Dimas A.S. Deutsch S. Stranger B.E. et al.Common regulatory variation impacts gene expression in a cell type-dependent manner.Science. 2009; 325: 1246-1250Crossref PubMed Scopus (584) Google Scholar and the procurement of relevant tissues remains a major limitation in population-based epigenome studies of adiposity traits. Second, unlike genotypes, DNA methylation and other epigenetic modifications are malleable and may change in response to environmental exposures or disease states.15Fraga M.F. Ballestar E. Paz M.F. et al.Epigenetic differences arise during the lifetime of monozygotic twins.Proc Natl Acad Sci U S A. 2005; 102: 10604-10609Crossref PubMed Scopus (2672) Google Scholar, 16Busche S. Shao X. Caron M. et al.Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.Genome Biol. 2015; 16: 290Crossref PubMed Scopus (64) Google Scholar Third, DNA methylation and other epigenetic modifications also partly are under genetic control and influenced by nearby genetic sequence variants,17Gibbs J.R. van der Brug M.P. Hernandez D.G. et al.Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.PLoS Genet. 2010; 6: e1000952Crossref PubMed Scopus (600) Google Scholar, 18Bell J.T. Pai A.A. Pickrell J.K. et al.DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.Genome Biol. 2011; 12: R10Crossref PubMed Scopus (392) Google Scholar, 19Drong A.W. Nicholson G. Hedman A.K. et al.The presence of methylation quantitative trait loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue.PLoS One. 2013; 8: e55923Crossref PubMed Scopus (62) Google Scholar, 20Gaunt T.R. Shihab H.A. Hemani G. et al.Systematic identification of genetic influences on methylation across the human life course.Genome Biol. 2016; 17: 61Crossref PubMed Scopus (329) Google Scholar, 21Shakhbazov K. Powell J.E. Hemani G. et al.Shared genetic control of expression and methylation in peripheral blood.BMC Genomics. 2016; 17: 278Crossref PubMed Scopus (8) Google Scholar and thus are not entirely independent of genetic effects. Body mass index (BMI) and waist-to-hip ratio controlled for BMI (WHRadjBMI) are simple measures of overall and abdominal adiposity, respectively. Both adiposity measures are associated with the development of metabolic complications of obesity. In 2007, Frayling et al22Frayling T.M. Timpson N.J. Weedon M.N. et al.A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity.Science. 2007; 316: 889-894Crossref PubMed Scopus (3341) Google Scholar showed that the FTO locus was associated with both BMI and diabetes, identifying the first common genetic locus for an adiposity measure and a cardiometabolic disease trait. It should be noted that for this locus and others, the closest gene often has been used to denote the locus, even when the causal gene is not known. By increasing sample sizes and power, international collaborative efforts performed successively larger meta-analyses of approximately 339,000 individuals for overall obesity, as measured using BMI,23Speliotes E.K. Willer C.J. Berndt S.I. et al.Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.Nat Genet. 2010; 42: 937-948Crossref PubMed Scopus (2234) Google Scholar, 24Locke A.E. Kahali B. Berndt S.I. et al.Genetic studies of body mass index yield new insights for obesity biology.Nature. 2015; 518: 197-206Crossref PubMed Scopus (2645) Google Scholar, 25Willer C.J. Speliotes E.K. Loos R.J. et al.Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.Nat Genet. 2009; 41: 25-34Crossref PubMed Scopus (1374) Google Scholar, 26Thorleifsson G. Walters G.B. Gudbjartsson D.F. et al.Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.Nat Genet. 2009; 41: 18-24Crossref PubMed Scopus (1063) Google Scholar, 27Loos R.J. Lindgren C.M. Li S. et al.Common variants near MC4R are associated with fat mass, weight and risk of obesity.Nat Genet. 2008; 40: 768-775Crossref PubMed Scopus (1026) Google Scholar and approximately 224,000 individuals for central obesity, as measured using WHRadjBMI.28Lindgren C.M. Heid I.M. Randall J.C. et al.Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution.PLoS Genet. 2009; 5: e1000508Crossref PubMed Scopus (429) Google Scholar, 29Shungin D. Winkler T.W. Croteau-Chonka D.C. et al.New genetic loci link adipose and insulin biology to body fat distribution.Nature. 2015; 518: 187-196Crossref PubMed Scopus (928) Google Scholar, 30Heid I.M. Jackson A.U. Randall J.C. et al.Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.Nat Genet. 2011; 43: 1164Crossref Scopus (9) Google Scholar These studies have greatly expanded the number of implicated loci to 98 for BMI and 49 for WHRadjBMI, with no overlapping loci between the 2 adiposity traits (Figure 3 and Supplementary Table 1). Examination of the identified loci showed common variants in or near genes previously found in monogenic obesity studies in human beings or mice. Examples include mutations in POMC31Krude H. Biebermann H. Luck W. et al.Severe early-onset obesity, adrenal insufficiency and red hair pigmentation caused by POMC mutations in humans.Nat Genet. 1998; 19: 155-157Crossref PubMed Scopus (1386) Google Scholar and MC4R.7Vaisse C. Clement K. Guy-Grand B. et al.A frameshift mutation in human MC4R is associated with a dominant form of obesity.Nat Genet. 1998; 20: 113-114Crossref PubMed Scopus (858) Google Scholar, 8Yeo G.S. Farooqi I.S. Aminian S. et al.A frameshift mutation in MC4R associated with dominantly inherited human obesity.Nat Genet. 1998; 20: 111-112Crossref PubMed Scopus (896) Google Scholar Specifically, these findings showed that common variants with subtle effects on the function or expression of these genes can influence population BMI, whereas severe rare mutations can lead to early onset monogenic obesity. A study assessing genetic associations with the tails of the BMI and WHR distribution in the general population of adults32Berndt S.I. Gustafsson S. Magi R. et al.Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.Nat Genet. 2013; 45: 501-512Crossref PubMed Scopus (420) Google Scholar highlighted the same loci as the top findings in the population-based approaches (Figure 3). Once again, this highlighted the observation that similar genes can influence common and extremes of obesity in the general population. The remarkable overlap between genes identified from studies in the general population, extremes of distribution, and severe early onset monogenic disorders suggest that targeting the genes identified in adiposity GWAS with small effect sizes could have strong effects on preventing obesity. As proof of principle, for example, the common SNP at the HMG-CoA reductase locus has a small effect size in relation to increased low-density lipoprotein (LDL) cholesterol, where each effect allele increases LDL cholesterol by only 2.5 mg/dL.33Teslovich T.M. Musunuru K. Smith A.V. et al.Biological, clinical and population relevance of 95 loci for blood lipids.Nature. 2010; 466: 707-713Crossref PubMed Scopus (2781) Google Scholar However, statin therapy, which directly inhibits the HMG-CoA reductase enzyme, has a large effect on LDL cholesterol levels. Statins routinely lower LDL cholesterol by 30%–50%,34Collins R. Reith C. Emberson J. et al.Interpretation of the evidence for the efficacy and safety of statin therapy.Lancet. 2016; 388: 2532-2561Abstract Full Text Full Text PDF PubMed Scopus (1128) Google Scholar and reductions of more than 100 mg/dL can occur for some individuals, which is an approximately 40 times greater effect than that observed with naturally occurring genetic variation. Furthermore, the adiposity GWAS shows that many of the identified common variants do not fall in the coding regions of genes. This suggests that most SNPs identified in adiposity GWAS may regulate the magnitude of gene expression, rather than cause severe changes to the coding part of the gene that can precipitate syndromic changes. After identifying adiposity-related loci, it is possible to examine the effects of genetic variants identified in adiposity GWAS on the development of obesity-related metabolic disorders. As expected, there was enrichment for variants that increase both obesity and metabolic diseases, such as type 2 diabetes, dyslipidemia, and cardiovascular disease, although some variants have the opposite effect (see the Pleiotropic Effects section). To identify tissues, genes, and pathways that influence adiposity traits, investigators integrated genetic sequence variants with gene expression across tissues and grouped genes by related pathways. These integrative analyses showed that the nervous system, in general, and the hypothalamus, hippocampus, and limbic system, specifically, play prominent roles for regulating BMI (Figure 4).24Locke A.E. Kahali B. Berndt S.I. et al.Genetic studies of body mass index yield new insights for obesity biology.Nature. 2015; 518: 197-206Crossref PubMed Scopus (2645) Google Scholar Further analyses highlighted genes related to synaptic function and neurotransmitter signaling (ELAVL4, GRID1, CADM2, NRXN3, NEGR1, and SCG3), and energy homeostasis (HNF4G, TLR4, BDNF, POMC, MC4R, and ETV5) as important for influencing overall obesity. For abdominal obesity, in contrast, integrative analyses highlighted effects in abdominal and subcutaneous adipose tissues (Figure 4).29Shungin D. Winkler T.W. Croteau-Chonka D.C. et al.New genetic loci link adipose and insulin biology to body fat distribution.Nature. 2015; 518: 187-196Crossref PubMed Scopus (928) Google Scholar Highlighted genes function in adiponectin signaling, insulin sensitivity and regulation of glucose levels, skeletal growth, angiogenesis (VEGFA, VEGFB, RSPO3, STAB1, WARS2, PLXND1, MEIS1, FGF2, SMAD6, and CALCRL), transcriptional regulation (CEBPA, PPARG, MSC, SMAD6, HOXA, HOXC, ZBTB7B, JUND, KLF13, MEIS1, RFX7, NKX2-6, and HMGA1), and adipose tissue development (CEBPA, PPARG, BMP2, HOXC-mir196, SPRY1, TBX15, and PEMT).29Shungin D. Winkler T.W. Croteau-Chonka D.C. et al.New genetic loci link adipose and insulin biology to body fat distribution.Nature. 2015; 518: 187-196Crossref PubMed Scopus (928) Google Scholar Taken together, integrating genetic variation with multitissue gene expression helps to dissect the causal biological susceptibility to identify new targets for therapeutic interventions. Although BMI and WHR are easy to measure in the population, they do not directly quantify fat mass or fat depots, which are likely more relevant in disease development. GWAS analysis in approximately 100,000 individuals identified 12 loci associated with body fat percentage (BF%), as measured by bioimpedance analysis or dual-energy X-ray absorptiometry.35Lu Y. Day F.R. Gustafsson S. et al.New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk.Nat Commun. 2016; 7: 10495Crossref PubMed Scopus (186) Google Scholar The majority of BF% loci overlap with BMI findings, and one, COBLL1/GRB14, with WHRadjBMI (Figure 3). The BF% increasing allele at COBLL1/GRB14 was associated with lower WHRadjBMI, suggesting that the risk variant promotes gluteal rather than abdominal fat storage. Seven loci showed a larger effect on BF% than on BMI, suggestive of a primary association with adiposity in particular. Five loci showed larger effects on BMI than on BF%, which may be explained by an association with increases in both fat and lean mass. The ratio of visceral adipose tissue to subcutaneous adipose tissue (VAT/SAT) is an alternative measure of body fat distribution with cardiometabolic disease relevancy because a higher VAT/SAT is correlated with the development of metabolic complications.36Kaess B.M. Pedley A. Massaro J.M. et al.The ratio of visceral to subcutaneous fat, a metric of body fat distribution, is a unique correlate of cardiometabolic risk.Diabetologia. 2012; 55: 2622-2630Crossref PubMed Scopus (208) Google Scholar Fox et al37Fox C.S. Liu Y. White C.C. et al.Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.PLoS Genet. 2012; 8: e1002695Crossref PubMed Scopus (204) Google Scholar performed a GWAS analysis of VAT/SAT in approximately 10,000 individuals. They found that a variant at the LYPLAL1 locus, previously identified in association with WHR, also was associated with a VAT/SAT ratio with larger effect sizes in women as compared with men. The strongest association for SAT was within the FTO locus. Unlike SAT, the largest effect sizes for VAT were seen at a variant near THNSL2, also with greater effects in women as compared with men. Thus, examining the genetic associations of complementary measures of adiposity (BMI, %BF, SAT, VAT) can begin to show the underlying biology by which specific fat deposition may contribute to disease development. SNPs within the first intron (ie, the noncoding part) of the FTO gene have been reported to be associated robustly with common obesity since 2007. Recent studies have suggested a recessive effect, in which individuals carrying zero vs one BMI-raising allele have a similar BMI, however, individuals with zero vs two BMI-raising alleles at the FTO locus had an average BMI of 27.3 vs 28.1 kg/m2, respectively.38Wood A.R. Tyrrell J. Beaumont R. et al.Variants in the FTO and CDKAL1 loci have recessive effects on risk of obesity and type 2 diabetes, respectively.Diabetologia. 2016; 59: 1214-1221Crossref PubMed Scopus (40) Google Scholar The strongest effect of the FTO locus was observed in individuals younger than 50 years of age.39Winkler T.W. Justice A.E. Graff M. et al.The influence of age and sex on genetic associations with adult body size and shape: a large-scale genome-wide interaction study.PLoS Genet. 2015; 11: e1005378Crossref PubMed Scopus (228) Google Scholar There is some evidence from observational studies in human beings that the FTO SNP effect on adiposity is modified by physical activity level40Kilpelainen T.O. Qi L. Brage S. et al.Physical activity attenuates the influence of FTO variants on obesity risk: a meta-analysis of 218,166 adults and 19,268 children.PLoS Med. 2011; 8: e1001116Crossref PubMed Scopus (396) Google Scholar, 41Young A.I. Wauthier F. Donnelly P. Multiple novel gene-by-environment interactions modify the effect of FTO variants on body mass index.Nat Commun. 2016; 7: 12724Crossref PubMed Scopus (87) Google Scholar and may affect dietary preferences.42Qi Q. Kilpelainen T.O. Downer M.K. et al.FTO genetic variants, dietary intake and body mass index: insights from 177,330 individuals.Hum Mol Genet. 2014; 23: 6961-6972Crossref PubMed Scopus (120) Google Scholar However, the association of FTO locus variation and obesity is not completely explained by interactions or mediation by lifestyle factors. So how do these FTO variants actually exert their effect on BMI? Smemo et al43Smemo S. Tena J.J. Kim K.H. et al.Obesity-associated variants within FTO form long-range functional connections with IRX3.Nature. 2014; 507: 371-375Crossref PubMed Scopus (807) Google Scholar found that obesity-increasing noncoding variants within the first FTO intron are associated with increased expression of the neighboring gene IRX3, but not with FTO in human brains. Furthermore, Irx3-deficient mice had a reduction in body weight of 25%–30%, primarily through the loss of fat mass and increase in basal metabolic rate, with browning of white adipose tissue. Previous work has shown that IRX3 and other homeobox transcription factors were overexpressed in adipocytes after weight loss, indicating that changes in these genes were important in weight regulation.44Dankel S.N. Fadnes D.J. Stavrum A.K. et al.Switch from stress response to homeobox transcription factors in adipose tissue after profound fat loss.PLoS One. 2010; 5: e11033Crossref PubMed Scopus (97) Google Scholar Claussnitzer et al45Claussnitzer M. Dankel S.N. Kim K.H. et al.FTO obesity variant circuitry and adipocyte browning in humans.N Engl J Med. 2015; 373: 895-907Crossref PubMed Scopus (799) Google Scholar combined information on regulatory elements and methylation patterns to show that the FTO SNP rs1421085 disrupts the binding site of the ARID5B repressor. The disruption of the repressor led to increased expression of IRX3 and IRX5 during adipocyte differentiation, causing energy-consuming beige adipocytes to become energy-storing white adipocytes. This decade-long effort to understand the biology of one of the earliest and most robust association signals for adiposity highlights the challenges and rewards in translating genomic discoveries to validated, potentially actionable, biology. Although obesity is known to increase the risk of metabolic diseases, some extremely obese individuals do not develop adiposity-related metabolic diseases. Why this is the case is not completely understood. This phenomenon also has been observed in genetic studies, in which a few recently identified genetic variants that increase adiposity also protect against the development of metabolic diseases.24Locke A.E. Kahali B. Berndt S.I. et al.Genetic studies of body mass index yield new insights for obesity biology.Nature. 2015; 518: 197-206Crossref PubMed Scopus (2645) Google Scholar, 46Kilpelainen T.O. Zillikens M.C. Stancakova A. et al.Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.Nat Genet. 2011; 43: 753-760Crossref PubMed Scopus (242) Google Scholar This observation suggests that genetics can dissociate epidemiologically correlated traits and identify mechanisms by which metabolic disease can be abrogated even in the obese. For example, the minor allele rs2943650 near the IRS1 (encoding the insulin-receptor substrate 1) gene was associated with a higher BF% (especially in men),46Kilpelainen T.O. Zillikens M.C. Stancakova A. et al.Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.Nat Genet. 2011; 43: 753-760Crossref PubMed Scopus (242) Google Scholar however, paradoxically, it also was associated with a favorable lipid profile, and a decreased risk of type 2 diabetes and coronary heart disease.46Kilpelainen T.O. Zillikens M.C. Stancakova A. et al.Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.Nat Genet. 2011; 43: 753-760Crossref PubMed Scopus (242) Google Scholar Gene expression profiles have shown that the variant was related to a higher expression of the IRS1 gene in adipose tissue, but not in liver, brain, or blood, suggesting that the adipose tissue may be the tissue in which it acts to have its effect. Furthermore, they found that the allele was associated with a decreased VAT/SAT r

