Evidence for sex-specific associations between variation in acid phosphatase locus 1 (ACP1) and insulin sensitivity in Mexican-Americans

A genome-wide association study identifies novel candidate genes for susceptibility to diabetes mellitus in non-obese cats

Diabetes mellitus (DM) is a common feline endocrinopathy, which is similar to human type 2 diabetes (T2DM) in terms of its pathophysiology. T2DM occurs due to peripheral insulin resistance and/or β-cell dysfunction. Several studies have identified genetic and environmental factors that contribute to susceptibility to human T2DM. In cats, environmental factors such as obesity and physical inactivity have been linked with DM, although to date, the only genetic association that has been demonstrated is with a polymorphism in the feline MC4R gene. The aim of this study was to perform a genome-wide association study (GWAS) to identify polymorphisms associated with feline DM. Illumina Infinium 63k iSelect DNA arrays were used to analyse genomic DNA samples from 200 diabetic domestic shorthair cats and 399 non-diabetic control cats. Data was analysed using PLINK whole genome data analysis toolset. A linear model analysis, EMMAX, was done to test for population structure and HAPLOVIEW was used to identify haplotype blocks surrounding the significant SNPs to assist with candidate gene nomination. A total of 47,497 SNPs were available for analysis. Four SNPs were identified with genome-wide significance: chrA2.4150731 (praw = 9.94 x10-8); chrUn17.115508 (praw = 6.51 x10-8); chrUn17.394136 (praw = 2.53 x10-8); chrUn17.314128 (praw = 2.53 x10-8) as being associated with DM. The first SNP is located within chromosome A2, less than 4kb upstream of the dipeptidyl-peptidase-9 (DPP9) gene, a peptidase involved in incretin inactivation. The remaining three SNPs are located within a haplotype block towards the end of chromosome A3; within this region, genes of interest include TMEM18 and ACP1, both previously associated with T2DM. This study indicates a polygenic component to susceptibility to DM in cats and has highlighted several loci and candidate genes worthy of further investigation.

Protein tyrosine phosphatases in cardiac physiology and pathophysiology

More than any other organ, the heart is particularly sensitive to gene expression deregulation, often leading in the long run to impaired contractile performances and excessive fibrosis deposition progressing to heart failure. Recent investigations provide evidences that the protein phosphatases (PPs), as their counterpart protein kinases, are important regulators of cardiac physiology and development. Two main groups, the protein serine/threonine phosphatases and the protein tyrosine phosphatases (PTPs), constitute the PPs family. Here, we provide an overview of the role of PTP subfamily in the development of the heart and in cardiac pathophysiology. Based on recent in silico studies, we highlight the importance of PTPs as therapeutic targets for the development of new drugs to restore PTPs signaling in the early and late events of heart failure.

A diet high in sugar-sweetened beverage and low in fruits and vegetables is associated with adiposity and a pro-inflammatory adipokine profile

Diet, obesity and adipokines play important roles in diabetes and CVD; yet, limited studies have assessed the relationship between diet and multiple adipokines. This cross-sectional study assessed associations between diet, adiposity and adipokines in Mexican Americans. The cohort included 1128 participants (age 34·7±8·2 years, BMI 29·5±5·9 kg/m2, 73·2 % female). Dietary intake was assessed by 12-month food frequency questionnaire. Adiposity was measured by BMI, total percentage body fat and percentage trunk fat using dual-energy X-ray absorptiometry. Adiponectin, apelin, C-reactive protein (CRP), dipeptidyl peptidase-4 (DPP-IV), IL-1β, IL-1ra, IL-6, IL-18, leptin, lipocalin, monocyte chemo-attractant protein-1 (MCP-1), resistin, secreted frizzled protein 4 (SFRP-4), SFRP-5, TNF-α and visfatin were assayed with multiplex kits or ELISA. Joint multivariate associations between diet, adiposity and adipokines were analysed using canonical correlations adjusted for age, sex, energy intake and kinship. The median (interquartile range) energy intake was 9514 (7314, 11912) kJ/d. Overall, 55 % of total intake was accounted for by carbohydrates (24 % from sugar). A total of 66 % of the shared variation between diet and adiposity, and 34 % of diet and adipokines were explained by the top canonical correlation. The diet component was most represented by sugar-sweetened beverages (SSB), fruit and vegetables. Participants consuming a diet high in SSB and low in fruits and vegetables had higher adiposity, CRP, leptin, and MCP-1, but lower SFRP-5 than participants with high fruit and vegetable and low SSB intake. In Mexican Americans, diets high in SSB but low in fruits and vegetables contribute to adiposity and a pro-inflammatory adipokine profile.

