Genome-Wide Studies of Type 2 Diabetes and Lipid Traits in Hispanics

Large-scale multi-omics analyses in Hispanic/Latino populations identify genes for cardiometabolic traits

Here, we present a multi-omics study of type 2 diabetes and quantitative blood lipid and lipoprotein traits conducted to date in Hispanic/Latino populations (nmax = 63,184). We conduct a meta-analysis of 16 type 2 diabetes and 19 lipid trait GWAS, identifying 20 genome-wide significant loci for type 2 diabetes, including one novel locus and novel signals at two known loci, based on fine-mapping. We also identify sixty-one genome-wide significant loci across the lipid/lipoprotein traits, including nine novel loci, and novel signals at 19 known loci through fine-mapping. Next, we analyze genetically regulated expression, perform Mendelian randomization, and analyze association with transcriptomic and proteomic measure using multi-omics data from a Hispanic/Latino population. Using this approach, we identify genes linked to type 2 diabetes and lipid/lipoprotein traits, including TMEM205 and NEDD9 for HDL cholesterol, TREH for triglycerides, and ANXA4 for type 2 diabetes.

Beyond borders: A commentary on the benefit of promoting immigrant populations in genome-wide association studies

Immigrants are an important part of many high-income nations, in that they contribute to the sociocultural tapestry, economic well-being, and demographic diversity of their receiving countries and communities. Yet, genomic studies to date have generally focused on non-immigrant, European-ancestry populations. Although this approach has proven fruitful in discovering and validating genomic loci, within the context of racially/ethnically diverse countries like the United States-wherein half of immigrants hail from Latin America and another quarter from Asia-this approach is insufficient. There is a persistent diversity gap in genomic research in terms of both current samples and genome-wide association studies, meaning that the field's understanding of genetic architecture and gene-environmental interactions is being hampered. In this commentary, I provide motivating examples of recent research developments related to the following: (1) how the increased ancestral diversity, such as seen among Latin American immigrants, improves power to discover and document genomic loci, (2) informs how environmental factors, such as immigration-related exposures, interact with genotypes to influence phenotypes, and (3) how inclusion can be promoted through community-engaged research programs and policies. I conclude that greater inclusion of immigrants in genomic research can move the field forward toward novel discoveries and interventions to address racial/ethnic health disparities.

Alteration of oral microbiome composition in children living with pesticide-exposed farm workers

Our prior work shows that azinphos-methyl pesticide exposure is associated with altered oral microbiomes in exposed farmworkers. Here we extend this analysis to show the same association pattern is also evident in their children. Oral buccal swab samples were analyzed at two time points, the apple thinning season in spring-summer 2005 for 78 children and 101 adults and the non-spray season in winter 2006 for 62 children and 82 adults. The pesticide exposure for the children were defined by the farmworker occupation of the cohabitating household adult and the blood azinphos-methyl detection of the cohabitating adult. Oral buccal swab 16S rRNA sequencing determined taxonomic microbiota proportional composition from concurrent samples from both adults and children. Analysis of the identified bacteria showed significant proportional changes for 12 of 23 common oral microbiome genera in association with azinphos-methyl detection and farmworker occupation. The most common significantly altered genera had reductions in the abundance of Streptococcus, suggesting an anti-microbial effect of the pesticide. Principal component analysis of the microbiome identified two primary clusters, with association of principal component 1 to azinphos-methyl blood detection and farmworker occupational status of the household. The children's buccal microbiota composition clustered with their household adult in ∼95% of the households. Household adult farmworker occupation and household pesticide exposure is associated with significant alterations in their children's oral microbiome composition. This suggests that parental occupational exposure and pesticide take-home exposure pathways elicit alteration of their children's microbiomes.

Understanding the growing epidemic of type 2 diabetes in the Hispanic population living in the United States

The prevalence and incidence of type 2 diabetes (T2D) among the Hispanic population in the United States are higher than the national average. This is partly due to sociocultural factors, such as lower income and decreased access to education and health care, as well as a genetic susceptibility to obesity and higher insulin resistance. This review focuses on understanding the Hispanic population living in the United States from a multidisciplinary approach and underlines the importance of cultural, social, and biological factors in determining the increased risk of T2D in this population. An overview of the acute and chronic complications of T2D upon this population is included, which is of paramount importance to understand the toll that diabetes has upon this population, the health system, and society as a whole. Specific interventions directed to the Hispanic populations are needed to prevent and alleviate some of the burdens of T2D. Different prevention strategies based on medications, lifestyle modifications, and educational programmes are discussed herein. Diabetes self-management education (DSME) is a critical element of care of all people with diabetes and is considered necessary to improve patient outcomes. To be more effective, programmes should take into consideration cultural factors that influence the development and progression of diabetes. These interventions aim to enhance long-term effects by reducing the incidence, morbidity, and mortality of T2D in the Hispanic population of the United States.