Comprehensive metabolite profiling captures many highly heritable traits, including amino acid levels, which are potentially sensitive biomarkers for disease pathogenesis. To better understand the contribution of genetic variation to amino acid levels, we performed single variant and gene-based tests of association between nine serum amino acids (alanine, glutamine, glycine, histidine, isoleucine, leucine, phenylalanine, tyrosine, and valine) and 16.6 million genotyped and imputed variants in 8545 non-diabetic Finnish men from the METabolic Syndrome In Men (METSIM) study with replication in Northern Finland Birth Cohort (NFBC1966). We identified five novel loci associated with amino acid levels (P = < 5×10−8): LOC157273/PPP1R3B with glycine (rs9987289, P = 2.3×10−26); ZFHX3 (chr16:73326579, minor allele frequency (MAF) = 0.42%, P = 3.6×10−9), LIPC (rs10468017, P = 1.5×10−8), and WWOX (rs9937914, P = 3.8×10−8) with alanine; and TRIB1 with tyrosine (rs28601761, P = 8×10−9). Gene-based tests identified two novel genes harboring missense variants of MAF <1% that show aggregate association with amino acid levels: PYCR1 with glycine (Pgene = 1.5×10−6) and BCAT2 with valine (Pgene = 7.4×10−7); neither gene was implicated by single variant association tests. These findings are among the first applications of gene-based tests to identify new loci for amino acid levels. In addition to the seven novel gene associations, we identified five independent signals at established amino acid loci, including two rare variant signals at GLDC (rs138640017, MAF=0.95%, Pconditional = 5.8×10−40) with glycine levels and HAL (rs141635447, MAF = 0.46%, Pconditional = 9.4×10−11) with histidine levels. Examination of all single variant association results in our data revealed a strong inverse relationship between effect size and MAF (Ptrend<0.001). These novel signals provide further insight into the molecular mechanisms of amino acid metabolism and potentially, their perturbations in disease.

