Strong Parent-of-Origin Effects in the Association of KCNQ1 Variants With Type 2 Diabetes in American Indians

Parent-of-origin effects were observed in an Icelandic population for several genetic variants associated with type 2 diabetes, including those in KLF14 (rs4731702), MOB2 (rs2334499), and KCNQ1 (rs2237892, rs231362). We analyzed parent-of-origin effects for these variants, along with two others in KCNQ1 identified in previous genome-wide association studies (rs2237895, rs2299620), in 7,351 Pima Indians from 4,549 nuclear families; 34% of participants had diabetes. In a subset of 287 normoglycemic individuals, acute insulin secretion was measured by an intravenous glucose tolerance test. Statistically significant (P < 0.05) parent-of-origin effects were seen for association with type 2 diabetes for all variants. The strongest effect was seen at rs2299620 in KCNQ1; the C allele was associated with increased diabetes when maternally derived (odds ratio [OR], 1.92; P = 4.1 × 10⁻¹²), but not when paternally derived (OR, 0.93; P = 0.47; P = 9.9 × 10⁻⁶ for difference in maternal and paternal effects). A maternally derived C allele also was associated with a 28% decrease in insulin secretion (P = 0.002). This study confirms parent-of-origin effects in the association with type 2 diabetes for variants in KLF14, MOB2, and KCNQ1. In Pima Indians, the effect of maternally derived KCNQ1 variants appears to be mediated through decreased insulin secretion and is particularly strong, accounting for 4% of the variance in liability to diabetes.Several single nucleotide polymorphisms (SNPs) reproducibly associated with type 2 diabetes recently have been identified (1–4). Many of these are in regions of the genome that are imprinted, and studies of an Icelandic population suggest that there are parent-of-origin effects at four of these variants (5); in other words, the extent of association with the risk allele depends on whether it is inherited from the mother or from the father. The SNPs for which parent-of-origin effects have been observed include one in KLF14 (rs4731702), one near MOB2 (rs2334499), and two independent SNPs in KCNQ1 (rs231362 and rs2237892) (5). The presence of parent-of-origin effects at these SNPs is consistent with imprinting and may have important implications for the mechanisms by which variants in or near these genes confer susceptibility to type 2 diabetes. However, for some of the SNPs, the current statistical evidence for parent-of-origin effects is modest. Furthermore, to our knowledge, these effects have not been replicated in other ethnic groups, nor have parent-of-origin effects been analyzed for metabolic traits that underlie the risk of type 2 diabetes, perhaps because few large studies have family data. In the current study, we have analyzed parent-of-origin effects at these SNPs in Pima Indians, an American Indian population in which the prevalence of type 2 diabetes is extraordinarily high (6) and in which family and detailed metabolic data were obtained.     

Common genetic variation in the glucokinase gene (GCK) is associated with type 2 diabetes and rates of carbohydrate oxidation and energy expenditure

Aims/hypothesis

Glucokinase (GCK) plays a role in glucose metabolism and glucose-stimulated insulin secretion. Rare mutations in GCK cause MODY. We investigated whether common variation (minor allele frequency ≥0.01) in GCK is associated with metabolic traits and type 2 diabetes.

Methods

Four exonic single-nucleotide polymorphisms (SNPs) and three SNPs predicted to cause loss of promoter function were identified in whole-genome sequence data from 234 Pima Indians. These seven tag SNPs and rs4607517, a type 2 diabetes variant established in other studies, were analysed in 415 full-heritage non-diabetic Pima Indians characterised for metabolic traits, and 7,667 American Indians who had data on type 2 diabetes and BMI.

Results

A novel 3′ untranslated region (3′UTR) SNP, chr7:44184184-G/A, was associated with the rate of carbohydrate oxidation post-absorptively (β?=?0.22 mg [kg estimated metabolic body size (EMBS)]^?1?min^?1, p?=?0.005) and during a hyperinsulinaemic–euglycaemic clamp (β?=?0.24 mg [kg EMBS]^?1?min^?1, p?=?0.0002), the rate of carbohydrate oxidation in a respiratory chamber (β?=?311 kJ/day, p?=?0.03) and 24 h energy expenditure, which was attributable to the thermic effect of food (β?=?520 kJ/day, p?=?3.39?×?10^?6). This 3′UTR SNP was also associated with diabetes (OR 1.36, 95% CI 1.11, 1.65, p?=?0.002), where the A allele (allele frequency 0.05) was associated with a lower rate of carbohydrate oxidation, lower 24 h energy expenditure and higher risk for diabetes. In a Cox proportional hazards model, a rate of insulin-stimulated carbohydrate oxidation lower than the mean rate at baseline predicted a higher risk for developing diabetes than for those above the mean (hazard rate ratio 2.2, 95% CI 1.3, 3.6, p?=?0.002).

Conclusions/interpretation

Common variation in GCK influences the rate of carbohydrate oxidation, 24 h energy expenditure and diabetes risk in Pima Indians.     

