Polymorphism in the calsequestrin 1 (CASQ1) gene on chromosome 1q21 is associated with type 2 diabetes in the old order Amish

Association between Genotype and the Glycemic Response to an Oral Glucose Tolerance Test: A Systematic Review

The inter-individual variability of metabolic response to foods may be partly due to genetic variation. This systematic review aims to assess the associations between genetic variants and glucose response to an oral glucose tolerance test (OGTT). Three databases (PubMed, Web of Science, Embase) were searched for keywords in the field of genetics, OGTT, and metabolic response (PROSPERO: CRD42021231203). Inclusion criteria were available data on single nucleotide polymorphisms (SNPs) and glucose area under the curve (gAUC) in a healthy study cohort. In total, 33,219 records were identified, of which 139 reports met the inclusion criteria. This narrative synthesis focused on 49 reports describing gene loci for which several reports were available. An association between SNPs and the gAUC was described for 13 gene loci with 53 different SNPs. Three gene loci were mostly investigated: transcription factor 7 like 2 (TCF7L2), peroxisome proliferator-activated receptor gamma (PPARγ), and potassium inwardly rectifying channel subfamily J member 11 (KCNJ11). In most reports, the associations were not significant or single findings were not replicated. No robust evidence for an association between SNPs and gAUC after an OGTT in healthy persons was found across the identified studies. Future studies should investigate the effect of polygenic risk scores on postprandial glucose levels.

The interplay of inflammation, exosomes and Ca2+ dynamics in diabetic cardiomyopathy

Diabetes mellitus is one of the prime risk factors for cardiovascular complications and is linked with high morbidity and mortality. Diabetic cardiomyopathy (DCM) often manifests as reduced cardiac contractility, myocardial fibrosis, diastolic dysfunction, and chronic heart failure. Inflammation, changes in calcium (Ca²⁺) handling and cardiomyocyte loss are often implicated in the development and progression of DCM. Although the existence of DCM was established nearly four decades ago, the exact mechanisms underlying this disease pathophysiology is constantly evolving. Furthermore, the complex pathophysiology of DCM is linked with exosomes, which has recently shown to facilitate intercellular (cell-to-cell) communication through biomolecules such as micro RNA (miRNA), proteins, enzymes, cell surface receptors, growth factors, cytokines, and lipids. Inflammatory response and Ca²⁺ signaling are interrelated and DCM  has been known to adversely affect many of these signaling molecules either qualitatively and/or quantitatively. In this literature review, we have demonstrated that Ca²⁺ regulators are tightly controlled at different molecular and cellular levels during various biological processes in the heart. Inflammatory mediators, miRNA and exosomes are shown to interact with these regulators, however how these mediators are linked to Ca²⁺ handling during DCM pathogenesis remains elusive. Thus, further investigations are needed to understand the mechanisms to restore cardiac Ca²⁺ homeostasis and function, and to serve as potential therapeutic targets in the treatment of DCM.

Detecting the Critical States of Type 2 Diabetes Mellitus Based on Degree Matrix Network Entropy by Cross-Tissue Analysis

Type 2 diabetes mellitus (T2DM) is a metabolic disease caused by multiple etiologies, the development of which can be divided into three states: normal state, critical state/pre-disease state, and disease state. To avoid irreversible development, it is important to detect the early warning signals before the onset of T2DM. However, detecting critical states of complex diseases based on high-throughput and strongly noisy data remains a challenging task. In this study, we developed a new method, i.e., degree matrix network entropy (DMNE), to detect the critical states of T2DM based on a sample-specific network (SSN). By applying the method to the datasets of three different tissues for experiments involving T2DM in rats, the critical states were detected, and the dynamic network biomarkers (DNBs) were successfully identified. Specifically, for liver and muscle, the critical transitions occur at 4 and 16 weeks. For adipose, the critical transition is at 8 weeks. In addition, we found some "dark genes" that did not exhibit differential expression but displayed sensitivity in terms of their DMNE score, which is closely related to the progression of T2DM. The information uncovered in our study not only provides further evidence regarding the molecular mechanisms of T2DM but may also assist in the development of strategies to prevent this disease.