Exome Sequencing Identifies Genetic Variants Associated with Circulating Lipid Levels in Mexican Americans: The Insulin Resistance Atherosclerosis Family Study (IRASFS)

Genome-wide association studies have identified numerous variants associated with lipid levels; yet, the majority are located in non-coding regions with unclear mechanisms. In the Insulin Resistance Atherosclerosis Family Study (IRASFS), heritability estimates suggest a strong genetic basis: low-density lipoprotein (LDL, h² = 0.50), high-density lipoprotein (HDL, h² = 0.57), total cholesterol (TC, h² = 0.53), and triglyceride (TG, h² = 0.42) levels. Exome sequencing of 1,205 Mexican Americans (90 pedigrees) from the IRASFS identified 548,889 variants and association and linkage analyses with lipid levels were performed. One genome-wide significant signal was detected in APOA5 with TG (rs651821, P_TG = 3.67 × 10^-10, LOD_TG = 2.36, MAF = 14.2%). In addition, two correlated SNPs (r² = 1.0) rs189547099 (P_TG = 6.31 × 10^-08, LOD_TG = 3.13, MAF = 0.50%) and chr4:157997598 (P_TG = 6.31 × 10^-08, LOD_TG = 3.13, MAF = 0.50%) reached exome-wide significance (P < 9.11 × 10^-08). rs189547099 is an intronic SNP in FNIP2 and SNP chr4:157997598 is intronic in GLRB. Linkage analysis revealed 46 SNPs with a LOD > 3 with the strongest signal at rs1141070 (LOD_LDL = 4.30, P_LDL = 0.33, MAF = 21.6%) in DFFB. A total of 53 nominally associated variants (P < 5.00 × 10^-05, MAF ≥ 1.0%) were selected for replication in six Mexican-American cohorts (N = 3,280). The strongest signal observed was a synonymous variant (rs1160983, P_LDL = 4.44 × 10^-17, MAF = 2.7%) in TOMM40. Beyond primary findings, previously reported lipid loci were fine-mapped using exome sequencing in IRASFS. These results support that exome sequencing complements and extends insights into the genetics of lipid levels.

Physiologic Interpretation of GWAS Signals for Type 2 Diabetes

This chapter reviews both statistical and physiologic issues related to the pathophysiologic effects of genetic variation in the context of type 2 diabetes. The goal is to review current methodologies used to analyze disease-related quantitative traits for those who do not have extensive quantitative and physiologic background, as an attempt to bridge that gap. We leverage mathematical modeling to illustrate the strengths and weaknesses of different approaches and attempt to reinforce with real data analysis. Topics reviewed include phenotype selection, phenotype specificity, multiple variant analysis via the genetic risk score, and consideration of multiple disease-related phenotypes. Type 2 diabetes is used as the example, not only because of the extensive existing knowledge at the genetic, physiologic, clinical, and epidemiologic levels, but also because type 2 diabetes has been at the forefront of complex disease genetics, with many examples to draw from.

A Comprehensive Analysis of Common and Rare Variants to Identify Adiposity Loci in Hispanic Americans: The IRAS Family Study (IRASFS)

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 (n_max = 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%, P_DOM = 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%, P_DOM = 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 (n_max = 4156) and the strongest signal was rs1471880 (P_DOM = 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.

Association between phosphatase related gene variants and coronary artery disease: case-control study and meta-analysis

Recent studies showed that the serum alkaline phosphatase is an independent predictor of the coronary artery disease (CAD). In this work, we aimed to summarize the association between three phosphatase related single nucleotide polymorphisms (rs12526453, rs11066301 and rs3828329) and the risk of CAD in Han Chinese. Our results showed that the rs3828329 of the ACP1 gene was closely related to the risk of CAD in Han Chinese (OR = 1.45, p = 0.0006). This significant association of rs3828329 with CAD was only found in the females (Additive model: OR = 1.80, p = 0.001; dominant model: OR = 1.69, p = 0.03; recessive model: OR = 1.96, p = 0.0008). Moreover, rs3828329 was likely to exert its effect in females aged 65 years and older (OR = 2.27, p = 0.001). Further meta-analyses showed that the rs12526453 of PHACTR11 gene (OR = 1.14, p < 0.0001, random-effect method) and the rs11066301 of PTPN11 gene (OR = 1.15, p < 0.0001, fixed-effects method) were associated with CAD risk in multiple populations. Our results showed that the polymorphisms rs12526453 and rs11066301 are significantly associated with the CAD risk in multiple populations. The rs3828329 of ACP1 gene is also a risk factor of CAD in Han Chinese females aged 65 years and older.