From Sea to Shining Sea and the Great Plains to Patagonia: A Review on Current Knowledge of Diabetes Mellitus in Hispanics/Latinos in the US and Latin America

The past two decades have witnessed many advances in the prevention, treatment, and control of diabetes mellitus (DM) and its complications. Increased screening has led to a greater recognition of type 2 diabetes mellitus (type 2 DM) and prediabetes; however, Hispanics/Latinos, the largest minority group in the US, have not fully benefited from these advances. The Hispanic/Latino population is highly diverse in ancestries, birth places, cultures, languages, and socioeconomic backgrounds, and it populates most of the Western Hemisphere. In the US, the prevalence of DM varies among Hispanic/Latino heritage groups, being higher among Mexicans, Puerto Ricans, and Dominicans, and lower among South Americans. The risk and prevalence of diabetes among Hispanics/Latinos are significantly higher than in non-Hispanic Whites, and nearly 40% of Hispanics/Latinos with diabetes have not been formally diagnosed. Despite these striking facts, the representation of Hispanics/Latinos in pharmacological and non-pharmacological clinical trials has been suboptimal, while the prevalence of diabetes in these populations continues to rise. This review will focus on the epidemiology, etiology and prevention of type 2 DM in populations of Latin American origin. We will set the stage by defining the terms Hispanic, Latino, and Latin American, explaining the challenges identifying Hispanics/Latinos in the scientific literature and databases, describing the epidemiology of diabetes-including type 2 DM and gestational diabetes mellitus (GDM)-and cardiovascular risk factors in Hispanics/Latinos in the US and Latin America, and discussing trends, and commonalities and differences across studies and populations, including methodology to ascertain diabetes. We will discuss studies on mechanisms of disease, and research on prevention of type 2 DM in Hispanics/Latinos, including women with GDM, youth and adults; and finalize with a discussion on lessons learned and opportunities to enhance research, and, consequently, clinical care oriented toward preventing type 2 DM in Hispanics/Latinos in the US and Latin America.

Association of genetic variants in RETN, NAMPT and ADIPOQ gene with glycemic, metabolic traits and diabetes risk in a Chinese population

Abnormal serum levels of adipokine have been established to be a strong predictor of developing several human diseases including type 2 diabetes mellitus (T2DM). Association studies have reported several genetic variants in genes coding adipokines with contributions to T2DM susceptibility as well as some glycemic and metabolic traits, of which the single nucleotide polymorphisms (SNPs) of RETN, NAMPT, and ADIPOQ gene were well documented. However, little is known about contributions of these SNPs to above phenotypes in Chinese. In the current study, with availably quantitative glycemic and metabolic data from a total of 185 T2DM patients and 191 healthy controls, we tested associations between four SNPs of RETN, NAMPT, ADIPOQ gene and 13 glycemic and metabolic traits. The results showed that the rs1862513 and rs34861192 of RETN gene were functional and negatively correlated with the levels of serum creatinine and cholesterol, respectively. The rs16861194 of ADIPOQ gene was positively correlated with the aspartate aminotransferase (AST) and AST/alanine aminotransferase level. Moreover, the rs34861192 and rs13237989 of NAMPT gene synergistically affected the levels of insulin and glycemic index. However, due to the limited sample size, only the rs16861194 exerted a significant increased risk on T2DM. These results underscore the contributions of SNPs in RETN, NAMPT, ADIPOQ gene to glycemic and metabolic traits as well as T2DM susceptibility in Chinese.

Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure

In a longitudinal agricultural community cohort sampling of 65 adult farmworkers and 52 adult nonfarmworkers, we investigated agricultural pesticide exposure-associated changes in the oral buccal microbiota. We found a seasonally persistent association between the detected blood concentration of the insecticide azinphos-methyl and the taxonomic composition of the buccal swab oral microbiome. Blood and buccal samples were collected concurrently from individual subjects in two seasons, spring/summer 2005 and winter 2006. Mass spectrometry quantified blood concentrations of the organophosphate insecticide azinphos-methyl. Buccal oral microbiome samples were 16S rRNA gene DNA sequenced, assigned to the bacterial taxonomy, and analyzed after "centered-log-ratio" transformation to handle the compositional nature of the proportional abundances of bacteria per sample. Nonparametric analysis of the transformed microbiome data for individuals with and without azinphos-methyl blood detection showed significant perturbations in seven common bacterial taxa (>0.5% of sample mean read depth), including significant reductions in members of the common oral bacterial genus Streptococcus Diversity in centered-log-ratio composition between individuals' microbiomes was also investigated using principal-component analysis (PCA) to reveal two primary PCA clusters of microbiome types. The spring/summer "exposed" microbiome cluster with significantly less bacterial diversity was enriched for farmworkers and contained 27 of the 30 individuals who also had azinphos-methyl agricultural pesticide exposure detected in the blood.

IMPORTANCE

In this study, we show in human subjects that organophosphate pesticide exposure is associated with large-scale significant alterations of the oral buccal microbiota composition, with extinctions of whole taxa suggested in some individuals. The persistence of this association from the spring/summer to the winter also suggests that long-lasting effects on the commensal microbiota have occurred. The important health-related outcomes of these agricultural community individuals' pesticide-associated microbiome perturbations are not understood at this time. Future investigations should index medical and dental records for common and chronic diseases that may be interactively caused by this association between pesticide exposure and microbiome alteration.

Analysis of Whole Exome Sequencing with Cardiometabolic Traits Using Family-Based Linkage and Association in the IRAS Family Study

Family-based methods are a potentially powerful tool to identify trait-defining genetic variants in extended families, particularly when used to complement conventional association analysis. We utilized two-point linkage analysis and single variant association analysis to evaluate whole exome sequencing (WES) data from 1205 Hispanic Americans (78 families) from the Insulin Resistance Atherosclerosis Family Study. WES identified 211,612 variants above the minor allele frequency threshold of ≥0.005. These variants were tested for linkage and/or association with 50 cardiometabolic traits after quality control checks. Two-point linkage analysis yielded 10,580,600 logarithm of the odds (LOD) scores with 1148 LOD scores ≥3, 183 LOD scores ≥4, and 29 LOD scores ≥5. The maximal novel LOD score was 5.50 for rs2289043:T>C, in UNC5C with subcutaneous adipose tissue volume. Association analysis identified 13 variants attaining genome-wide significance (P < 5 × 10^-08 ), with the strongest association between rs651821:C>T in APOA5 and triglyceride levels (P  =  3.67 × 10^-10 ). Overall, there was a 5.2-fold increase in the number of informative variants detected by WES compared to exome chip analysis in this population, nearly 30% of which were novel variants relative to the Database of Single Nucleotide Polymorphisms (dbSNP) build 138. Thus, integration of results from two-point linkage and single-variant association analysis from WES data enabled identification of novel signals potentially contributing to cardiometabolic traits.

Association between -308G/A TNFA Polymorphism and Susceptibility to Type 2 Diabetes Mellitus: A Systematic Review

Diabetes mellitus (DM) is considered to be a worldwide epidemic disease and its type 2 form comprises more than 95% of all cases. Tumor necrosis factor-alpha (TNF-α) is a proinflammatory cytokine. Its dysregulation has been implicated in a variety of human diseases, including type 2 diabetes mellitus (T2DM). The control of expression of this cytokine is associated with insulin resistance and has a strong genetic influence. In order to understand this relationship, the literature from all case-control studies since 2000 to date was reviewed. The genotypes frequency results presented in ten publications with different ethnicities were compared. The correlation between the TNFA promoter genotypes and the risk of developing T2DM remains controversial due to the many discrepancies between the different studies available. Ethnic differences may play a role in these conflicting results, since the distribution of TNFA promoter polymorphisms is distinctive between individuals of dissimilar racial origin. Hence, although the relationship between T2DM incidence and presence of polymorphisms at position -308 of the TNFA gene is not entirely clear, the results of these studies suggest the need for further investigation.