The association of dietary patterns with dietary inflammatory index, systemic inflammation, and insulin resistance, in apparently healthy individuals with obesity

Inflammation is considered a key mechanism leading to obesity. Dietary patterns and certain food items influence inflammation. Few studies have investigated the contribution of major dietary patterns to biological measures of inflammation. Therefore, the present study aimed to examine the associations of different dietary patterns with dietary inflammatory index (DII), systemic inflammation, and insulin resistance (IR) in the apparently healthy obese. In this cross-sectional study, 151 abdominally obese subjects were recruited from the Northwest of Iran. Dietary intake, demographic data, anthropometric indices, and physical activity (PA) was assessed. DII scores were calculated based on a validated 168-item food frequency questionnaire (FFQ). Three dietary patterns were identified, using principal component analysis. Basal blood samples were collected to determine biochemical parameters. Linear regression test with adjusted beta estimates was applied for data analysis. Three dietary patterns were extracted as Healthy, Western, and Traditional. Body mass index (BMI) (p < 0.01) and fat mass (p < 0.001) were directly associated with the Western dietary pattern. Conversely, serum lipopolysaccharide-binding protein (LBP) (b = - 0.1, p < 0.04) was negatively associated with Healthy dietary pattern, after controlling for confounders. The Traditional pattern was found to be inversely related to DII (b = - 0.3, p < 0.001). The association was also reveresed between Traditional pattern and IR (Odds Ratio: 0.3 (95% Confidence Interval 0.1-0.9)). The results suggested that the Western dietary pattern was related to higher BMI and fat mass. In addition, the Healthy pattern was associated with decreased levels of LBP. Adherence to the Traditional dietary pattern was inversely related to DII as well as IR.

Calsequestrin: a well-known but curious protein in skeletal muscle

Calsequestrin (CASQ) was discovered in rabbit skeletal muscle tissues in 1971 and has been considered simply a passive Ca²⁺-buffering protein in the sarcoplasmic reticulum (SR) that provides Ca²⁺ ions for various Ca²⁺ signals. For the past three decades, physiologists, biochemists, and structural biologists have examined the roles of the skeletal muscle type of CASQ (CASQ1) in skeletal muscle and revealed that CASQ1 has various important functions as (1) a major Ca²⁺-buffering protein to maintain the SR with a suitable amount of Ca²⁺ at each moment, (2) a dynamic Ca²⁺ sensor in the SR that regulates Ca²⁺ release from the SR to the cytosol, (3) a structural regulator for the proper formation of terminal cisternae, (4) a reverse-directional regulator of extracellular Ca²⁺ entries, and (5) a cause of human skeletal muscle diseases. This review is focused on understanding these functions of CASQ1 in the physiological or pathophysiological status of skeletal muscle.

Calsequestrin, a key protein in striated muscle health and disease

Calsequestrin (CASQ) is the most abundant Ca²⁺ binding protein localized in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. The genome of vertebrates contains two genes, CASQ1 and CASQ2. CASQ1 and CASQ2 have a high level of homology, but show specific patterns of expression. Fast-twitch skeletal muscle fibers express only CASQ1, both CASQ1 and CASQ2 are present in slow-twitch skeletal muscle fibers, while CASQ2 is the only protein present in cardiomyocytes. Depending on the intraluminal SR Ca²⁺ levels, CASQ monomers assemble to form large polymers, which increase their Ca²⁺ binding ability. CASQ interacts with triadin and junctin, two additional SR proteins which contribute to localize CASQ to the junctional region of the SR (j-SR) and also modulate CASQ ability to polymerize into large macromolecular complexes. In addition to its ability to bind Ca²⁺ in the SR, CASQ appears also to be able to contribute to regulation of Ca²⁺ homeostasis in muscle cells. Both CASQ1 and CASQ2 are able to either activate and inhibit the ryanodine receptors (RyRs) calcium release channels, likely through their interactions with junctin and triadin. Additional evidence indicates that CASQ1 contributes to regulate the mechanism of store operated calcium entry in skeletal muscle via a direct interaction with the Stromal Interaction Molecule 1 (STIM1). Mutations in CASQ2 and CASQ1 have been identified, respectively, in patients with catecholamine-induced polymorphic ventricular tachycardia and in patients with some forms of myopathy. This review will highlight recent developments in understanding CASQ1 and CASQ2 in health and diseases.