Variations in peptide YY and Y2 receptor genes are associated with severe obesity in Pima Indian men

Peptide YY (PYY) and Y2 receptor (Y2R) may be important in the central regulation of body weight and food intake. To determine whether genetic variation in PYY and/or Y2R may contribute to morbid obesity in humans, these genes were sequenced in 83 extremely obese Pima Indians (BMI > or = 50 kg/m2). Sequencing of PYY identified three single nucleotide polymorphisms (SNPs) in the untranslated region. Sequencing of the Y2R coding region identified one missense (Ala172Thr) substitution and two silent substitutions. Eight additional SNPs in the 5' untranslated region of Y2R were identified from public databases. These SNPs were genotyped in 489 full-heritage adult Pimas (362 severely obese and 127 nondiabetic, nonobese subjects), who are not first-degree relatives, for association analysis. The PYY variants were not associated with obesity, whereas four variants from two haplotype blocks in Y2R were marginally associated (P = 0.054-0.067) with obesity. However, if the analysis was restricted to men (n = 167, 100 obese and 67 lean), the PYY variants and two SNPs in Y2R that were in complete linkage disequilibrium were significantly associated with severe obesity (P = 0.001 and P = 0.002, respectively). Our data suggest that the PYY-Y2R pathway may influence body weight through a sex-specific mechanism, but this finding requires confirmation in other populations.     

SIRT1 is associated with a decrease in acute insulin secretion and a sex specific increase in risk for type 2 diabetes in Pima Indians

Genetic variation in SIRT1 affects obesity-related phenotypes in several populations. The purpose of this study was to determine whether variation in SIRT1 affects susceptibility to obesity or type 2 diabetes in Pima Indians, a population with very high prevalence and incidence rates of these diseases. Genotypic data from single nucleotide polymorphisms (SNPs) identified by sequencing regions of SIRT1 combined with SNPs in/near SIRT1 from a prior genome-wide association study determined that 4 tag SNPs (rs7895833, rs10509291, rs7896005, and rs4746720) could capture information across this gene and its adjacent 5′ region. The tag SNPs were genotyped in a population-based sample of 3501 Pima Indians (44% had diabetes, 58% female) for association with type 2 diabetes and BMI. Metabolic trait data and adipose biopsies were available on a subset of these subjects. Two tag SNPs, rs10509291 and rs7896005, were nominally associated with type 2 diabetes (P = 0.01, OR = 1.25 95%CI 1.05–1.48, and P = 0.02, OR = 1.17 95%CI 1.02–1.34, respectively; additive P values adjusted for age, sex, birth year, and family membership), but not BMI (adjusted P values 0.52 and 0.45, respectively). Among metabolically characterized subjects with normal glucose tolerance (N = 243), those carrying the diabetes risk allele (T) for rs10509291 and (G) for rs7896005 had a reduced acute insulin response (AIR) to an intravenous glucose bolus (adjusted P = 0.045 and 0.035, respectively). SIRT1 expression in adipose biopsies was negatively correlated with BMI (adjusted P = 0.00001). We conclude that variation in SIRT1 is nominally associated with reduced AIR and increased risk for type 2 diabetes. SIRT1 expression in adipose is correlated with BMI, but it remains unknown whether this is a cause or consequence of obesity.     

ABCC8 R1420H Loss-of-Function Variant in a Southwest American Indian Community: Association With Increased Birth Weight and Doubled Risk of Type 2 Diabetes

Missense variants in KCNJ11 and ABCC8, which encode the KIR6.2 and SUR1 subunits of the β-cell K_ATP channel, have previously been implicated in type 2 diabetes, neonatal diabetes, and hyperinsulinemic hypoglycemia of infancy (HHI). To determine whether variation in these genes affects risk for type 2 diabetes or increased birth weight as a consequence of fetal hyperinsulinemia in Pima Indians, missense and common noncoding variants were analyzed in individuals living in the Gila River Indian Community. A R1420H variant in SUR1 (ABCC8) was identified in 3.3% of the population (N = 7,710). R1420H carriers had higher mean birth weights and a twofold increased risk for type 2 diabetes with a 7-year earlier onset age despite being leaner than noncarriers. One individual homozygous for R1420H was identified; retrospective review of his medical records was consistent with HHI and a diagnosis of diabetes at age 3.5 years. In vitro studies showed that the R1420H substitution decreases K_ATP channel activity. Identification of this loss-of-function variant in ABCC8 with a carrier frequency of 3.3% affects clinical care as homozygous inheritance and potential HHI will occur in 1/3,600 births in this American Indian population.     