Dyslipidemia is common in the general population and increases the risk of cardiovascular disease. Treatment of dyslipidemia is effective in decreasing morbidity from cardiovascular disease. Because the liver is the primary source of cholesterol and other lipids in the body, medications for dyslipidemia, such as statins, target genes in the liver. Furthermore, the liver plays a role in the metabolism of many drugs, including those that are used to treat dyslipidemia. It is not surprising, therefore, that many practitioners are hesitant to prescribe medicines to treat dyslipidemia in the setting of liver disease. This update is aimed at summarizing current understanding of the safety of treating patients who have various liver diseases and dyslipidemia with lipid-lowering drugs (Table 1).Table 1Best Practice Advice: Treatment of Dyslipidemia in Liver DiseaseDILIBPA #1 Statins often (3%) cause benign elevations in serum ALT or AST levels and should not be considered contraindicated in patients with liver disease.BPA #2 Liver biochemical tests are recommended before starting a statin but do not need to be checked routinely while statins are taken unless clinically significant side effects develop.BPA #3 Increases in serum ALT or AST levels to >3 times ULN with evidence of cholestasis (bilirubin >2 times ULN) (in the absence of biliary obstruction) after statins are started generally require that the statin be stopped. A work-up for DILI should include testing for the presence of other underlying causes of liver disease or other medications that may have precipitated the reaction besides or in addition to the statin.BPA #4 If DILI or ALF occurs in a patient taking a statin, other statins should be avoided in that patient.BPA #5 DILI and ALF caused by statins are rare (1 in 100,000 and 1 in 1,000,000, respectively), so fear of developing these effects should not be used to justify avoidance of statins when an individual may benefit from them.BPA #6 Statins are contraindicated in patients with ALF because of the patients’ poor prognosis.BPA #7 Other lipid-lowering medications, such as niacin, ezetimibe, or fibrates, may cause DILI, but such instances are exceedingly rare and should not prevent starting these medications in a patient who may benefit from them.NAFLDBPA #8 Although NAFLD and NASH are not considered traditional risk factors for cardiovascular disease, they are associated with dyslipidemia. The 2013 ACC/AHA guidelines should be used to assess cardiovascular risk in patients with NAFLD and to guide the need for lipid-lowering pharmacotherapy.BPA #9 Statins, ezetimibe, omega-3 fatty acids, and fibrates are safe and well tolerated in the setting of NAFLD and NASH.BPA #10 A statin is first-line treatment of elevated serum LDL levels in patients with NAFLD who are deemed to be at increased risk for adverse cardiovascular disease outcomes. Statin therapy is associated with reductions in serum LDL levels and cardiovascular disease prevention in patients with NAFLD.BPA #11 Ezetimibe may also be used for treatment of elevated LDL levels, either as primary therapy in patients who are statin intolerant or in addition to a statin when the statin is insufficient to reduce LDL levels. Ezetimibe is associated with reductions in LDL levels, but its efficacy for cardiovascular disease prevention is unknown.BPA #12 Omega-3 fatty acids and fibrates are indicated for the treatment of isolated hypertriglyceridemia.BPA #13 There is no conclusive evidence that treatment of dyslipidemia with any agent (statin, fibrate, fish oil) improves the histology of NASH or liver-related outcomes.Viral HepatitisBPA #14 Despite causing a reduction in serum lipid levels, chronic HCV infection is associated with an increased risk of acute myocardial infarction. Serum LDL and total cholesterol levels rebound after spontaneous and treatment-induced viral clearance. Therefore, lipid levels should be monitored after HCV clearance to determine if a patient has a new indication for treatment of dyslipidemia.BPA #15 The impact of chronic HBV infection on serum lipid levels is not well described, but HBV infection may decrease serum triglyceride and HDL levels.BPA #16 Management of patients with HBV or HCV infection and dyslipidemia should be guided by standard recommendations for the treatment of dyslipidemia.BPA #17 Statins are safe to use in patients with either chronic HCV or HBV infection, but attention should be paid to potential interactions between statins and antiviral agents.PBCBPA #18 Dyslipidemia in the form of elevated serum cholesterol and triglyceride levels is common in PBC, does not increase the risk of cardiovascular disease, and does not need to be treated with lipid-lowering agents unless other concomitant cardiovascular risk factors are present.BPA #19 Lipid-lowering agents, such as statins, are not contraindicated in patients with PBC with compensated liver disease but should not be used in patients with decompensated disease.BPA #20 Second-line treatments for PBC, such as fibrates and OCA, can affect lipid levels. Until more is known about the effect of OCA on cardiovascular disease, OCA in particular should be avoided in patients with PBC who have cardiovascular disease or risk factors for disease. OCA should be dosed weekly rather than daily in PBC patients with Child-Pugh class B or C cirrhosis.BPA #21 There is no compelling evidence that statins can improve outcomes in patients with PBC; they should not be used as primary agents for treatment of this disease.CirrhosisBPA #22 Statins can be safely used in patients with Child-Pugh class A cirrhosis for cardiovascular risk reduction if indicated.BPA #23 Statins should be avoided in patients with Child-Pugh class B or C cirrhosis because of the patients’ poor prognosis, not because of increased hepatotoxicity.Post-Transplant DyslipidemiaBPA #24 Dyslipidemia is common following liver transplantation, affecting up to 62% of transplant recipients. Pretransplant obesity and diabetes mellitus increase the risk of post-transplant dyslipidemia. Post-transplant weight gain and immunosuppressant medications, including calcineurin inhibitors and the mTOR inhibitor sirolimus, also increase the risk of post-transplant dyslipidemia.BPA #25 Lipid-lowering agents, specifically statins, are not associated with an increased risk of hepatotoxicity in the post-transplant population and may be used as needed to treat dyslipidemia.BPA #26 Calcineurin inhibitors, like several statins, are metabolized by CYP3A4 and may increase the risk of statin-associated myopathy. Pravastatin and fluvastatin are not metabolized by CYP3A4 and do not increase the risk of statin-associated myopathy when used with a calcineurin inhibitor.ALT, alanine aminotransferase; ACC, American College of Cardiology; AHA, American Heart Association; ALF, acute liver failure; AST, alanine aminotransferase; BPA, best practice advice; CYP, cytochrome P-450; DILI, drug-induced liver injury; HBV, hepatitis B virus; HCV, hepatitis C virus; HDL, high-density lipoprotein; LDL, low-density lipoprotein; mTOR, mechanistic target of rapamycin; NAFLD, nonalcoholic fatty liver disease; NASH, nonalcoholic steatohepatitis; OCA, obeticholic acid; PBC, primary biliary cholangitis; ULN, upper limit of normal. Open table in a new tab ALT, alanine aminotransferase; ACC, American College of Cardiology; AHA, American Heart Association; ALF, acute liver failure; AST, alanine aminotransferase; BPA, best practice advice; CYP, cytochrome P-450; DILI, drug-induced liver injury; HBV, hepatitis B virus; HCV, hepatitis C virus; HDL, high-density lipoprotein; LDL, low-density lipoprotein; mTOR, mechanistic target of rapamycin; NAFLD, nonalcoholic fatty liver disease; NASH, nonalcoholic steatohepatitis; OCA, obeticholic acid; PBC, primary biliary cholangitis; ULN, upper limit of normal. The 2013 American College of Cardiology/American Heart Association guidelines, published in 2014, should be used to guide treatment of dyslipidemia in patients with the liver diseases discussed in this update.1Stone N.J. Robinson J.G. Lichtenstein A.H. et al.2013 ACC/AHA guideline on the treatment of blood cholesterol to reduce atherosclerotic cardiovascular risk in adults: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines.J Am Coll Cardiol. 2014; 63: 2889-2934Crossref PubMed Scopus (3312) Google Scholar The guidelines recommend that adults with cardiovascular disease or a low-density lipoprotein (LDL) level ≥190 mg/dL be treated with high-intensity statins, with the goal of reducing LDL levels by 50%. Individuals 45–70 years of age with diabetes mellitus and a serum LDL level <189 mg/dL or persons with a >7.5% global 10-year risk of cardiovascular disease can be treated with moderate-intensity statins, with the goal of reducing LDL levels by 30%–50% (Table 2).Table 2Indications for Pharmacologic Reduction of Serum LDL Levels in the General PopulationPresence of clinical atherosclerotic cardiovascular disease (coronary heart disease, symptomatic carotid artery disease, stroke/transient ischemic attack, peripheral artery disease, abdominal aortic aneurysm)Adults 40–77 years of age with diabetes mellitus and LDL levels of 70–189 mg/dLAdults 40–75 years of age with a global 10-year risk of cardiovascular disease ≥7.5% and an LDL level of 70–189 mg/dLAdults with an LDL level ≥190 mg/dLAdapted from 2013 American Heart Association/American College of Cardiology guidelines.1Stone N.J. Robinson J.G. Lichtenstein A.H. et al.2013 ACC/AHA guideline on the treatment of blood cholesterol to reduce atherosclerotic cardiovascular risk in adults: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines.J Am Coll Cardiol. 2014; 63: 2889-2934Crossref PubMed Scopus (3312) Google ScholarLDL, low-density lipoproteins. Open table in a new tab Adapted from 2013 American Heart Association/American College of Cardiology guidelines.1Stone N.J. Robinson J.G. Lichtenstein A.H. et al.2013 ACC/AHA guideline on the treatment of blood cholesterol to reduce atherosclerotic cardiovascular risk in adults: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines.J Am Coll Cardiol. 2014; 63: 2889-2934Crossref PubMed Scopus (3312) Google Scholar LDL, low-density lipoproteins. From 8% to 9% of persons in the general population have an elevated aminotransferase level, a common clinical problem.2Clark J.M. Brancati F.L. Diehl A.M. The prevalence and etiology of elevated aminotransferase levels in the United States.Am J Gastroenterol. 2003; 98: 960-967Crossref PubMed Scopus (1090) Google Scholar In these persons, an evaluation to determine the cause of the aminotransferase elevation is warranted, particularly before a new drug is started, because they may have a common underdiagnosed condition, such as nonalcoholic fatty liver disease (NAFLD), excessive alcohol use, or viral hepatitis. Statins (3-hydroxy-3-methyl-glutaryl-coenzyme A reductase inhibitors) are by far the most common medication used to treat dyslipidemia and are known to cause elevations of serum alanine aminotransferase (ALT) levels in persons with previously normal levels. Overall, persons on low-to-moderate statin doses have, on average, a 1% chance of having an elevated ALT level.3Calderon R.M. Cubeddu L.X. Goldberg R.B. et al.Statins in the treatment of dyslipidemia in the presence of elevated liver aminotransferase levels: a therapeutic dilemma.Mayo Clin Proc. 2010; 85: 349-356Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar At most, 3% of patients on statins develop elevations in serum ALT levels.3Calderon R.M. Cubeddu L.X. Goldberg R.B. et al.Statins in the treatment of dyslipidemia in the presence of elevated liver aminotransferase levels: a therapeutic dilemma.Mayo Clin Proc. 2010; 85: 349-356Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar The effect is generally dose dependent, with higher doses of statins increasing the chances of an elevated ALT level. These mild elevations do not generally indicate serious toxicity. Elevations in aminotransferase level indicative of serious liver injury caused by a drug are rare but can be life threatening. Zimmermann4Zimmermann H. Drug-induced liver disease.in: Hepatotoxicity, the adverse effects of drugs and other chemicals on the liver. 1st ed. Appleton-Century-Crofts, New York1978: 351-353Crossref Scopus (79) Google Scholar, 5Zimmermann H. Drug-induced liver disease.in: The adverse effects of drugs and other chemicals on the liver. 2nd ed. Lippincott Williams & Wilkins, Philadelphia1999: 428-433Google Scholar observed that jaundiced patients with elevated aminotransferase levels had a poorer prognosis than patients with elevated aminotransferase levels without jaundice. That observation was further developed into Hy’s Law to identify patients with potentially fatal drug-induced liver injury (DILI).6Administration US Department of Health and Human Services Food and Drug Administration, for CfDEaRCC, Center for Biologics Evaluation and Research (CBER) BEaR. Guidance for industry, drug-induced liver injury: premarketing clinical evaluation 2009, 2014.Google Scholar To meet criteria for DILI, patients must have elevations of ALT or aspartate aminotransferase levels ≥3 times the upper limit of normal (ULN) and have elevations of the total serum bilirubin level >2 times the ULN with no other identified cause of the increased liver biochemical tests (eg, biliary obstruction, another liver disease, other drug toxicity) except for the offending drug.6Administration US Department of Health and Human Services Food and Drug Administration, for CfDEaRCC, Center for Biologics Evaluation and Research (CBER) BEaR. Guidance for industry, drug-induced liver injury: premarketing clinical evaluation 2009, 2014.Google Scholar DILI from statins occurs in 1 in 100,000 persons and can have a variety of histologic presentations.7Thapar M. Russo M.W. Bonkovsky H.L. Statins and liver injury.Gastroenterol Hepatol (NY). 2013; 9: 605-606PubMed Google Scholar, 8Russo M.W. Hoofnagle J.H. Gu J. et al.Spectrum of statin hepatotoxicity: experience of the Drug-Induced Liver Injury Network.Hepatology. 2014; 60: 679-686Crossref PubMed Scopus (154) Google Scholar There can be an asymptomatic rise in the ALT level (<3 times ULN) that can improve with continued stain use, so-called adaptation; hepatitis with an ALT level >3 times ULN and clinical liver disease; cholestatic hepatitis with development of jaundice; and autoantibody-associated DILI with the development of positive antinuclear antibodies and antimitochondrial or smooth muscle antibodies with or without plasma cells in liver biopsy specimens. In general, however, statins can be used in individuals with autoimmune disorders including autoimmune hepatitis. General care should be taken to ensure that medications taken for autoimmune hepatitis or other disorders do not affect the catabolism or excretion of statins, thereby altering their effective dose. Statins can also cause acute liver failure in 1 in 1,000,000 persons. The liver safety of statins has recently been reviewed and guidelines published for their use.9Bays H. Cohen D.E. Chalasani N. et al.An assessment by the Statin Liver Safety Task Force: 2014 update.J Clin Lipidol. 2014; 8: S47-S57Abstract Full Text Full Text PDF PubMed Scopus (159) Google Scholar It is recommended that liver biochemical tests be checked before a statin is started. However, routine periodic monitoring of serum ALT levels does not seem to detect or prevent serious liver injury in association with statin use and is not recommended. Only if and when a patient shows clinical signs, such as fever or jaundice, of adverse effects from a statin should liver biochemical tests be rechecked. If DILI from a statin is suspected, then a full work-up should be initiated to ensure that the cause is the statin and not a secondary liver disease or another drug (reviewed in Ref.9Bays H. Cohen D.E. Chalasani N. et al.An assessment by the Statin Liver Safety Task Force: 2014 update.J Clin Lipidol. 2014; 8: S47-S57Abstract Full Text Full Text PDF PubMed Scopus (159) Google Scholar). Niacin, ezetimibe, and fibrates, which are also used to treat serum lipid disorders, have all been reported to cause DILI. If a patient had DILI or acute liver failure from a statin, this class of medications should not be used in that patient again, and an alternative class of lipid-lowering drugs can be tried.7Thapar M. Russo M.W. Bonkovsky H.L. Statins and liver injury.Gastroenterol Hepatol (NY). 2013; 9: 605-606PubMed Google Scholar Statins are contraindicated in patients with decompensated liver disease or acute liver failure (see later) but are otherwise safe, even at high doses, and efficacious in lowering lipid levels in patients with compensated liver disease.10Lewis J.H. Mortensen M.E. Zweig S. et al.Efficacy and safety of high-dose pravastatin in hypercholesterolemic patients with well-compensated chronic liver disease: results of a prospective, randomized, double-blind, placebo-controlled, multicenter trial.Hepatology. 2007; 46: 1453-1463Crossref PubMed Scopus (244) Google Scholar Dyslipidemia is common among persons with NAFLD and plays a critical role in the development of cardiovascular disease, the leading cause of mortality among these persons. Dyslipidemia associated with NAFLD is typically characterized by a pattern of hypertriglyceridemia, increased LDL levels, and reduced high-density lipoprotein (HDL) levels. Although patients with NAFLD have a higher risk of cardiovascular complications compared with the general population, NAFLD and nonalcoholic steatohepatitis (NASH) are not considered traditional risk factors for cardiovascular disease. Therefore, cardiovascular risk should be assessed according to the 2013 American College of Cardiology/American Heart Association guidelines, which use presence of known coronary artery disease, cardiovascular risk factors, and 10-year cardiovascular event risk assessment to determine the need for treatment with lipid-lowering agents and to establish LDL targets for primary and secondary cardiovascular risk prevention (Table 2; discussed later). Diet and exercise are the first-line approaches to reduce LDL levels. When diet and exercise are insufficient, statins are the first-line pharmacologic agents for LDL reduction and have proven benefit for primary and secondary prevention of cardiovascular disease. Several studies have demonstrated that statins are effective in reducing LDL levels and cardiovascular events and are safe in patients with NAFLD. Intensive statin therapy (eg, pravastatin, 80 mg daily) was associated with a significant reduction in LDL levels compared with placebo among patients with chronic liver disease primarily caused by NAFLD (mean percentage LDL reduction, 30.6%; standard deviation, 16.5%).10Lewis J.H. Mortensen M.E. Zweig S. et al.Efficacy and safety of high-dose pravastatin in hypercholesterolemic patients with well-compensated chronic liver disease: results of a prospective, randomized, double-blind, placebo-controlled, multicenter trial.Hepatology. 2007; 46: 1453-1463Crossref PubMed Scopus (244) Google Scholar In a post hoc analysis of the ATTEMPT study, a greater benefit in primary cardiovascular disease prevention was observed among patients with NAFLD and metabolic syndrome in whom LDL reduction was aggressive with intensive statin therapy (atorvastatin titrated from 10 to 80 mg daily) aimed to reduce LDL levels to <100 mg/dL compared with those in whom the LDL reduction was aimed to reduce the level to <130 mg/dL.11Athyros V.G. Tziomalos K. Gossios T.D. et al.Safety and efficacy of long-term statin treatment for cardiovascular events in patients with coronary heart disease and abnormal liver tests in the Greek Atorvastatin and Coronary Heart Disease Evaluation (GREACE) Study: a post-hoc analysis.Lancet. 2010; 376: 1916-1922Abstract Full Text Full Text PDF PubMed Scopus (559) Google Scholar Post hoc analyses of 2 large randomized controlled trials (RCTs) (GREACE and IDEAL studies) also found superior secondary cardiovascular disease prevention benefit in association with intensive statin therapy among patients with increased aminotransferase levels attributed to NAFLD. In the IDEAL study, compared with moderate statin therapy, intensive statin therapy (atorvastatin, 80 mg daily) was associated with a 44% relative risk reduction in secondary cardiovascular events (hazard ratio, 0.556; 95% confidence interval, 0.367–0.842).12Tikkanen M.J. Fayyad R. Faergeman O. et al.Effect of intensive lipid lowering with atorvastatin on cardiovascular outcomes in coronary heart disease patients with mild-to-moderate baseline elevations in alanine aminotransferase levels.Int J Cardiol. 2013; 168: 3846-3852Abstract Full Text Full Text PDF PubMed Scopus (138) Google Scholar In the GREACE study, compared with usual care, intensive statin therapy (atorvastatin titrated from 10 to 80 mg daily for an LDL goal of <100 mg/dL) was associated with a 68% relative risk reduction (P < .0001).11Athyros V.G. Tziomalos K. Gossios T.D. et al.Safety and efficacy of long-term statin treatment for cardiovascular events in patients with coronary heart disease and abnormal liver tests in the Greek Atorvastatin and Coronary Heart Disease Evaluation (GREACE) Study: a post-hoc analysis.Lancet. 2010; 376: 1916-1922Abstract Full Text Full Text PDF PubMed Scopus (559) Google Scholar Both studies found greater cardiovascular benefit among patients with increased aminotransferase levels than in those with normal levels. Statins are well tolerated and not associated with liver-related adverse events among patients with NAFLD and dyslipidemia.10Lewis J.H. Mortensen M.E. Zweig S. et al.Efficacy and safety of high-dose pravastatin in hypercholesterolemic patients with well-compensated chronic liver disease: results of a prospective, randomized, double-blind, placebo-controlled, multicenter trial.Hepatology. 2007; 46: 1453-1463Crossref PubMed Scopus (244) Google Scholar, 13Athyros V.G. Giouleme O. 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Zweig S. et al.Efficacy and safety of high-dose pravastatin in hypercholesterolemic patients with well-compensated chronic liver disease: results of a prospective, randomized, double-blind, placebo-controlled, multicenter trial.Hepatology. 2007; 46: 1453-1463Crossref PubMed Scopus (244) Google Scholar Observational studies have similarly reported significant reductions in aminotransferase levels and steatosis on liver biopsy specimens in statin-treated patients with NAFLD. However, histologic improvements in ballooning and fibrosis have not been observed in association with statins. Experience with ezetimibe in patients with NAFLD is much less extensive than that with statins. Treatment with ezetimibe, 10 mg daily, was associated with significant reductions in LDL and total cholesterol levels among patients with NAFLD in several observational studies15Park H. Shima T. 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Takamura T. Honda M. et al.The effects of ezetimibe on non-alcoholic fatty liver disease and glucose metabolism: a randomised controlled trial.Diabetologia. 2014; 57: 878-890Crossref PubMed Scopus (93) Google Scholar However, there have been no studies looking at the effect of ezetimibe on cardiovascular disease prevention in patients with NAFLD. Ezetimibe may be associated with improvements in aminotransferase levels. Mixed results from studies evaluating the effect of ezetimibe on liver histology in patients with NASH suggest that ezetimibe may improve steatosis, NAFLD activity score, and hepatocyte ballooning but not fibrosis.15Park H. Shima T. Yamaguchi K. et al.Efficacy of long-term ezetimibe therapy in patients with nonalcoholic fatty liver disease.J Gastroenterol. 2011; 46: 101-107Crossref PubMed Scopus (158) Google Scholar, 17Yoneda M. Fujita K. 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Kohjima M. et al.NPC1L1 inhibitor ezetimibe is a reliable therapeutic agent for non-obese patients with nonalcoholic fatty liver disease.Lipids Health Dis. 2010; 9: 29Crossref PubMed Scopus (58) Google Scholar, 23Shiwa T. Kawanami Y. Yokoyama T. et al.The efficacy of ezetimibe on nonalcoholic fatty liver disease (NAFLD).Nihon Shokakibyo Gakkai Zasshi. 2011; 108: 1383-1392PubMed Google Scholar Omega-3 fatty acids and fenofibrates are safe and effective for the treatment of isolated hypertriglyceridemia. Neither medication is associated with improvement in liver histology in patients with NAFLD. In summary, statin therapy is indicated for treatment of increased LDL levels among patients with NAFLD who are at increased risk for adverse outcomes of cardiovascular disease. Statin therapy is associated with reductions in LDL levels and prevention of cardiovascular disease. Ezetimibe may also be used for treatment of increased LDL levels and is associated with reductions in these levels, but its efficacy for cardiovascular disease prevention is unknown. Omega-3 fatty acids and fibrates are indicated for the treatment of hypertriglyceridemia. All of these agents are safe and well tolerated in patients with NAFLD. However, there is no conclusive evidence to date that treatment of dyslipidemia with any agent (statins, fibrates, omega-3 fatty acids) improves histology or liver-related outcomes in patients with NASH. Hepatitis C virus (HCV) chronically infects up to 170 million individuals globally and can lead to the development of cirrhosis, hepatocellular carcinoma, and the need for liver transplantation.24Lavanchy D. The global burden of hepatitis C.Liver Int. 2009; 29: 74-81Crossref PubMed Scopus (1099) Google Scholar HCV replication impacts host lipid metabolism via several mechanisms. HCV virions interacts with circulating lipoproteins to infect hepatocytes via the LDL receptor and interacts with the cell surface markers Niemann-Pick C1-like 1, a receptor for cholesterol resorption, and scavenger receptor class B member 1, which promotes uptake of cholesterol from lipoproteins.25Andre P. Komurian-Pradel F. Deforges S. et al.Characterization of low- and very-low-density hepatitis C virus RNA-containing particles.J Virol. 2002; 76: 6919-6928Crossref PubMed Scopus (551) Google Scholar, 26Acuna-Alonzo V. Flores-Dorantes T. Kruit J.K. et al.A functional ABCA1 gene variant is associated with low HDL-cholesterol levels and shows evidence of positive selection in Native Americans.Hum Mol Genet. 2010; 19: 2877-2885Crossref PubMed Scopus (102) Google Scholar, 27Wunschmann S. Muller H.M. 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Abstract Background Prevalence of nonalcoholic fatty liver disease (NAFLD) is increasing in developing countries, but its causes are not known. We aimed to ascertain the prevalence and determinants of NAFLD in a new largely unmedicated population‐based cohort from the rapidly gentrifying region of Pinggu, China. Methods We randomized cluster sampled 4002 Pinggu residents aged 26 to 76 years. Data from 1238 men and 1928 women without significant alcohol drinking or hepatitis virus B or C infection were analysed. NAFLD was defined using a liver‐spleen ratio (L/S ratio) ≤1.1 on unenhanced abdominal computed tomography (CT) scanning. Results Of men and women, 26.5% and 20.1%, respectively, had NAFLD. NAFLD prevalence was highest in younger men and older women. In multivariate logistic regression models, higher body mass index, waist circumference, serum triglyceride, alanine transaminase, and haemoglobin A1c independently increased the odds of NAFLD in both men and women separately. Higher annual household income and systolic blood pressure for men and higher serum uric acid and red meat intake and lower physical activity levels for women also independently associated with higher odds of NAFLD. Individuals with L/S ratio ≤1.1 had linearly increasing rates of obesity, diabetes, and metabolic syndrome that paralleled fatty liver increase. Conclusions NAFLD is common in a gentrifying Chinese population particularly in younger men of high socioeconomic status and older women with sedentary behaviour who eat red meat. Demographic factors add independent risk of NAFLD above traditional metabolic risk factors. A CT L/S ratio of ≤1.1 identifies individuals at high risk of metabolic disease.

Nonalcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver disease and is highly correlated with metabolic disease. NAFLD results from environmental exposures acting on a susceptible polygenic background. This study performed the largest multiethnic investigation of exonic variation associated with NAFLD and correlated metabolic traits and diseases. An exome array meta-analysis was carried out among eight multiethnic population-based cohorts (n = 16 492) with computed tomography (CT) measured hepatic steatosis. A fixed effects meta-analysis identified five exome-wide significant loci (P < 5.30 × 10-7); including a novel signal near TOMM40/APOE. Joint analysis of TOMM40/APOE variants revealed the TOMM40 signal was attributed to APOE rs429358-T; APOE rs7412 was not associated with liver attenuation. Moreover, rs429358-T was associated with higher serum alanine aminotransferase, liver steatosis, cirrhosis, triglycerides and obesity; as well as, lower cholesterol and decreased risk of myocardial infarction and Alzheimer's disease (AD) in phenome-wide association analyses in the Michigan Genomics Initiative, United Kingdom Biobank and/or public datasets. These results implicate APOE in imaging-based identification of NAFLD. This association may or may not translate to nonalcoholic steatohepatitis; however, these results indicate a significant association with advanced liver disease and hepatic cirrhosis. These findings highlight allelic heterogeneity at the APOE locus and demonstrate an inverse link between NAFLD and AD at the exome level in the largest analysis to date.

•We evaluated the impact of SERPINA Pi∗MZ in a compensated cirrhosis cohort.•SERPINA1 Pi∗MZ was associated with an increased risk of decompensation vs. Pi∗MM.•Pi∗MZ was associated with an increased risk of liver-related death or liver transplant.•Findings were robust across several sensitivity analyses. Background & AimsAlpha-1 antitrypsin deficiency is caused by mutations in SERPINA1, most commonly homozygosity for the Pi∗Z variant, and can present as liver disease. While heterozygosity for Pi∗Z (Pi∗MZ) is linked to increased risk of cirrhosis, whether the Pi∗MZ genotype is associated with an increased rate of decompensation among patients who already have compensated cirrhosis is not known.MethodsThis was a retrospective study of Michigan Genomics Initiative participants with baseline compensated cirrhosis. The primary predictors were Pi∗MZ or Pi∗MS genotype (vs. Pi∗MM). The primary outcomes were hepatic decompensation with ascites, hepatic encephalopathy, or variceal bleeding, or the combined endpoint of liver-related death or liver transplant, both modeled with Fine-Gray competing risk models.ResultsWe included 576 patients with baseline compensated cirrhosis who had undergone genotyping, of whom 474 had Pi∗MM, 49 had Pi∗MZ, and 52 had Pi∗MS genotypes. Compared to Pi∗MM genotype, Pi∗MZ was associated with increased rates of hepatic decompensation (hazard ratio 1.81; 95% CI 1.22-2.69; p = 0.003) and liver transplant or liver-related death (hazard ratio 2.07; 95% CI 1.21-3.52; p = 0.078). These associations remained significant after adjustment for severity of underlying liver disease, and were robust across subgroup analyses based on etiology, sex, obesity, and diabetes status. Pi∗MS was not associated with decompensation or death/transplantation.ConclusionsThe SERPINA1 Pi∗MZ genotype is associated with an increased rate of hepatic decompensation and decreased transplant-free survival among patients with baseline compensated cirrhosis.Lay summaryThere is a mutation in the gene SERPINA1 called Pi∗MZ which increases risk of liver scarring (cirrhosis); however, it is not known what effect Pi∗MZ has if someone already has cirrhosis. In this study, we found that people who had cirrhosis and Pi∗MZ developed complications from cirrhosis faster than those who did not have the mutation. Alpha-1 antitrypsin deficiency is caused by mutations in SERPINA1, most commonly homozygosity for the Pi∗Z variant, and can present as liver disease. While heterozygosity for Pi∗Z (Pi∗MZ) is linked to increased risk of cirrhosis, whether the Pi∗MZ genotype is associated with an increased rate of decompensation among patients who already have compensated cirrhosis is not known. This was a retrospective study of Michigan Genomics Initiative participants with baseline compensated cirrhosis. The primary predictors were Pi∗MZ or Pi∗MS genotype (vs. Pi∗MM). The primary outcomes were hepatic decompensation with ascites, hepatic encephalopathy, or variceal bleeding, or the combined endpoint of liver-related death or liver transplant, both modeled with Fine-Gray competing risk models. We included 576 patients with baseline compensated cirrhosis who had undergone genotyping, of whom 474 had Pi∗MM, 49 had Pi∗MZ, and 52 had Pi∗MS genotypes. Compared to Pi∗MM genotype, Pi∗MZ was associated with increased rates of hepatic decompensation (hazard ratio 1.81; 95% CI 1.22-2.69; p = 0.003) and liver transplant or liver-related death (hazard ratio 2.07; 95% CI 1.21-3.52; p = 0.078). These associations remained significant after adjustment for severity of underlying liver disease, and were robust across subgroup analyses based on etiology, sex, obesity, and diabetes status. Pi∗MS was not associated with decompensation or death/transplantation. The SERPINA1 Pi∗MZ genotype is associated with an increased rate of hepatic decompensation and decreased transplant-free survival among patients with baseline compensated cirrhosis.

Background Visceral adipose tissue ( VAT ) and fatty liver differ in their associations with cardiovascular risk compared with subcutaneous adipose tissue ( SAT ). Several biomarkers have been linked to metabolic derangements and may contribute to the pathogenicity of fat depots. We examined the association between fat depots on multidetector computed tomography and metabolic regulatory biomarkers. Methods and Results Participants from the Framingham Heart Study (n=1583, 47% women) underwent assessment of SAT , VAT , and liver attenuation. We measured circulating biomarkers secreted by adipose tissue or liver (adiponectin, leptin, leptin receptor, fatty acid binding protein 4, fetuin‐A, and retinol binding protein 4). Using multivariable linear regression models, we examined relations of fat depots with biomarkers. Higher levels of fat depots were positively associated with leptin and fatty acid binding protein 4 but negatively associated with adiponectin (all P &lt;0.001). Associations with leptin receptor, fetuin‐A, and retinol binding protein 4 varied according to fat depot type or sex. When comparing the associations of SAT and VAT with biomarkers, VAT was the stronger correlate of adiponectin (β=−0.28 [women]; β=−0.30 [men]; both P &lt;0.001), whereas SAT was the stronger correlate of leptin (β=0.62 [women]; β=0.49 [men]; both P &lt;0.001; P &lt;0.001 for comparing VAT versus SAT ). Although fetuin‐A and retinol binding protein 4 are secreted by the liver in addition to adipose tissue, associations of liver attenuation with these biomarkers was not stronger than that of SAT or VAT . Conclusions SAT , VAT , and liver attenuation are associated with metabolic regulatory biomarkers with differences in the associations by fat depot type and sex. These findings support the possibility of biological differences between fat depots.

Abstract Background Inflammatory bowel disease (IBD) is associated with an increased risk of osteoporosis and bone fracture. The aims of this study were to (1) confirm the association between IBD and low bone density and (2) test for shared risk variants across diseases. Methods The study cohort included patients from the Michigan Genomics Initiative. Student’s t tests (continuous) and chi-square tests (categorical) were used for univariate analyses. Multivariable logistic regression was performed to test the effect of IBD on osteoporosis or osteopenia. Publicly available genome-wide association summary statistics were used to identify variants that alter the risk of IBD and bone density, and Mendelian randomization (MR) was used to identify causal effects of genetically predicted IBD on bone density. Results There were 51 405 individuals in the Michigan Genomics Initiative cohort including 10 378 (20.2%) cases of osteoporosis or osteopenia and 1404 (2.7%) cases of IBD. Patients with osteoporosis or osteopenia were more likely to be older (64 years of age vs 56 years of age; P &amp;lt; .001), female (67% vs 49%; P &amp;lt; .001), and have a lower body mass index (29 kg/m2 vs 30 kg/m2; P &amp;lt; .001). IBD patients with (odds ratio, 4.60; 95% confidence interval, 3.93-5.37) and without (odds ratio, 1.77; 95% confidence interval, 1.42-2.21) steroid use had a significantly higher risk of osteoporosis or osteopenia. Twenty-one IBD variants associated with reduced bone mineral density at P ≤ .05 and 3 IBD risk variants associated with reduced bone mineral density at P ≤ 5 × 10-8. Of the 3 genome-wide significant variants, 2 increased risk of IBD (rs12568930-T: MIR4418;ZBTB40; rs7236492-C: NFATC1). MR did not reveal a causal effect of genetically predicted IBD on bone density (MR Egger, P = .30; inverse variance weighted, P = .63). Conclusions Patients with IBD are at increased risk for low bone density, independent of steroid use. Variants in or near ZBTB40 and NFATC1 are associated with an increased risk of IBD and low bone density.

To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR).We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height.Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9610 211 ) and MSRA (WC, P = 8.9610 29 ).A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6610 28 ).The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution.By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.

Up to 25% of patients with nonalcoholic fatty liver disease (NAFLD) are not obese but may have a fat or muscle composition that predisposes them to NAFLD. Our aim was to determine whether body composition parameters associate with NAFLD and to identify genetic contributors to this association. This study included two cohorts. The first included 2,249 participants from the Framingham Heart Study who underwent a computed tomography scan to evaluate hepatic steatosis, dual‐energy x‐ray absorptiometry testing to assess body composition, and clinical examination. Body composition parameters were normalized to total body weight. A subset of participants underwent genotyping with an Affymetrix 550K single‐nucleotide polymorphism array. The second cohort, Michigan Genomics Initiative, included 19,239 individuals with genotyping on the Illumina HumanCoreExome v.12.1 array and full electronic health record data. Using sex‐stratified multivariable linear regression, greater central body fat associated with increased hepatic steatosis while greater lower extremity body fat associated with decreased hepatic steatosis. Greater appendicular lean mass was associated with decreased hepatic steatosis in men but not in women. A polygenic risk score for lipodystrophy (regional or global loss of adipose tissue) was associated with increased hepatic steatosis, increased liver fibrosis, and decreased lower extremity fat mass. Conclusion: Greater central body fat associated with increased hepatic steatosis, while greater lower extremity body fat and, in men, greater appendicular lean mass were associated with decreased hepatic steatosis. A genetic risk score for lipodystrophy was associated with NAFLD and liver fibrosis. Our results suggest that buffering of excess energy by peripheral fat and muscle may protect against NAFLD and liver fibrosis in the general population.

Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and approximately 2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 x 10(-)(8)), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.