Effect of insulin-glucose metabolism compared with obesity on adipose omentin gene expression in different models of diabetic C57BL/6 mice

BACKGROUND

Omentin, releasing by adipose-tissue may be related to glucose metabolism. The omentin circulating levels and the related mRNA expression in visceral adipose-tissue are different in types of diabetes and the exact function of this molecule is still unknown. The aim of this study was to examine omentin gene expression in adipose-tissues of type-1 and type-2 diabetic mice for the investigation of the effects of fat-mass and insulin-glucose metabolism.

METHODS

In this study, 36 C57BL/6 mice were divided into four experimental groups, including control, type-1 diabetes (inducted by streptozotocin), type-2 diabetes with obesity (high-fat diet + low-dose-streptozotocin [HFD + STZ]), and type-2 with normal weight (normal-pellet diet + low-dose-streptozotocin [NPD + STZ]). The present study involved the measurements of oral-glucose-tolerance-test and the levels of biochemical parameters, including blood glucose, omentin, insulin, lipid-profile, as well as aminotransferases. In addition, the omentin mRNA expression was evaluated by real-time polymerase-chain-reaction.

RESULTS

The results of omentin gene expression analysis showed a significant difference between mRNA expressions in the experimental groups. The plasma omentin levels were significantly higher in type-1 diabetes group and lower in type-2 diabetes with NPD + STZ; however, the plasma omentin levels were not changed in the HFD + STZ group. In addition, the findings of serum-biochemical analysis revealed significant differences, compared to the control-group.

CONCLUSIONS

The omentin expression may be affected by insulin and glucose levels in different types of diabetes more than fat-mass, and due to the local activity, the serum omentin may not comply with its gene expression.

Effect of Two Lipoprotein (a)-Associated Genetic Variants on Plasminogen Levels and Fibrinolysis

Two genetic variants (rs3798220 and rs10455872) in the apolipoprotein (a) gene (LPA) have been implicated in cardiovascular disease (CVD), presumably through their association with lipoprotein (a) [Lp(a)] levels. While Lp(a) is recognized as a lipoprotein with atherogenic and thrombogenic characteristics, it is unclear whether or not the two Lp(a)-associated genetic variants are also associated with markers of thrombosis (i.e., plasminogen levels and fibrinolysis). In the present study, we genotyped the two genetic variants in 2919 subjects of the Old Order Amish (OOA) and recruited 146 subjects according to the carrier and noncarrier status for rs3798220 and rs10455872, and also matched for gender and age. We measured plasma Lp(a) and plasminogen levels in these subjects, and found that the concentrations of plasma Lp(a) were 2.62- and 1.73-fold higher in minor allele carriers of rs3798220 and rs10455872, respectively, compared with noncarriers (P = 2.04 × 10⁻¹⁷ and P = 1.64 × 10⁻⁶, respectively). By contrast, there was no difference in plasminogen concentrations between carriers and noncarriers of rs3798220 and rs10455872. Furthermore, we observed no association between carrier status of rs3798220 or rs10455872 with clot lysis time. Finally, plasminogen mRNA expression in liver samples derived from 76 Caucasian subjects was not significantly different between carriers and noncarriers of these two genetic variants. Our results provide further insight into the mechanism of action behind two genetic variants previously implicated in CVD risk and show that these polymorphisms are not major modulating factors for plasma plasminogen levels and fibrinolysis.

Cardiac Affection in Type 1 Diabetic Patients in Relation to Omentin

AIM:

To evaluate cardiac affection in type 1 diabetes in relation to Omentin.