Prevalence of rib anomalies in normal Caucasian children and childhood cancer patients

Purpose. – To evaluate the prevalence of abnormalities of rib development in normal Caucasian children and patients with childhood cancer.Materials And Methods. – Chest radiographs of 881 Caucasian pediatric controls and 906 childhood cancer patients were reviewed, and independently scored by four blinded observers, using strict definitions. Prevalences of 6 major rib anomaly categories in controls were compared to their prevalence in the total group of childhood cancer patients, and the 12 individual larger tumor groups using Chi-square tests.Results. – Values in the control population were generated for the occurrence of six major rib anomaly categories; cervical rib anomalies were present in 6.1% of controls, aplasia of 12^th ribs in 6.6%, lumbar ribs in 0.9%, bifurcations in 0.7%, synostosis-bridging in 0.3%, and segmentations were not found. The overall prevalence of total rib anomalies in cases and controls was equal (14.9% and 14.2%, respectively). Cervical rib anomalies were found significantly more often in cases (8.6%) compared to controls (p-value=0.047), three groups accounting for this higher prevalence: 12.1% of acute lymphoblastic leukemia patients (p=0.011), 18.2% of astrocytoma patients (p=0.023), and 14.7% of germ cell tumor patients (p=0.046) had a cervical rib anomaly.Conclusion. – Prevalence figures for the presence and type of rib anomalies in a large group of normal Caucasian children were generated. In childhood cancer patients a significantly higher prevalence of cervical rib anomalies was demonstrated in patients with acute lymphoblastic leukemia, astrocytoma, and germ cell tumors.     

Evaluation of A2BP1 as an Obesity Gene

OBJECTIVE

A genome-wide association study (GWAS) in Pima Indians (n = 413) identified variation in the ataxin-2 binding protein 1 gene (A2BP1) that was associated with percent body fat. On the basis of this association and the obese phenotype of ataxin-2 knockout mice, A2BP1 was genetically and functionally analyzed to assess its potential role in human obesity.

RESEARCH DESIGN AND METHODS

Variants spanning A2BP1 were genotyped in a population-based sample of 3,234 full-heritage Pima Indians, 2,843 of whom were not part of the initial GWAS study and therefore could serve as a sample to assess replication. Published GWAS data across A2BP1 were additionally analyzed in French adult (n = 1,426) and children case/control subjects (n = 1,392) (Meyre et al. Nat Genet 2009;41:157–159). Selected variants were genotyped in two additional samples of Caucasians (Amish, n = 1,149, and German children case/control subjects, n = 998) and one additional Native American (n = 2,531) sample. Small interfering RNA was used to knockdown A2bp1 message levels in mouse embryonic hypothalamus cells.

RESULTS

No single variant in A2BP1 was reproducibly associated with obesity across the different populations. However, different variants within intron 1 of A2BP1 were associated with BMI in full-heritage Pima Indians (rs10500331, P = 1.9 × 10⁻⁷) and obesity in French Caucasian adult (rs4786847, P = 1.9 × 10⁻¹⁰) and children (rs8054147, P = 9.2 × 10⁻⁶) case/control subjects. Reduction of A2bp1 in mouse embryonic hypothalamus cells decreased expression of Atxn2, Insr, and Mc4r.

CONCLUSIONS

Association analysis suggests that variation in A2BP1 influences obesity, and functional studies suggest that A2BP1 could potentially affect adiposity via the hypothalamic MC4R pathway.Recent large-scale genome-wide association studies (GWASs) have uncovered common variants in several loci associated with obesity in multiple populations (1–7). Most of these studies have been done in populations of European ancestry. Additional GWASs in diverse ethnic groups could confirm previously identified obesity-associated genes, identify novel ethnic-specific susceptibility genes, or identify ethnic-specific variation within a previously identified gene. Several examples exist of common variation in a gene contributing to obesity in one population but unique, rare variation contributing to obesity in a different population. For example, a common obesity-associated variant, rs17782313, near MC4R has been widely replicated in Europeans (3,5,6), but this same variant is nearly monomorphic for the Caucasian nonrisk allele (T allele) in full-heritage Pima Indians, whereas rare coding variants in MC4R, one of which is a novel frameshift mutation that has not been reported in other populations, do contribute to obesity in Pima Indians (8,9). Similarly, a common obesity-associated variant in SIM1 has been reproducibly associated with obesity in Native Americans but not French Caucasians (10), whereas both rare deletions and rare missense variants in SIM1 have been reported to be associated with severe obesity in Caucasians (11–19).To search for loci that may be important in determining obesity in Pima Indians, we recently completed a GWAS using the Affymetrix 100K genotyping array in a group of 413 nondiabetic full-heritage Pima Indians who were phenotyped for various measures of body composition including percent body fat. Our most significant association with percent body fat was in the A2BP1 gene (rs10500331, P = 6.6 × 10⁻⁶), which encodes for the ataxin-2 binding protein 1 (also known as FOX-1) and is involved in tissue-specific alternative splicing (20). In addition to containing RNA-binding motifs, A2BP1 also interacts with ataxin-2 (ATXN2) (21), a protein thought to be involved with RNA metabolism (22). ATXN2 has been implicated in the neurodegenerative disorder spinocerebellar ataxia type 2 (SCA2) (22), and hyperphagia and obesity are two major clinical features reported in an Egyptian family with SCA2 (23). Consistent with this observation, ataxin-2 knockout mice (Sca^−/−) are reported to be much more obese than their wild-type littermates when both are fed a high-fat diet (24,25). Therefore, based on the genetic associations with percent body fat in our GWAS and the obese phenotype of the Sca2^−/− mouse, we studied A2BP1 as a potential candidate gene for human obesity.