Obesity is growing epidemic affecting 35% of adults in the United States. Previous genome-wide association studies (GWAS) have identified numerous loci associated with obesity. However, the majority of studies have been completed in Caucasians focusing on total body measures of adiposity. Here we report the results from genome-wide and exome chip association studies focusing on total body measures of adiposity including body mass index (BMI), percent body fat (PBF) and measures of fat deposition including waist circumference (WAIST), waist-hip ratio (WHR), subcutaneous adipose tissue (SAT), and visceral adipose tissue (VAT) in Hispanic Americans (nmax = 1263) from the Insulin Resistance Atherosclerosis Family Study (IRASFS). Five SNPs from two novel loci attained genome-wide significance (P<5.00x10-8) in IRASFS. A missense SNP in the isocitrate dehydrogenase 1 gene (IDH1) was associated with WAIST (rs34218846, MAF = 6.8%, PDOM = 1.62x10-8). This protein is postulated to play an important role in fat and cholesterol biosynthesis as demonstrated in cell and knock-out animal models. Four correlated intronic SNPs in the Zinc finger, GRF-type containing 1 gene (ZGRF1; SNP rs1471880, MAF = 48.1%, PDOM = 1.00x10-8) were strongly associated with WHR. The exact biological function of ZGRF1 and the connection with adiposity remains unclear. SNPs with p-values less than 5.00x10-6 from IRASFS were selected for replication. Meta-analysis was computed across seven independent Hispanic-American cohorts (nmax = 4156) and the strongest signal was rs1471880 (PDOM = 8.38x10-6) in ZGRF1 with WAIST. In conclusion, a genome-wide and exome chip association study was conducted that identified two novel loci (IDH1 and ZGRF1) associated with adiposity. While replication efforts were inconclusive, when taken together with the known biology, IDH1 and ZGRF1 warrant further evaluation.

Objective This study aimed to explore the genetic mechanisms of regional fat deposition, which is a strong risk factor for metabolic diseases beyond total adiposity. Methods A genome‐wide association study of 7,757,139 single‐nucleotide polymorphisms (SNPs) in 983 Mexican Americans ( n male = 403; n female = 580) from the Insulin Resistance Atherosclerosis Family Study was performed. Association analyses were performed with and without sex stratification for subcutaneous adipose tissue, visceral adipose tissue (VAT), and visceral‐subcutaneous ratio (VSR) obtained from computed tomography. Results The strongest signal identified was SNP rs2185405 (minor allele frequencies [MAF] = 40%; P VAT = 1.98 × 10 −8 ) with VAT. It is an intronic variant of the GLIS family zinc finger 3 gene ( GLIS3 ). In addition, SNP rs12657394 (MAF = 19%) was associated with VAT in males ( P male = 2.39×10 −8 ; P female = 2.5 × 10 −3 ). It is located intronically in the serum response factor binding protein 1 gene ( SRFBP1 ). On average, male carriers of the variant had 24.6 cm 2 increased VAT compared with noncarriers. Subsequently, genome‐wide SNP‐sex interaction analysis was performed. SNP rs10913233 (MAF = 14%; P int = 3.07 × 10 −8 ) in PAPPA2 and rs10923724 (MAF = 38%; P int = 2.89 × 10 −8 ) upstream of TBX15 were strongly associated with the interaction effect for VSR. Conclusions Six loci were identified with genome‐wide significant associations with fat deposition and interactive effects. These results provided genetic evidence for a differential basis of fat deposition between genders.

In this issue of the Journal, Luukkonen et al. explore the metabolic signature of "genetic" vs. "non-genetic" NAFLD. The authors recruit both bariatric and non-bariatric patients and carry out genetic, NMR metabolomic, as well as liver histologic analyses on participants. For one part of their study, participants were divided into 6 insulin resistance categories based on homeostatic model assessment for insulin resistance and into 6 categories based on a genetic risk score (GRS) derived from an unweighted analysis of 5 fatty liver disease-associated variants.

Evidence for a role for vitamin D in non-alcoholic fatty liver disease (NAFLD) pathogenesis is conflicting. As Mendelian randomisation (MR) avoids many limitations of conventional observational studies, this two-sample bidirectional MR analysis was conducted to determine the following: (i) whether genetically predicted 25-hydroxyvitamin D [25(OH)D] levels are a risk factor for NAFLD, and (ii) whether genetic risk for NAFLD influences 25(OH)D levels. Single-nucleotide polymorphisms (SNPs) associated with serum 25(OH)D levels were obtained from the European ancestry-derived SUNLIGHT consortium. SNPs associated with NAFLD or NASH (p-value &lt; 1 × 10−5) were extracted from previous studies and supplemented by genome-wide association studies (GWASs) performed in the UK Biobank. These GWASs were done both without (primary analysis) and with (sensitivity analysis) the population-level exclusion of other liver diseases (e.g., alcoholic liver diseases, toxic liver diseases, viral hepatitis, etc.). Subsequently, MR analyses were performed to obtain effect estimates using inverse variance weighted (IVW) random effect models. Cochran’s Q statistic, MR-Egger regression intercept, MR pleiotropy residual sum and outlier (MR-PRESSO) analyses were used to assess pleiotropy. No causal association of genetically predicted serum 25(OH)D (per standard deviation increase) with risk of NAFLD was identified in either the primary analysis: n = 2757 cases, n = 460,161 controls, odds ratio (95% confidence interval): 0.95 (0.76, −1.18), p = 0.614; or the sensitivity analysis. Reciprocally, no causal association was identified between the genetic risk of NAFLD and serum 25(OH)D levels, OR = 1.00 (0.99, 1.02, p = 0.665). In conclusion, this MR analysis found no evidence of an association between serum 25(OH)D levels and NAFLD in a large European cohort.

An elevated level of lipoprotein(a), or Lp(a), in the bloodstream has been causally linked to the development of atherosclerotic cardiovascular disease and calcific aortic valve stenosis. Steady state levels of circulating lipoproteins are modulated by their rate of clearance, but the identity of the Lp(a) uptake receptor(s) has been controversial. In this study, we performed a genome-scale CRISPR screen to functionally interrogate all potential Lp(a) uptake regulators in HuH7 cells. Strikingly, the top positive and negative regulators of Lp(a) uptake in our screen were LDLR and MYLIP, encoding the LDL receptor and its ubiquitin ligase IDOL, respectively. We also found a significant correlation for other genes with established roles in LDLR regulation. No other gene products, including those previously proposed as Lp(a) receptors, exhibited a significant effect on Lp(a) uptake in our screen. We validated the functional influence of LDLR expression on HuH7 Lp(a) uptake, confirmed in vitro binding between the LDLR extracellular domain and purified Lp(a), and detected an association between loss-of-function LDLR variants and increased circulating Lp(a) levels in the UK Biobank cohort. Together, our findings support a central role for the LDL receptor in mediating Lp(a) uptake by hepatocytes.

Linkage analysis of complex traits has had limited success in identifying trait-influencing loci. Recently, coding variants have been implicated as the basis for some biomedical associations. We tested whether coding variants are the basis for linkage peaks of complex traits in 42 African-American (n = 596) and 90 Hispanic (n = 1,414) families in the Insulin Resistance Atherosclerosis Family Study (IRASFS) using Illumina HumanExome Beadchips. A total of 92,157 variants in African Americans (34%) and 81,559 (31%) in Hispanics were polymorphic and tested using two-point linkage and association analyses with 37 cardiometabolic phenotypes. In African Americans 77 LOD scores greater than 3 were observed. The highest LOD score was 4.91 with the APOE SNP rs7412 (MAF = 0.13) with plasma apolipoprotein B (ApoB). This SNP was associated with ApoB (P-value = 4 × 10(-19)) and accounted for 16.2% of the variance in African Americans. In Hispanic families, 104 LOD scores were greater than 3. The strongest evidence of linkage (LOD = 4.29) was with rs5882 (MAF = 0.46) in CETP with HDL. CETP variants were strongly associated with HDL (0.00049 < P-value <4.6 × 10(-12)), accounting for up to 4.5% of the variance. These loci have previously been shown to have effects on the biomedical traits evaluated here. Thus, evidence of strong linkage in this genome wide survey of primarily coding variants was uncommon. Loci with strong evidence of linkage was characterized by large contributions to the variance, and, in these cases, are common variants. Less compelling evidence of linkage and association was observed with additional loci that may require larger family sets to confirm.

Glycogen storage diseases are rare. Increased glycogen in the liver results in increased attenuation.Investigate the association and function of a noncoding region associated with liver attenuation but not histologic nonalcoholic fatty liver disease.Genetics of Obesity-associated Liver Disease Consortium.Population-based.Computed tomography measured liver attenuation.Carriers of rs4841132-A (frequency 2%-19%) do not show increased hepatic steatosis; they have increased liver attenuation indicative of increased glycogen deposition. rs4841132 falls in a noncoding RNA LOC157273 ~190 kb upstream of PPP1R3B. We demonstrate that rs4841132-A increases PPP1R3B through a cis genetic effect. Using CRISPR/Cas9 we engineered a 105-bp deletion including rs4841132-A in human hepatocarcinoma cells that increases PPP1R3B, decreases LOC157273, and increases glycogen perfectly mirroring the human disease. Overexpression of PPP1R3B or knockdown of LOC157273 increased glycogen but did not result in decreased LOC157273 or increased PPP1R3B, respectively, suggesting that the effects may not all occur via affecting RNA levels. Based on electronic health record (EHR) data, rs4841132-A associates with all components of the metabolic syndrome (MetS). However, rs4841132-A associated with decreased low-density lipoprotein (LDL) cholesterol and risk for myocardial infarction (MI). A metabolic signature for rs4841132-A includes increased glycine, lactate, triglycerides, and decreased acetoacetate and beta-hydroxybutyrate.These results show that rs4841132-A promotes a hepatic glycogen storage disease by increasing PPP1R3B and decreasing LOC157273. rs4841132-A promotes glycogen accumulation and development of MetS but lowers LDL cholesterol and risk for MI. These results suggest that elevated hepatic glycogen is one cause of MetS that does not invariably promote MI.