PATIENTS AND METHODS:

Sixty two diabetics and 30 volunteer of the same age and sex were included as a control group. Blood sample was taken for assessment of omentin and oxidized low density lipoprotein (OxLDL), glycosylated hemoglobin (HbA1) and lipid profile. Urine sample was taken for assessment of albumin/creatinine ratio. 24 hour holter was also done. T-test, simple correlation followed by stepwise multiple regression analysis was used for analysis of data.

RESULTS:

Parameters of 24 hour holter were significantly lower in diabetics. Omentin was significantly lower, while OxLDL were significantly higher than controls. RMSSD, ST deviation and OxLDL were the parameters related to omentin by stepwise multiple regression analysis in diabetics.

CONCLUSION:

Diabetic patients had a cardiac autonomic neuropathy. A significant reduction of omentin and elevation OxLDL imply that they influence glucose metabolism in type 1 diabetes. Omentin had a significant relation to 24 hr holter which may reflect its role in cardiac affection. Omentin and OxLDL had a role in renal affection.

Genes, Genetics, and Environment in Type 2 Diabetes: Implication in Personalized Medicine

Type 2 diabetes (T2D) is a multifactorial anomaly involving 57 genes located on 16 different chromosomes and 136 single nucleotide polymorphisms (SNPs). Ten genes are located on chromosome 1, followed by seven genes on chromosome 11 and six genes on chromosomes 3. Remaining chromosomes harbor two to five genes. Significantly, chromosomes 13, 14, 16, 18, 21, 22, X, and Y do not have any associated diabetogenic gene. Genetic components have their own pathways encompassing insulin secretion, resistance, signaling, and β-cell dysfunction. Environmental factors include epigenetic changes, nutrition, intrauterine surroundings, and obesity. In addition, ethnicity plays a role in conferring susceptibility to T2D. This scenario poses a challenge toward the development of biomarker for quick disease diagnosis or for generating a consensus to delineate different categories of T2D patients. We believe, before prescribing a generic drug, detailed genotypic information with the background of ethnicity and environmental factors may be taken into consideration. This nonconventional approach is envisaged to be more robust in the context of personalized medicine and perhaps would cause lot less burden on the patient ensuring better management of T2D.

Changes of serum omentin-1 levels in normal subjects, type 2 diabetes and type 2 diabetes with overweight and obesity in Chinese adults

PURPOSE

Omentin-1 has been identified as interesting novel adipokines that may modulate insulin action. Its exact biological function is unclear. The aim of this study is to assay the levels of serum omentin-1 in normal subjects and type 2 diabetes mellitus (T2DM) with normal weight, overweight and obesity and to analyze the relationship between serum omentin-1 levels with body mass index (BMI), waist to hip ratio (WHR), glycosylated hemoglobin (HbA1c), plasma glucose, insulin resistance index (HOMA-IR) and serum lipid levels.

METHODS

There are eighty newly diagnosed type 2 diabetes patients, thirty-five type 2 diabetes patients with normal weight, twenty-nine type 2 diabetes patients with overweight, sixteen type 2 diabetes patients with obesity, and forty healthy control subjects were enrolled in this study. The levels of plasma glucose at fasting and 2-hour postprandial blood glucose and fasting serum levels of insulin, omentin-1and HbA1c were measured. HOMA-IR was calculated.

RESULTS

Serum omentin-1 levels were found to be significantly decreased in type 2 diabetes patients with normal weight (821.16 ± 312.50 ng/L), in type 2 diabetes patients with overweight (748.00±322.51 ng/L), and in type 2 diabetes patients with obesity (530.44±357.35 ng/L) compared with healthy control subjects (994.71±435.90 ng/L) at P<0.05. The level of serum omentin-1 was negatively correlated to BMI, HOMA-IR, WHR, fasting insulin (FINS), fasting plasma glucose (FPG), 2-hour postprandial blood glucose (2HPG), triglycerides (TG), and positively correlated to high-density lipoprotein (HDL). BMI was independent related factor that influenced the levels of serum omentin-1.