Longitudinal changes in insulin sensitivity and beta cell function between women with and without a history of gestational diabetes mellitus

AIMS/HYPOTHESIS

The aim of the study was to compare longitudinal changes in insulin sensitivity (SI) and beta cell function between women with and without a history of gestational diabetes mellitus (GDM).

METHODS

The prospective follow-up cohort included 235 parous non-diabetic Mexican-American women, 93 with and 142 without a history of GDM. The participants underwent dual-energy x-ray absorptiometry, OGTTs and IVGTTs at baseline and at a median of 4.1 years follow-up. The baseline values and rates of change of metabolic measures were compared between groups.

RESULTS

At baseline, women with prior GDM (mean age 36.3 years) had similar values of SI but higher percentages of body fat and trunk fat (p ≤ 0.02), a lower acute insulin response and poorer beta cell compensation (disposition index [DI]) (p < 0.0001) than women without GDM (mean age 37.9 years). During the follow-up, women with GDM had a faster decline in SI (p = 0.02) and DI (p = 0.02) than their counterparts without GDM, with no significant differences in changes of weight or fat (p > 0.50). Adjustment for baseline age, adiposity, calorie intake, physical activity, age at first pregnancy, additional pregnancies and changes in adiposity during follow-up increased the between-group differences in the rates of change of SI and DI (p ≤ 0.003).

CONCLUSIONS/INTERPRETATION

Mexican-American women with recent GDM had a faster deterioration in insulin sensitivity and beta cell compensation than their parous counterparts without GDM. The differences were not explained by differences in adiposity, suggesting more deleterious effects of existing fat and/or reduced beta cell robustness in women with GDM.

High-fat diet is associated with obesity-mediated insulin resistance and β-cell dysfunction in Mexican Americans

Consumption of energy-dense, nutrient-poor foods has contributed to the rising incidence of obesity and may underlie insulin resistance and β-cell dysfunction. Macronutrient intake patterns were examined in relation to anthropometric and metabolic traits in participants of BetaGene, a family-based study of obesity, insulin resistance, and β-cell dysfunction in Mexican Americans. Dietary intake, body composition, insulin sensitivity (SI), and β-cell function [Disposition Index (DI)] were assessed by food-frequency questionnaires, dual-energy X-ray absorptiometry, and intravenous glucose-tolerance tests, respectively. Patterns of macronutrient intake were identified by using a K-means model based on the proportion of total energy intake per day attributable to carbohydrate, fat, and protein and were tested for association with anthropometric and metabolic traits. Among 1150 subjects aged 18-65 y (73% female), tertiles of fat intake were associated with greater adiposity and lower SI, after adjustment for age, sex, and daily energy intake. Moreover, 3 distinct dietary patterns were identified: "high fat" (35% fat, 44% carbohydrate, 21% protein; n = 238), "moderate fat" (28% fat, 54% carbohydrate, 18% protein; n = 520), and "low fat" (20% fat, 65% carbohydrate, 15% protein; n = 392). Compared with the low-fat group, the high-fat group had higher age- and sex-adjusted mean body mass index, body fat percentage, and trunk fat and lower SI and DI. Further adjustment for daily energy intake by matching individuals across dietary pattern groups yielded similar results. None of the observed associations were altered after adjustment for physical activity; however, associations with SI and DI were attenuated after adjustment for adiposity. These findings suggest that high-fat diets may contribute to increased adiposity and concomitant insulin resistance and β-cell dysfunction in Mexican Americans.

Lack of association of ACP1 gene with inflammatory bowel disease: a case-control study

The red cell acid phosphatease (ACP1) gene, which encodes a low molecular weight phosphotyrosine phosphatase (LMW-PTP), has been suggested as a common genetic factor of autoimmunity. In the present study, we aimed to investigate the possible influence of ACP1 polymorphisms in the susceptibility of inflammatory bowel disease (IBD). A total of 1271 IBD Spanish patients [720 Crohn's disease (CD) and 551 ulcerative colitis (UC)] and 1877 healthy subjects were included. Four single-nucleotide polymorphisms (SNPs), rs10167992, rs11553742, rs7576247 and rs3828329, were genotyped using TaqMan SNP genotyping assays. Common ACP1 alleles (i.e. ACP1*A, ACP1*B and ACP1*C) were determined by two of these SNPs. After the analysis, no evidence of association of the ACP1 genetic variants was found with CD or UC. Therefore, our results suggest that the ACP1 gene may not play a relevant role in the development of IBD.