See “Heritability of nonalcoholic fatty liver disease” by Schwimmer JB, Celedon MA, Lavine JE, et al, on page 1585. See “Heritability of nonalcoholic fatty liver disease” by Schwimmer JB, Celedon MA, Lavine JE, et al, on page 1585. Over the last 25 years, the prevalence of obesity has increased to epidemic proportions. Certainly, this rise is in part due to a change in our environment; before the mid 1980s, the prevalence of obesity was relatively constant at about 10%.1Kopelman P.G. Obesity as a medical problem.Nature. 2000; 404: 635-643Crossref PubMed Scopus (3765) Google Scholar This increase in obesity is correlated with a higher prevalence of fat deposits in the liver, which leads to a condition called nonalcoholic fatty liver disease (NAFLD). NAFLD encompasses a spectrum of disease that ranges from simple fat deposition (steatosis) to inflammation around the fat (steatohepatitis) and scarring (cirrhosis); some individuals with NAFLD go on to develop liver failure. However, even in today's “obesogenic” environment, not all people become obese. Similarly, why some individuals deposit fat in their liver and others do not and why some of those that deposit fat go on to develop nonalcoholic steatohepatitis, cirrhosis, and liver failure remains to be determined. One possibility is that genetics influence the observed heterogeneity in the development of these traits. One way to determine the overall genetic contribution to a trait is to measure its heritability.2Neale M.C. Cardon L.R. Methodology for genetic studies of twins and families. Kluwer Academic Publishers, 1992Crossref Google Scholar Heritability is the proportion of population phenotype variation that is attributable to genetic variation. In simple mathematical terms, phenotype variation is the sum of variation owing to environment plus variation owing to genotype. Heritability is measured relative to the genetic and environmental factors of the population and is not absolute. The degree of relatedness influences the accuracy and degree of heritability estimates; for example, the heritability of BMI studied in twins is usually higher than that obtained from family studies, which is higher than that observed in adoption studies.3Loos R.J. Bouchard C. Obesity—is it a genetic disorder?.J Intern Med. 2003; 254: 401-425Crossref PubMed Scopus (194) Google Scholar Heritability describes a population characteristic, not an individual's. For example, if a trait is 40% heritable, then the variation in the population attributable to a familial component genetics is 40%, not the variation found in the individual. The most commonly used obesity measure is body mass index (BMI). Twin and family studies show that the heritability of BMI ranges from 20% to 90% (reviewed in Maes et al4Maes H.H. Neale M.C. Eaves L.J. Genetic and environmental factors in relative body weight and human adiposity.Behav Genet. 1997; 27: 325-351Crossref PubMed Scopus (1185) Google Scholar). This suggests that the variation in BMI observed in the population is part of familial origin. Work evaluating the genetic nature of NAFLD has been much more limited. Fatty liver clusters in families,5Struben V.M. Hespenheide E.E. Caldwell S.H. Nonalcoholic steatohepatitis and cryptogenic cirrhosis within kindreds.Am J Med. 2000; 108: 9-13Abstract Full Text Full Text PDF PubMed Scopus (271) Google Scholar, 6Willner I.R. Waters B. Patil S.R. et al.Ninety patients with nonalcoholic steatohepatitis: insulin resistance, familial tendency, and severity of disease.Am J Gastroenterol. 2001; 96: 2957-2961Crossref PubMed Google Scholar suggesting a possible genetic component to the condition. A recent study of fatty liver in 157 individuals with familial combined hyperlipidemia found that the heritability of fatty liver in this group was 40%.7Brouwers M.C. Cantor R.M. Kono N. et al.Heritability and genetic loci of fatty liver in familial combined hyperlipidemia.J Lipid Res. 2006; 47: 2799-2807Abstract Full Text Full Text PDF PubMed Scopus (51) Google Scholar The heritability of fatty liver in individuals without known genetic lipid abnormalities has not been addressed. The accompanying paper by Schwimmer et al8Schwimmer J.B. Celedon M.A. Lavine J.E. et al.Heritability of nonalcoholic fatty liver disease.Gastroenterology. 2009; 136: 1585-1592Abstract Full Text Full Text PDF PubMed Scopus (370) Google Scholar aims to fill this gap in knowledge. The strength of this paper is that the authors took on the challenging task of measuring fatty liver using magnetic resonance imaging in family members of probands with and without biopsy-proven NAFLD. Using variance components methods, they determined that the heritability of fatty liver measured as a continuous trait was 58%; after controlling for age, gender, race, and BMI, it was reduced to 39%. Such a range is often seen with many common traits9McQueen M.B. Bertram L. Rimm E.B. et al.A QTL genome scan of the metabolic syndrome and its component traits.BMC Genet. 2003; 4: S96Crossref PubMed Google Scholar and suggests that about half of the population variance in fatty liver may have a genetic origin. The authors calculated further the heritability of fatty liver as a dichotomous trait. In this case, they obtained a higher heritability of 85% and, after correction for age, gender, race, and BMI it increased to close to 100%. Both the continuous and dichotomous analyses were done using a multivariate t-distribution in SOLAR, a program that uses variance component methods algorithms to determine the contribution of genetic and other influences on a trait. Because both the continuous and certainly the dichotomous fatty liver traits are not normally distributed and the underlying methodology of variance component methods requires normality, analysis of these traits in SOLAR may be limited. Although the multivariate t-distribution can be used to model non-normal traits, numerical problems with modeling dichotomous traits in particular may lead to faulty parameter estimates. Thus, the dichotomous analyses of fatty liver should be viewed with caution The authors go on to show that BMI correlates with fatty liver in individuals with NAFLD whereas BMI correlates less well with liver fat in those without NAFLD. One possible explanation for this nonlinear correlation is that some individuals with a genetic predisposition to develop fatty liver disease with increasing BMI deposit fat in their livers, whereas in those not predisposed it may be harder to accumulate fat in the liver. The finding that BMI and NAFLD are heritable suggests that there are genetic components that predispose to these traits. Finding genetic variants that affect population traits has been challenging and elusive until recently. Several publications have reported reproducible associations of single nucleotide polymorphisms with BMI. The first common genetic variants convincingly associated with BMI were found in the first intron of the gene FTO (Table 1).10Frayling T.M. Timpson N.J. Weedon M.N. et al.A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity.Science. 2007; 316: 889-894Crossref PubMed Scopus (3505) Google Scholar, 11Scuteri A. Sanna S. Chen W.M. et al.Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits.PLoS Genet. 2007; 3: e115Crossref PubMed Scopus (1355) Google Scholar These variants confer an increased odds of being overweight or obese of about 1.14 and 1.25 per risk allele.12Willer C.J. Speliotes E.K. Loos R.J. et al.Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.Nat Genet. 2009; 41: 25-34Crossref PubMed Scopus (1416) Google Scholar Since that time, another 10 variants have been reported.12Willer C.J. Speliotes E.K. Loos R.J. et al.Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.Nat Genet. 2009; 41: 25-34Crossref PubMed Scopus (1416) Google Scholar, 13Thorleifsson G. Walters G.B. Gudbjartsson D.F. et al.Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.Nat Genet. 2009; 41: 18-24Crossref PubMed Scopus (1099) Google Scholar Many of these variants have small effect sizes and often map to noncoding regions of the genome. Thus far, common single nucleotide polymorphisms captured by current genotyping platforms with large effect sizes for affecting BMI have not been uncovered in the populations being studied. Finally, 1 study12Willer C.J. Speliotes E.K. Loos R.J. et al.Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.Nat Genet. 2009; 41: 25-34Crossref PubMed Scopus (1416) Google Scholar has found recently an association of a deletion with increased BMI, suggesting that other forms of genetic variation may contribute to variation in BMI.Table 1Variants That Associate With Increasing Body Mass Index (BMI) or SteatosisSingle nucleotide polymorphismChromosomePositionBMI/Steatosis increasing alleleNearest geneBMI rs99396091652378028AFTO rs65482382624905CTMEM18 rs177823131856002077CMC4R rs10938397445023455GGNPDA2 rs74986651628790742GSH2B1 rs110847531939013977GKCTD15 rs108387381147619625GMTCH2 rs2815752172524461ANEGR1 rs40741341127603861GBDNF rs76473053187316984CETV5 rs109134691176180142CSEC16BSteatosis rs7384092242649628GPNPLA3 rs60064002228925243GPNPLA3NOTE: Data from references 12Willer C.J. Speliotes E.K. Loos R.J. et al.Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.Nat Genet. 2009; 41: 25-34Crossref PubMed Scopus (1416) Google Scholar, 13Thorleifsson G. Walters G.B. Gudbjartsson D.F. et al.Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.Nat Genet. 2009; 41: 18-24Crossref PubMed Scopus (1099) Google Scholar, 19Romeo S. Kozlitina J. Xing C. et al.Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2008; 40: 1461-1465Crossref PubMed Scopus (2433) Google Scholar. Open table in a new tab NOTE: Data from references 12Willer C.J. Speliotes E.K. Loos R.J. et al.Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.Nat Genet. 2009; 41: 25-34Crossref PubMed Scopus (1416) Google Scholar, 13Thorleifsson G. Walters G.B. Gudbjartsson D.F. et al.Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity.Nat Genet. 2009; 41: 18-24Crossref PubMed Scopus (1099) Google Scholar, 19Romeo S. Kozlitina J. Xing C. et al.Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2008; 40: 1461-1465Crossref PubMed Scopus (2433) Google Scholar. Although these associations implicate some genes known previously to associate with body weight, they also implicate novel loci whose contribution to BMI was heretofore unsuspected. Two variants that affect BMI map near the genes MC4R and BDNF. Severe mutations in these genes both in humans and in mice are associated with hyperphagia and obesity.14Lyons W.E. Mamounas L.A. Ricaurte G.A. et al.Brain-derived neurotrophic factor-deficient mice develop aggressiveness and hyperphagia in conjunction with brain serotonergic abnormalities.Proc Natl Acad Sci U S A. 1999; 96: 15239-15244Crossref PubMed Scopus (736) Google Scholar, 15Huszar D. Lynch C.A. Fairchild-Huntress V. et al.Targeted disruption of the melanocortin-4 receptor results in obesity in mice.Cell. 1997; 88: 131-141Abstract Full Text Full Text PDF PubMed Scopus (2612) Google Scholar, 16Farooqi I.S. Keogh J.M. Yeo G.S. et al.Clinical spectrum of obesity and mutations in the melanocortin 4 receptor gene.N Engl J Med. 2003; 348: 1085-1095Crossref PubMed Scopus (1342) Google Scholar, 17Han J.C. Liu Q.R. Jones M. et al.Brain-derived neurotrophic factor and obesity in the WAGR syndrome.N Engl J Med. 2008; 359: 918-927Crossref PubMed Scopus (251) Google Scholar Other variants that are reproducibly associated with BMI map near the gene SH2B1, a member of the leptin signaling pathway. Sh2b1-null mice develop obesity and hyperphagia.18Ren D. Li M. Duan C. et al.Identification of SH2-B as a key regulator of leptin sensitivity, energy balance, and body weight in mice.Cell Metab. 2005; 2: 95-104Abstract Full Text Full Text PDF PubMed Scopus (199) Google Scholar The detection of variants near candidate genes that are clearly involved in the regulation of body weight by an unbiased scan of the human genome serves as a positive control, and illustrates that this approach is likely to yield loci that have real effects on BMI. Excitingly, 8 more loci have been reproducibly associated with BMI; however, the precise genes that mediate these effects and their mechanism of action remain to be determined. Seven of the 8 genes located closest to the strongest signals of association are expressed in the cerebral cortex and hypothalamus,12Willer C.J. Speliotes E.K. Loos R.J. et al.Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.Nat Genet. 2009; 41: 25-34Crossref PubMed Scopus (1416) Google Scholar suggesting a possible contribution of the central nervous system to the influence of body weight. Furthermore, these new loci in aggregate account for <1% of the population variation in BMI, suggesting that many more BMI-influencing variants remain to be discovered. In support of the proposed contribution of genetic inheritance to NAFLD, nonsynonymous variants in PNPLA3 have been associated recently with this phenotype.19Romeo S. Kozlitina J. Xing C. et al.Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease.Nat Genet. 2008; 40: 1461-1465Crossref PubMed Scopus (2433) Google Scholar The investigators measured fat in the liver using proton magnetic resonance spectroscopy in 2,111 European, African, and Latino individuals. They conducted an association analysis of nonsynonymous variants across the genome with NAFLD and discovered a missense variant in PNPLA3 (rs738409, encoding I148M) that associated with hepatic fat. Hepatic fat was >2-fold higher in individuals carrying 2 alleles of this variant than in those who did not carry any. They identified other variants by resequencing the coding region of PNPLA3 in individuals at the extremes of the liver fat distribution, and genotyped the 6 most common of these in their full sample. One of them (rs6006460, encoding S453I) was associated with decreased hepatic fat content. PNPLA3 encodes a protein of unknown function with homology to lipid acyl hydrolases of the patanin-like phospholipase family. These associations with PNPLA3 need to be replicated in other samples with a direct measure of fat in the liver, but variants near this region were also associated with population based levels of ALT,20Yuan X. Waterworth D. Perry J.R. et al.Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.Am J Hum Genet. 2008; 83: 520-528Abstract Full Text Full Text PDF PubMed Scopus (348) Google Scholar a nonspecific marker for liver insult, including NAFLD, suggesting that they may be real. Furthermore, the precise mechanisms by which variation around this locus leads to development of NAFLD remain to be determined. Nevertheless, these findings and the paper by Schwimmer et al8Schwimmer J.B. Celedon M.A. Lavine J.E. et al.Heritability of nonalcoholic fatty liver disease.Gastroenterology. 2009; 136: 1585-1592Abstract Full Text Full Text PDF PubMed Scopus (370) Google Scholar in this issue of Gastroenterology suggest that a human genetic approach to the study of NAFLD is feasible and tractable. Possible overlap in the contribution of variants to obesity and NAFLD is an active area of research. The upcoming years hold great promise for using a human genetic approach to not only get new insights into the biology of obesity and NAFLD, but also into possible new targets for therapeutic intervention. Heritability of Nonalcoholic Fatty Liver DiseaseGastroenterologyVol. 136Issue 5PreviewNonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in the United States. The etiology is believed to be multifactorial with a substantial genetic component; however, the heritability of NAFLD is undetermined. Therefore, a familial aggregation study was performed to test the hypothesis that NAFLD is highly heritable. Full-Text PDF

Insulin resistance is a risk marker for non-alcoholic fatty liver disease, and a risk factor for liver disease progression. We assessed temporal trajectories of insulin resistance and β-cell response to serum glucose concentration throughout adulthood and their association with diabetes risk in non-alcoholic fatty liver disease.Three thousand and sixty participants from Coronary Artery Risk Development in Young Adults, a prospective bi-racial cohort of adults age 18-30 years at baseline (1985-1986; Y0) who completed up to 5 exams over 25 years and had fasting insulin and glucose measurement were included. At Y25 (2010-2011), non-alcoholic fatty liver disease was assessed by noncontrast computed tomography after exclusion of other liver fat causes. Latent mixture modelling identified 25-year trajectories in homeostatic model assessment insulin resistance and β-cell response homeostatic model assessment-β.Three distinct trajectories were identified, separately, for homeostatic model assessment insulin resistance (low-stable [47%]; moderate-increasing [42%]; and high-increasing [12%]) and homeostatic model assessment-β (low-decreasing [16%]; moderate-decreasing [63%]; and high-decreasing [21%]). Y25 non-alcoholic fatty liver disease prevalence was 24.5%. Among non-alcoholic fatty liver disease, high-increasing homeostatic model assessment insulin resistance (referent: low-stable) was associated with greater prevalent (OR 95% CI = 8.0, 2.0-31.9) and incident (OR = 10.5, 2.6-32.8) diabetes after multivariable adjustment including Y0 or Y25 homeostatic model assessment insulin resistance. In contrast, non-alcoholic fatty liver disease participants with low-decreasing homeostatic model assessment-β (referent: high-decreasing) had the highest odds of prevalent (OR = 14.1, 3.9-50.9) and incident (OR = 10.3, 2.7-39.3) diabetes.Trajectories of insulin resistance and β-cell response during young and middle adulthood are robustly associated with diabetes risk in non-alcoholic fatty liver disease. Thus, how persons with non-alcoholic fatty liver disease develop resistance to insulin provides important information about risk of diabetes in midlife above and beyond degree of insulin resistance at the time of non-alcoholic fatty liver disease assessment.

Abstract Background Inflammatory bowel disease is associated with an increased risk of skin cancer. The aims of this study were to determine whether IBD susceptibility variants are also associated with skin cancer susceptibility and if such risk is augmented by use of immune-suppressive therapy. Methods The discovery cohort included participants in the UK Biobank. The validation cohort included participants in the Michigan Genomics Initiative. The primary outcome of interest was skin cancer, subgrouped into nonmelanoma skin cancers (NMSC) and melanoma skin cancers (MSC). Multivariable logistic regression with matched controls (3 controls:1 case) was performed to identify genomic predictors of skin malignancy in the discovery cohort. Variants with P &amp;lt; .05 were tested for replication in the validation cohort. Validated Single nucleotide polymorphisms were then evaluated for effect modification by immune-suppressive medications. Results The discovery cohort included 10,247 cases of NMSC and 1883 cases of MSC. The validation cohort included 7334 cases of NMSC and 3304 cases of MSC. Twenty-nine variants were associated with risk of NMSC in the discovery cohort, of which 5 replicated in the validation cohort (increased risk, rs7773324-A [DUSP22; IRF4], rs2476601-G [PTPN22], rs1847472-C [BACH2], rs72810983-A [CPEB4]; decreased risk, rs6088765-G [PROCR; MMP24]). Twelve variants were associated with risk of MSC in the discovery cohort, of which 4 were replicated in the validation cohort (increased risk, rs61839660-T [IL2RA]; decreased risk, rs17391694-C [GIPC2; MGC27382], rs6088765-G [PROCR; MMP24], and rs1728785-C [ZFP90]). No effect modification was observed. Conclusions The results of this study highlight shared genetic susceptibility across IBD and skin cancer, with increased risk of NMSC in those who carry risk variants in IRF4, PTPN22, CPEB4, and BACH2 and increased risk of MSC in those who carry a risk variant in IL2RA.