CONCLUSION

Decreased omentin-1 levels may contribute to the development of insulin resistance, T2DM and particularly to obesity in Chinese adults, however, its role in these diseases needs to be fully elucidated.

Genetic associations with diabetes: meta-analyses of 10 candidate polymorphisms

Aims

The goal of our study is to investigate the combined contribution of 10 genetic variants to diabetes susceptibility.

Methods

Bibliographic databases were searched from 1970 to Dec 2012 for studies that reported on genetic association study of diabetes. After a comprehensive filtering procedure, 10 candidate gene variants with informative genotype information were collected for the current meta-anlayses. Using the REVMAN software, odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to evaluate the combined contribution of the selected genetic variants to diabetes.

Results

A total of 37 articles among 37,033 cases and 54,716 controls were involved in the present meta-analyses of 10 genetic variants. Three variants were found to be significantly associated with type 1 diabetes (T1D): NLRP1 rs12150220 (OR = 0.71, 95% CI = 0.55–0.92, P = 0.01), IL2RA rs11594656 (OR = 0.86, 95% CI = 0.82–0.91, P<0.00001), and CLEC16A rs725613 (OR = 0.71, 95% CI = 0.55–0.92, P = 0.01). APOA5 −1131T/C polymorphism was shown to be significantly associated with of type 2 diabetes (T2D, OR = 1.27, 95% CI = 1.03–1.57, P = 0.03). No association with diabetes was showed in the meta-analyses of other six genetic variants, including SLC2A10 rs2335491, ATF6 rs2070150, KLF11 rs35927125, CASQ1 rs2275703, GNB3 C825T, and IL12B 1188A/C.

Conclusion

Our results demonstrated that IL2RA rs11594656 and CLEC16A rs725613 are protective factors of T1D, while NLRP1 rs12150220 and APOA5 −1131T/C are risky factors of T1D and T2D, respectively.

The human protein disulfide isomerase gene family

Enzyme-mediated disulfide bond formation is a highly conserved process affecting over one-third of all eukaryotic proteins. The enzymes primarily responsible for facilitating thiol-disulfide exchange are members of an expanding family of proteins known as protein disulfide isomerases (PDIs). These proteins are part of a larger superfamily of proteins known as the thioredoxin protein family (TRX). As members of the PDI family of proteins, all proteins contain a TRX-like structural domain and are predominantly expressed in the endoplasmic reticulum. Subcellular localization and the presence of a TRX domain, however, comprise the short list of distinguishing features required for gene family classification. To date, the PDI gene family contains 21 members, varying in domain composition, molecular weight, tissue expression, and cellular processing. Given their vital role in protein-folding, loss of PDI activity has been associated with the pathogenesis of numerous disease states, most commonly related to the unfolded protein response (UPR). Over the past decade, UPR has become a very attractive therapeutic target for multiple pathologies including Alzheimer disease, Parkinson disease, alcoholic and non-alcoholic liver disease, and type-2 diabetes. Understanding the mechanisms of protein-folding, specifically thiol-disulfide exchange, may lead to development of a novel class of therapeutics that would help alleviate a wide range of diseases by targeting the UPR.

Potential regulatory role of calsequestrin in platelet Ca(2+) homeostasis and its association with platelet hyperactivity in diabetes mellitus

BACKGROUND

Altered Ca(2+) homeostasis contributes significantly to platelet hyperactivity in diabetes mellitus. Calsequestrin (CSQ), as a Ca(2+) buffer protein in the sarcoplasmic reticulum, also regulates the Ca(2+) release process in muscles. We hypothesized that CSQ may be expressed in platelets, but is altered and involved in diabetic platelet Ca(2+) abnormalities and hyperaggregability.

METHODS

CSQ expression in platelets from streptozotocin-induced type 1 diabetes rats, type 2 diabetes volunteers and Goto-Kakizaki rats were analyzed by western blotting and RT-qPCR. Platelet Ca(2+) and aggregation were evaluated with Fura2 and an aggregometer, respectively.