Nonalcoholic fatty liver disease (NAFLD) is prevalent worldwide. NAFLD is associated with elevated serum triglycerides (TG), low-density lipoprotein cholesterol (LDL), and reduced high-density lipoprotein cholesterol (HDL). Both NAFLD and blood lipid levels are genetically influenced and may share a common genetic etiology. We used genome-wide association studies (GWAS)-ranked genes and gene-set enrichment analysis to identify pathways that affect serum lipids and NAFLD. We identified credible genes in these pathways and characterized missense variants in these for effects on serum traits. We used MAGENTA to identify 58 enriched pathways from publicly available TG, LDL, and HDL GWAS (n = 99,000). Three of these pathways were also enriched for associations with European-ancestry NAFLD GWAS (n = 7176). One pathway, farnesoid X receptor (FXR)/retinoid X receptor (RXR) activation, was replicated for association in an African-ancestry NAFLD GWAS (n = 3214) and plays a role in serum lipids and NAFLD. Credible genes (proteins) in FXR/RXR activation include those associated with cholesterol/bile/bilirubin transport/absorption (ABCC2 (MRP2) [ATP binding cassette subfamily C member (multidrug resistance-associated protein 2)], ABCG5, ABCG8 [ATP-binding cassette (ABC) transporters G5 and G8], APOB (APOB) [apolipoprotein B], FABP6 (ILBP) [fatty acid binding protein 6 (ileal lipid-binding protein)], MTTP (MTP) [microsomal triglyceride transfer protein], SLC4A2 (AE2) [solute carrier family 4 member 2 (anion exchange protein 2)]), nuclear hormone-mediated control of metabolism (NR0B2 (SHP) [nuclear receptor subfamily 0 group B member 2 (small heterodimer partner)], NR1H4 (FXR) [nuclear receptor subfamily 1 group H member 4 (FXR)], PPARA (PPAR) [peroxisome proliferator activated receptor alpha], FOXO1 (FOXO1A) [forkhead box O1]), or other pathways (FETUB (FETUB) [fetuin B]). Missense variants in ABCC2 (MRP2), ABCG5 (ABCG5), ABCG8 (ABCG8), APOB (APOB), MTTP (MTP), NR0B2 (SHP), NR1H4 (FXR), and PPARA (PPAR) that associate with serum LDL levels also associate with serum liver function tests in UK Biobank. Conclusion: Genetic variants in NR1H4 (FXR) that protect against liver steatosis increase serum LDL cholesterol while variants in other members of the family have congruent effects on these traits. Human genetic pathway enrichment analysis can help guide therapeutic development by identifying effective targets for NAFLD/serum lipid manipulation while minimizing side effects. In addition, missense variants could be used in companion diagnostics to determine their influence on drug effectiveness.

Human genome-wide association studies found single-nucleotide polymorphisms (SNPs) near LYPLAL1 (Lysophospholipase-like protein 1) that have sex-specific effects on fat distribution and metabolic traits. To determine whether altering LYPLAL1 affects obesity and metabolic disease, we created and characterized a mouse knockout (KO) of Lyplal1. We fed the experimental group of mice a high-fat, high-sucrose (HFHS) diet for 23 weeks, and the controls were fed regular chow diet. Here, we show that CRISPR-Cas9 whole-body Lyplal1 KO mice fed an HFHS diet showed sex-specific differences in weight gain and fat accumulation as compared to chow diet. Female, not male, KO mice weighed less than WT mice, had reduced body fat percentage, had white fat mass, and had adipocyte diameter not accounted for by changes in the metabolic rate. Female, but not male, KO mice had increased serum triglycerides, decreased aspartate, and decreased alanine aminotransferase. Lyplal1 KO mice of both sexes have reduced liver triglycerides and steatosis. These diet-specific effects resemble the effects of SNPs near LYPLAL1 in humans, suggesting that LYPLAL1 has an evolutionary conserved sex-specific effect on adiposity. This murine model can be used to study this novel gene-by-sex-by-diet interaction to elucidate the metabolic effects of LYPLAL1 on human obesity.

<h3>Background & Aims</h3> Non-alcoholic fatty liver disease (NAFLD), and its progressive form steatohepatitis (NASH), represent a genetically and phenotypically diverse entity for which there is no approved therapy, making it imperative to define the spectrum of pathways contributing to its pathogenesis. Rare variants in genes encoding nuclear envelope proteins cause lipodystrophy with early-onset NAFLD/NASH; we hypothesized that common variants in nuclear envelope-related genes might also contribute to hepatic steatosis and NAFLD. <h3>Methods</h3> Using hepatic steatosis as the outcome of interest, we performed an association meta-analysis of nuclear envelope-related coding variants in three large discovery cohorts (N >120,000 participants), followed by phenotype association studies in large validation cohorts (N >600,000) and functional testing of the top steatosis-associated variant in cell culture. <h3>Results</h3> A common protein-coding variant, rs6461378 (<i>SUN1</i> H118Y), was the top steatosis-associated variant in our association meta-analysis (<i>p</i> <0.001). In ancestrally distinct validation cohorts, rs6461378 associated with histologic NAFLD and with NAFLD-related metabolic traits including increased serum fatty acids, type 2 diabetes, hypertension, cardiovascular disease, and decreased HDL. SUN1 H118Y was subject to increased proteasomal degradation relative to wild-type SUN1 in cells, and SUN1 H118Y-expressing cells exhibited insulin resistance and increased lipid accumulation. <h3>Conclusions</h3> Collectively, these data support a potential causal role for the common <i>SUN1</i> variant rs6461378 in NAFLD and metabolic disease. <h3>Impact and implications</h3> Non-alcoholic fatty liver disease (NAFLD), with an estimated global prevalence of nearly 30%, is a growing cause of morbidity and mortality for which there is no approved pharmacologic therapy. Our data provide a rationale for broadening current concepts of NAFLD genetics and pathophysiology to include the nuclear envelope, and particularly Sad1 and UNC84 domain containing 1 (SUN1), as novel contributors to this common liver disease. Furthermore, if future studies confirm causality of the common <i>SUN1</i> H118Y variant, it has the potential to become a broadly relevant therapeutic target in NAFLD and metabolic disease.

Glucagon-like peptide 1 receptor agonists (GLP-1RAs) are approved for treatment of type 2 diabetes mellitus (T2DM) and weight loss in people with overweight, and semaglutide is in phase 3 clinical trials for treatment of nonalcoholic fatty liver disease (NAFLD). GLP-1RAs reduce alanine aminotransferase (ALT) levels, and in phase 2 trials, semaglutide resulted in histologic improvement in steatohepatitis.1,2

The object of this investigation was to determine whether glutamate uptake affects the apparent potency of the competitive antagonists DL-2-amino-5-phosphonovalerate and CGS-19755 in blocking NMDA receptor-mediated neurotoxicity. In astrocyte-rich rat cortical cultures we observed that DL-2-amino-5-phosphonovalerate and CGS-19755 were 24 and 16 times more potent against NMDA than against glutamate-induced toxicity. In contrast, DL-2-amino-5-phosphonovalerate was equipotent against the two agonists in astrocyte-poor cultures, in which dendrites are directly exposed to the extracellular medium. With the noncompetitive NMDA antagonist MK-801, similar potencies were observed against glutamate (212 +/- 16 nM) and against NMDA (155 +/- 9 nM) neurotoxicity. These results may be explained if we assume that the neuronal cell body is less susceptible than the dendrites to NMDA receptor-mediated toxicity, and that the action of glutamate in astrocyte-rich cultures is confined to the cell body. In this case, one would expect that higher concentrations of glutamate would be needed to produce toxicity in astrocyte-rich cultures, and that higher concentrations of competitive antagonists would be needed to overcome this toxicity. Our observations help explain the pharmacology of the competitive NMDA antagonists against NMDA receptor-mediated neurotoxicity but also suggest the possibility that, because the cell body and dendrites may be distinct sites for neurotoxicity, they might also involve different mechanisms of toxicity.

Vandervell Foundation and Wellcome Trust (068545/Z/02, GR072960, GR076113, GR069224, 086596/Z/08/Z)

Nat. Genet. 42, 949–960 (2010); published online 10 October 2010; corrected after print 12 October 2011 In the version of this article initially published, there were errors in Table 1. Specifically, for eight SNPs, the effect allele frequencies were reversed. The correct effect allele frequencies for rs9491696, rs984222, rs4846567, rs1011731, rs718314, rs1294421, rs6795735 and rs2076529 are 0.

Myocyte-specific enhancer binding factor 2 (MEF2C) is a transcription factor expressed at high levels in brain. In this study, the distribution of MEF2C expression in brain was studied in normal adult gerbils and in adult gerbils subjected to 10 min of global cerebral ischemia. In normal animals, MEF2C-immunoreactivity and messenger RNA expression were detected in cortex, hippocampus, caudate-putamen, thalamus, hypothalamus, and amygdala. Within the hippocampus, MEF2C-immunoreactivity and MEF2C messenger RNA were found in interneurons scattered through the CA fields, a subset of which are parvalbumin-immunoreactive. MEF2C-immunoreactivity and MEF2C messenger RNA were also present in granule cells in the dentate gyrus. MEF2C-immunoreactivity was also detected in microglia in the hippocampus. After transient forebrain ischemia, CA1 pyramidal neurons, which are MEF2C-negative, degenerate whereas MEF2C-positive interneurons survive. Our results thus indicate that MEF2C is a marker for hippocampal neurons that are resistant to ischemia. It remains to be determined whether MEF2C plays a direct role in protecting the neurons that express it from ischemic injury. In addition, MEF2C-immunoreactivity is present in microglia, and, after ischemia, there were increased numbers of MEF2C-immunoreactive microglia in CA1, so MEF2C-immunoreactivity is a marker of both resting and activated microglia.

Abstract Carotid artery atherosclerotic disease (CAAD) is a risk factor for stroke. We used a genome‐wide association (GWAS) approach to discover genetic variants associated with CAAD in participants in the electronic Medical Records and Genomics (eMERGE) Network. We identified adult CAAD cases with unilateral or bilateral carotid artery stenosis and controls without evidence of stenosis from electronic health records at eight eMERGE sites. We performed GWAS with a model adjusting for age, sex, study site, and genetic principal components of ancestry. In eMERGE we found 1793 CAAD cases and 17,958 controls. Two loci reached genome‐wide significance, on chr6 in LPA (rs10455872, odds ratio [OR] (95% confidence interval [CI]) = 1.50 (1.30–1.73), p = 2.1 × 10 −8 ) and on chr7, an intergenic single nucleotide variant (SNV; rs6952610, OR (95% CI) = 1.25 (1.16–1.36), p = 4.3 × 10 −8 ). The chr7 association remained significant in the presence of the LPA SNV as a covariate. The LPA SNV was also associated with coronary heart disease (CHD; 4199 cases and 11,679 controls) in this study (OR (95% CI) = 1.27 (1.13–1.43), p = 5 × 10 −5 ) but the chr7 SNV was not (OR (95% CI) = 1.03 (0.97–1.09), p = .37). Both variants replicated in UK Biobank. Elevated lipoprotein(a) concentrations ([Lp(a)]) and LPA variants associated with elevated [Lp(a)] have previously been associated with CAAD and CHD, including rs10455872. With electronic health record phenotypes in eMERGE and UKB, we replicated a previously known association and identified a novel locus associated with CAAD.

Objective: To derive and validate a polygenic risk score (PRS) to predict the occurrence and severity of diverticulitis and to understand the potential for incorporation of a PRS in current decision-making. Background: PRS quantifies genetic variation into a continuous measure of risk. There is a need for improved risk stratification to guide surgical decision-making that could be fulfilled by PRS. It is unknown how surgeons might integrate PRS in decision-making. Methods: We derived a PRS with 44 single-nucleotide polymorphisms associated with diverticular disease in the UK Biobank and validated this score in the Michigan Genomics Initiative (MGI). We performed a discrete choice experiment of practicing colorectal surgeons. Surgeons rated the influence of clinical factors and a hypothetical polygenic risk prediction tool. Results: Among 2812 MGI participants with diverticular disease, 1964 were asymptomatic, 574 had mild disease, and 274 had severe disease. PRS was associated with occurrence and severity. Patients in the highest PRS decile were more likely to have diverticulitis [odds ratio (OR)=1.84; 95% confidence interval (CI), 1.42–2.38)] and more likely to have severe diverticulitis (OR=1.61; 95% CI, 1.04–2.51) than the bottom 50%. Among 213 surveyed surgeons, extreme disease-specific factors had the largest utility (3 episodes in the last year, +74.4; percutaneous drain, + 69.4). Factors with strongest influence against surgery included 1 lifetime episode (−63.3), outpatient management (−54.9), and patient preference (−39.6). PRS was predicted to have high utility (+71). Conclusions: A PRS derived from a large national biobank was externally validated, and found to be associated with the incidence and severity of diverticulitis. Surgeons have clear guidance at clinical extremes, but demonstrate equipoise in intermediate scenarios. Surgeons are receptive to PRS, which may be most useful in marginal clinical situations. Given the current lack of accurate prognostication in recurrent diverticulitis, PRS may provide a novel approach for improving patient counseling and decision-making.

In the last few decades, dengue virus, an arbovirus, has spread to over 120 countries. Although a vaccine has been approved in some countries, limitations on its effectiveness and a lack of effective antiviral treatments reinforce the need for additional research. The functions of several viral nonstructural proteins are essentially unknown. To better understand the functions of these proteins and thus dengue virus pathogenesis, we embarked on a genomewide transposon mutagenesis screen with next-generation sequencing to determine sites in the viral genome that tolerate 15-nucleotide insertions. Using this approach, we generated support for several published predicted transmembrane and enzymatic domains. Next, we created 7 mutants containing the 15-nucleotide insertion from the original selection and found 6 of them were capable of replication in both mammalian and mosquito tissue culture cells. Interestingly, one mutation had a significant impairment of viral assembly, and this mutation may lead to a better understanding of viral assembly and release. In addition, we created a fully infectious virus expressing a functionally tagged NS4B protein, which will provide a much-needed tool to elucidate the role of NS4B in viral pathogenesis.IMPORTANCE Dengue virus is a mosquito-borne virus distributed in tropical and subtropical regions globally that can result in hospitalization and even death in some cases. Although a vaccine exists, its limitations and a lack of approved antiviral treatments highlight our limited understanding of dengue virus pathogenesis and host immunity. The functions of many viral proteins are poorly understood. We used a previously published approach using transposon mutagenesis to develop tools to study these proteins' functions by adding insertions randomly throughout the viral genomes. These genomes were transferred into cells, and infectious progeny were recovered to determine sites that tolerated insertions, as only the genomes that tolerated insertions would be able to propagate. Using these results, we created viruses with epitope tags, one in the viral structural protein Capsid and one in the viral nonstructural protein NS4B. Further investigation of these mutants may elucidate the roles of Capsid and NS4B during dengue virus infections.