RESULTS

Platelets from diabetic patients and rats exhibited increased resting Ca(2+) levels, and hyperactive Ca(2+) and aggregation responses to agonists. This enhanced basal Ca(2+) was largely dependent on intracellular Ca(2+) and insensitive to inositol 1,4,5-trisphosphate receptor (IP(3)R) antagonism. Additionally, the expression of the skeletal CSQ isotype (CSQ-1) was detected in both rat and human platelets, but its levels were significantly lowered in diabetic platelets as compared with normal platelets. Impairment of CSQ by trifluoperazine caused concentration-dependent Ca(2+) release in normal platelets and HEK293 cells. Knocking down CSQ-1 in HEK293 cells resulted in increased leakage of Ca(2+), which was also insensitive to IP(3)R inhibition, and exaggerated Ca(2+) release following carbachol treatment.

CONCLUSIONS

Downregulation of CSQ-1 in diabetic platelets and impairment of CSQ-1 in normal cells leads to disturbed Ca(2+) release, demonstrating a potential role for CSQ-1 in the regulation of the platelet Ca(2+) release process and a possible causal contribution to diabetic platelet hyperactivity.

Serum omentin-1 and chemerin levels are interrelated in patients with Type 2 diabetes mellitus with or without ischaemic heart disease

AIMS

Omentin-1 and chemerin have been identified as interesting novel adipokines that may modulate insulin action. Also, they have been suggested to be linked to obesity-induced insulin resistance. The aim of this study was to analyse the relationship between these adipokines and interleukin-6, insulin resistance and anthropometric and metabolic variables in patients with Type 2 diabetes mellitus and in patients with Type 2 diabetes who have ischaemic heart disease.

METHODS

Seventy-five individuals with Type 2 diabetes and 15 healthy control subjects were enrolled in this study. Insulin levels, interleukin-6, omentin-1 and chemerin were measured by ELISA.

RESULTS

Serum omentin-1 levels were found to be significantly decreased in patients with Type 2 diabetes (19.7 ± 1 ng/ml) and in patients with Type 2 diabetes with ischaemic heart disease (18.5 ± 1.6 ng/ml) compared with healthy control subjects (27.4 ± 2.6 ng/ml) at P < 0.01. Moreover, serum chemerin levels were found to be significantly increased in patients with Type 2 diabetes (347 ± 14 ng/ml) and in patients with Type 2 diabetes with ischaemic heart disease (341 ± 16.5 ng/ml) compared with healthy control subjects (281 ± 13 ng/ml) at P < 0.01. Interestingly, omentin-1 and chemerin levels were found to be significantly correlated negatively with each other as well as being individually correlated with some selected anthropometric, biochemical and clinical variables. In conclusion, both omentin-1 and chemerin might play as a pivotal role in obesity and its associated disorders as Type 2 diabetes; however, their role in cardiovascular diseases needs to be fully elucidated.

Calsequestrin distribution, structure and function, its role in normal and pathological situations and the effect of thyroid hormones

Calsequestrin is the main calcium binding protein of the sarcoplasmic reticulum, serving as an important regulator of Ca(2+). In mammalian muscles, it exists as a skeletal isoform found in fast- and slow-twitch skeletal muscles and a cardiac isoform expressed in the heart and slow-twitch muscles. Recently, many excellent reviews that summarised in great detail various aspects of the calsequestrin structure, localisation or function both in skeletal and cardiac muscle have appeared. The present review focuses on skeletal muscle: information on cardiac tissue is given, where differences between both tissues are functionally important. The article reviews the known multiple roles of calsequestrin including pathology in order to introduce this topic to the broader scientific community and to stimulate an interest in this protein. Newly we describe our results on the effect of thyroid hormones on skeletal and cardiac calsequestrin expression and discuss them in the context of available literary data on this topic.

FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals

We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR. It combines features of the Genome-wide Rapid Association using Mixed Model And Regression approach (GRAMMAR) with Model-Based MDR (MB-MDR). We focus on continuous traits, although the method is general and can be used for outcomes of any type, including binary and censored traits. When comparing FAM-MDR with Pedigree-based Generalized MDR (PGMDR), which is a generalization of Multifactor Dimensionality Reduction (MDR) to continuous traits and related individuals, FAM-MDR was found to outperform PGMDR in terms of power, in most of the considered simulated scenarios. Additional simulations revealed that PGMDR does not appropriately deal with multiple testing and consequently gives rise to overly optimistic results. FAM-MDR adequately deals with multiple testing in epistasis screens and is in contrast rather conservative, by construction. Furthermore, simulations show that correcting for lower order (main) effects is of utmost importance when claiming epistasis. As Type 2 Diabetes Mellitus (T2DM) is a complex phenotype likely influenced by gene-gene interactions, we applied FAM-MDR to examine data on glucose area-under-the-curve (GAUC), an endophenotype of T2DM for which multiple independent genetic associations have been observed, in the Amish Family Diabetes Study (AFDS). This application reveals that FAM-MDR makes more efficient use of the available data than PGMDR and can deal with multi-generational pedigrees more easily. In conclusion, we have validated FAM-MDR and compared it to PGMDR, the current state-of-the-art MDR method for family data, using both simulations and a practical dataset. FAM-MDR is found to outperform PGMDR in that it handles the multiple testing issue more correctly, has increased power, and efficiently uses all available information.

Polymorphisms of the IGF1R gene and their genetic effects on chicken early growth and carcass traits

BACKGROUND

The insulin-like growth factor I receptor (IGF1R) has an important effect on growth, carcass, and meat quality traits in many species. However, few studies on associations of the IGF1R gene with growth and carcass traits have been reported in chickens. The objectives of the present study were to study the associations of the IGF1R gene with chicken early growth and carcass traits using a neutral test, variation scan of the gene, genetic diversity, linkage disequilibrium and association analyses.

RESULTS

The tree generated from the amino acid sequences of 15 species showed that the IGF1R gene was conservative in the whole evolution among the mammalian animals and chickens. In a total of 10,818 bp of sequence, 70 single nucleotide polymorphisms were identified in the chicken IGF1R gene. The allelic and genotypic frequency distribution, genetic diversity and linkage disequilibrium of 18 single nucleotide polymorphisms (SNPs) in the Xinghua and White Recessive Rock chickens showed that six of them were possibly associated with growth traits. Association analyses showed that the A17299834G SNP was significantly associated with chicken carcass body weight, eviscerated weight with giblets, eviscerated weight, body weights at 28, 35, and 56 d of age, leg length at 56 d of age, and daily weight gain at 0-4 weeks. The haplotypes of the A17307750G and A17307494G were associated with early growth traits. The haplotypes of the A17299834G and C17293932T were significantly associated with most of the early growth traits and carcass traits.

CONCLUSION

There were rich polymorphisms in the chicken IGF1R gene. Several SNPs associated with chicken early growth traits and carcass traits were identified in the IGF1R gene by genetic diversity, linkage disequilibrium, and association analyses in the present study.

Type 2 diabetes susceptibility genes on chromosome 1q21-24

Type 2 diabetes (T2D) has been linked to chromosome 1q21-24 in multiple samples, including a Utah family sample. Variants in 13 of the numerous candidate genes in the 1q region were tested for association with T2D in a Utah case-control sample. The most promising, 19 variants in 6 candidates, were genotyped on the Utah family sample. Herein, we tested the 19 variants individually and in pairs for an effect on T2D risk in family members using a logistic regression model that accounted for gender, age, and BMI and attributed residual genetic effects to a polygenic component. Seven variants increased risk significantly through 5 pairs of interactions. The significant variant pairs were apolipoprotein A-II (APOA2) rs6413453 interacting with calsequestrin 1 (CASQ1) rs617698, dual specificity phosphatase 12 (DUSP12) rs1503814, and retinoid X receptor gamma (RXRG) rs10918169, a poly-T insertion-deletion polymorphism in liver pyruvate kinase (PKLR) interacting with APOA2 rs12143180, and DUSP12 rs1027702 interacting with RXRG rs10918169. Genotypes of these 5 variant pairs accounted for 25.8% of the genetic variance in T2D in these pedigrees.