We previously identified a low-frequency (1.1 %) coding variant (G45R; rs200573126) in the adiponectin gene (ADIPOQ) which was the basis for a multipoint microsatellite linkage signal (LOD = 8.2) for plasma adiponectin levels in Hispanic families. We have empirically evaluated the ability of data from targeted common variants, exome chip genotyping, and genome-wide association study data to detect linkage and association to adiponectin protein levels at this locus. Simple two-point linkage and association analyses were performed in 88 Hispanic families (1,150 individuals) using 10,958 SNPs on chromosome 3. Approaches were compared for their ability to map the functional variant, G45R, which was strongly linked (two-point LOD = 20.98) and powerfully associated (p value = 8.1 × 10−50). Over 450 SNPs within a broad 61 Mb interval around rs200573126 showed nominal evidence of linkage (LOD > 3) but only four other SNPs in this region were associated with p values < 1.0 × 10−4. When G45R was accounted for, the maximum LOD score across the interval dropped to 4.39 and the best p value was 1.1 × 10−5. Linked and/or associated variants ranged in frequency (0.0018–0.50) and type (coding, non-coding) and had little detectable linkage disequilibrium with rs200573126 (r 2 < 0.20). In addition, the two-point linkage approach empirically outperformed multipoint microsatellite and multipoint SNP analysis. In the absence of data for rs200573126, family-based linkage analysis using a moderately dense SNP dataset, including both common and low-frequency variants, resulted in stronger evidence for an adiponectin locus than association data alone. Thus, linkage analysis can be a useful tool to facilitate identification of high-impact genetic variants.

Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure.These studies also have pointed to thousands of loci with promising but not yet compelling association evidence.To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the ''Metabochip,'' a custom genotyping array that assays nearly 200,000 SNP markers.Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation.The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits.The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.

Linkage studies of complex genetic diseases have been largely replaced by genome-wide association studies, due in part to limited success in complex trait discovery. However, recent interest in rare and low-frequency variants motivates re-examination of family-based methods. In this study, we investigated the performance of two-point linkage analysis for over 1.6 million single-nucleotide polymorphisms (SNPs) combined with single variant association analysis to identify high impact variants, which are both strongly linked and associated with cardiometabolic traits in up to 1414 Hispanics from the Insulin Resistance Atherosclerosis Family Study (IRASFS). Evaluation of all 50 phenotypes yielded 83 557 000 LOD (logarithm of the odds) scores, with 9214 LOD scores ⩾3.0, 845 ⩾4.0 and 89 ⩾5.0, with a maximal LOD score of 6.49 (rs12956744 in the LAMA1 gene for tumor necrosis factor-α (TNFα) receptor 2). Twenty-seven variants were associated with P<0.005 as well as having an LOD score >4, including variants in the NFIB gene under a linkage peak with TNFα receptor 2 levels on chromosome 9. Linkage regions of interest included a broad peak (31 Mb) on chromosome 1q with acute insulin response (max LOD=5.37). This region was previously documented with type 2 diabetes in family-based studies, providing support for the validity of these results. Overall, we have demonstrated the utility of two-point linkage and association in comprehensive genome-wide array-based SNP genotypes.

Sum of cells within 5° latitudinal bins for all model classes, binary thresholds and climate scenarios.

Non-alcoholic fatty liver disease (NAFLD) is caused by excess lipid accumulation in hepatocytes. Genome-wide association studies have identified a strong association of NAFLD with non-synonymous E167K amino acid mutation in the transmembrane 6 superfamily member 2 (TM6SF2) protein. The E167K mutation reduces TM6SF2 stability, and its carriers display increased hepatic lipids and lower serum triglycerides. However, the effects of TM6SF2 on hepatic lipid metabolism are not completely understood. We overexpressed wild-type or E167K variant of TM6SF2 or knocked down TM6SF2 expression in lipid-treated Huh-7 cells and used untargeted lipidomic analysis, RNAseq transcriptome analysis, and fluorescent imaging to determine changes in hepatic lipid metabolism. Both TM6SF2 knockdown and E167K overexpression increased hepatic lipid accumulation, while wild-type overexpression decreased acylglyceride levels. We also observed lipid chain remodeling for acylglycerides by TM6SF2 knockdown, leading to a relative increase in species with shorter, more saturated side chains. RNA-sequencing revealed differential expression of several lipid metabolizing genes, including genes belonging to AKR1 family and lipases, primarily in cells with TM6SF2 knockdown. Taken together, our data show that overexpression of TM6SF2 gene or its loss-of-function changes hepatic lipid species composition and expression of lipid metabolizing genes. Additionally, our data further confirms a loss-of-function effect for the E167K variant.

Watch a video presentation of this article Watch the interview with the author In April 2018, the American Gastroenterology Association (AGA) published a clinical practice update on management of dyslipidemia in individuals with liver disease.1 Dyslipidemia is common in the general population and increases the risk for cardiovascular disease. Treatment of dyslipidemia is effective in decreasing morbidity from cardiovascular disease. Because the liver is the primary source of cholesterol and other lipids in the body, medications for dyslipidemia, such as statins, target genes in the liver. Furthermore, the liver plays a role in the metabolism of many drugs, including those that are used to treat dyslipidemia. It is not surprising, therefore, that many practitioners are hesitant to prescribe medicines to treat dyslipidemia in the setting of liver disease. This update is aimed at summarizing current understanding of the safety of treating with lipid-lowering drugs patients who have various liver diseases and dyslipidemia (Table 1). Please listen to Dr. Elizabeth K. Speliotes discuss the important updates and impact on patient management from this publication.

Nonalcoholic fatty liver disease (NAFLD) affects 20‐30% of US adults, yet its underlying cause is unknown. Excess intake of sugar‐sweetened beverages (SSB), the largest source of added sugar intake in the American diet, is a potential risk factor for NAFLD. We examined the cross‐sectional association between SSB intake and fatty liver in members of the Framingham Offspring cohort (n=1,061; 57% women; mean age 59 y). Liver fat was measured using CT scan, and fatty liver was defined as a liver to phantom ratio &lt;0.33. Cumulative intakes of SSB and diet soda were estimated from FFQ collected at 3 exam cycles over 7 years. Participants were defined as SSB non‐consumers or consumers (3 categories: 1 drink/mo to &lt;1 drink/wk, 1 drink/wk to &lt; 1 drink/d, and 蠅1 drink/d). Participants were also categorized into 4 groups according to diet soda intake as described above. Covariates examined included age, sex, BMI, smoking status, energy intake, alcohol intake, dietary fiber, total fat, and fruit and vegetable intake. After multivariate adjustment, 14.3% (95%CI: 9.1, 19.5%) of non‐SSB consumers and 26.9% (95%CI: 19.5, 34.2%) of daily SSB consumers had fatty liver, P for trend =0.02. No significant association was observed between diet soda intake and fatty liver. In this study sample, daily SSB consumers had nearly 2 fold higher prevalence of fatty liver compared to non‐SSB consumers. Grant Funding Source : Supoorted by the NIH/NHLIBI's Framingham Heart Study, Boston University School of Medicine, and USDA

Summary The R644C variant of lamin A is controversial, as it has been linked to multiple phenotypes in familial studies, but has also been identified in apparently healthy volunteers. Here we present data from a large midwestern US cohort showing that this variant associates genetically with hepatic steatosis, and with related traits in additional publicly available datasets, while in vitro testing demonstrated that this variant increased cellular lipid droplet accumulation. Taken together, these data support this LMNA variant’s potential pathogenicity in lipodystrophy and metabolic liver disease.

ABSTRACT Background &amp; Aims A common genetic variant near MBOAT7 (rs641738C&gt;T) has been previously associated with hepatic fat and advanced histology in non-alcoholic fatty liver disease (NAFLD), however, these findings have not been consistently replicated in the literature. We aimed to establish whether rs641738C&gt;T is a risk factor across the spectrum of NAFLD and characterize its role in the regulation of related metabolic phenotypes through meta-analysis. Methods We performed meta-analysis of studies with data on the association between rs641738C&gt;T genotype and: liver fat, NAFLD histology, and serum ALT, lipids, or insulin. These included directly genotyped studies and population-level data from genome-wide association studies (GWAS). We performed random effects meta-analysis using recessive, additive, and dominant genetic models. Results Data from 1,047,265 participants (8,303 with liver biopsies) across 42 studies was included in the meta-analysis. rs641738C&gt;T was associated with higher liver fat on CT/MRI (+0.03 standard deviations [95% CI: 0.02 - 0.05]) and diagnosis of NAFLD (OR 1.22 [95% CI 1.08 - 1.39]) in Caucasian adults. The variant was also positively associated with presence of severe steatosis, NASH, and advanced fibrosis (OR: 1.32 [95% CI: 1.06 - 1.63]) in Caucasian adults using a recessive model of inheritance (CC+CT vs. TT). Meta-analysis of data from previous GWAS found the variant to be associated with higher ALT (P z =0.002) and lower serum triglycerides (P z =1.5×10 −4 ). rs641738C&gt;T was not associated with fasting insulin and no effect was observed in children with NAFLD. Conclusion Our study validates rs641738C&gt;T near MBOAT7 as a risk factor for the presence and severity of NAFLD in individuals of European descent.

Background and Aim: Free fatty acid-induced hepatocyte cytotoxicity is deeply associated with morbidity of Non-alcoholic fatty liver disease (NAFLD) (Malhi et al, 2008, Gastroenterology).Saturated free fatty acids induce hepatocyte lipoapoptosis via endoplasmic reticulum stress (ER) response, which leads to translational activation of DR5 and BH3 only protein Bim (Cazanave et al, JBC, 2011).We previously reported that X-box binding protein-1 (XBP-1) is activated downstream of IRE-1 arm of ER stress by free fatty acid treatment upon its splicing (Akazawa et al, 2009, J Hepatol).However, role of XBP-1 during hepatocyte lipoapoptosis remains relatively unexplored.We examined the impact of inhibiting XBP-1 on hepatocyte lipoapoptosis and steatosis employing Toyocamycin, which was recently reported to inhibit ER stress-mediated XBP-1 splicing (Ri M et al, Blood Cancer J. 2012).Methods: We employed hepatocellular carcinoma cell line, Huh-7 cells, for these studies.Cells were incubated with palmitate (200~800μM) in presence or absence of Toyocamycin (0.1~3μM).Apoptosis was assessed by DAPI staining and caspase 3/7 activity assay.Steatosis was assessed by Nile red staining.mRNA expression of Bim and DR5 was examined by real time PCR.Expression of Bim protein and phosphorylation of JNK was assessed by immunoblotting.Results: As expected, Toyocamycin inhibited palmitate-mediated XBP-1 splicing without affecting amount of total RNA.Toyocamycin significantly reduced palmitateinduced hepatocyte lipoapoptosis (p<0.05) and caspase 3/7 activity (p<0.05) in dose dependent manner.Interestingly, Toyocamycin also attenuated free fatty acid-induced steatosis.In addition, Toyocamycin attenuated expression of Bim protein and mRNA (p<0.05) following palmitate treatment.Furthermore, PA mediated-transcriptional activation of DR5 was reduced by Toyocamycin (p<0.05).In contrast, palmitate-induced JNK phosphorylation, which also occurs downstream of IRE-1 arm of ER stress, was not inhibited by Toyocamycin.Conclusions: These data imply that Toyocamycin attenuates hepatocyte lipotoxicity as well as steatosis, likely through inhibition of XBP-1 splicing.Toyocamycin might be beneficial for NASH treatment.

Obesity is a rising global concern as it substantially contributes to cardiovascular disease (CVD) and CVD risk factors (e.g. insulin resistance, dyslipidemia, Type 2 Diabetes). BMI (body mass index) is an easily obtained measure of obesity, which is highly heritable, and often used as a proxy when searching for genetic risk factors. Previous analyses of genome-wide association studies (GWAS) in the GIANT (Genetic Investigation of ANthropometric Traits) Consortium identified 32 loci containing common variants associated with BMI in adults of European ancestry. To enhance discovery of common causal variants for BMI, GIANT has expanded to include 82 studies with GWAS data and 43 studies with Metabochip data in more ancestrally diverse populations including up to 339,224 individuals. We performed a meta-analysis of the study-specific summary statistics for the BMI associations, assuming an additive model and using a fixed-effects inverse variance method. SNPs in 97 loci reached genome-wide significance (P MC4R, POMC, GRID1, NAV1 ). Our analyses also highlight loci with genes in pathways that were previously less apparent, such as those related to glucose and insulin homeostasis ( TCF7L2 , GIPR ), lipid metabolism ( APOE -cluster, NPC1 , NR1H3 ), the immune system ( TLR4) , and others. Additionally, many of the newly associated variants are in high LD with previously identified SNPs associated with related phenotypes, including other CVD risk factors (e.g. SNPs nearby IRS1 associated with T2D, adiposity, HDL, TG, adiponectin levels, and CHD; and SNPs near NT5C2 associated with CHD and blood pressure variables). This large-scale meta-analysis has greatly increased the number of identified obesity-susceptibility loci and continues to contribute to our understanding of the complex biology of adiposity. Our results have highlighted overlapping GWAS signals and important pathways which connect BMI and other CVD risk factors supporting the importance of pleiotropic effects in the pathogenesis of common complex diseases.

Sequencing of the human genome has opened up many opportunities to learn about our own genetic susceptibilities to disease. In this Foreword to this issue of Seminars in Liver Disease, I provide some required background to understanding genome-wide association analyses in general, including a list of terms ([Table 1]) often used in such studies. Five areas of particular significance are then reviewed in detail in the articles that follow.