Omentin plasma levels and gene expression are decreased in obesity

Central obesity and the accumulation of visceral fat are risk factors for the development of type 2 diabetes and cardiovascular disease. Omentin is a protein expressed and secreted from visceral but not subcutaneous adipose tissue that increases insulin sensitivity in human adipocytes. To determine the impact of obesity-dependent insulin resistance on the regulation of two omentin isoforms, gene expression and plasma levels were measured in lean, overweight, and obese subjects. Omentin 1 was shown to be the major circulating isoform in human plasma. Lean subjects had significantly higher plasma omentin 1 levels than obese and overweight subjects. In addition, higher plasma omentin 1 levels were detected in women compared with men. Plasma omentin 1 levels were inversely correlated with BMI, waist circumference, leptin levels, and insulin resistance as measured by homeostasis model assessment and positively correlated with adiponectin and HDL levels. Both omentin 1 and omentin 2 gene expression were decreased with obesity and were highly correlated with each other in visceral adipose tissue. In summary, decreased omentin levels are associated with increasing obesity and insulin resistance. Therefore, omentin levels may be predictive of the metabolic consequences or co-morbidities associated with obesity.

Evidence that Rho guanine nucleotide exchange factor 11 (ARHGEF11) on 1q21 is a type 2 diabetes susceptibility gene in the Old Order Amish

Rho guanine nucleotide exchange factor 11 (ARHGEF11), located on chromosome 1q21, is involved in G protein signaling and is a pathway known to play a role in both insulin secretion and action. We genotyped 52 single nucleotide polymorphims (SNPs) in ARHGEF11 and compared the genotype frequencies of subjects with type 2 diabetes (n = 145) or type 2 diabetes/impaired glucose tolerance (IGT) (n = 293) with those of control subjects with normal glucose tolerance (NGT) (n = 358). Thirty SNPs, spanning the entire gene, were significantly associated with type 2 diabetes or type 2 diabetes/IGT. The most significantly associated SNP was rs6427340 (intron 2), in which the less common allele was the risk allele (odds ratio [OR] 1.82 [95% CI 1.20-2.70], P = 0.005 for type 2 diabetes vs. NGT and 1.79 [1.27-2.50], P = 0.0008 for type 2 diabetes/IGT vs. NGT). In an expanded set of nondiabetic subjects (n = 754), most of the type 2 diabetes-and IGT-associated SNPs were significantly associated with glucose levels during an oral glucose tolerance test, with the same SNP (rs6427340) showing the most significant associations (P = 0.007). All type 2 diabetes-and IGT-associated SNPs were in high linkage disequilibrium and constitute a single 133-kb haplotype block. These results, coupled with similar findings in Pima Indians, suggest that sequence variation in ARHGEF11 may influence risk of type 2 diabetes.

The search for type 2 diabetes susceptibility loci: the chromosome 1q story

The unbiased approach of genome-wide linkage analysis has shown evidence for linkage of type 2 diabetes mellitus to the chromosome 1q21-25 region in at least eight independent studies. More than 26 candidate genes have already been evaluated, but to date none explain the evidence for linkage in this gene-dense region. Considerable data suggest that multiple genes account for this linkage result. The search for these genes is now the focus of an international consortium of groups reporting linkage of type 2 diabetes to this region of chromosome 1q21-q25.

Polymorphisms in the glucokinase-associated, dual-specificity phosphatase 12 (DUSP12) gene under chromosome 1q21 linkage peak are associated with type 2 diabetes

Linkage of type 2 diabetes to chromosome 1q21-q23 is well replicated across populations. In an initial 50-kb marker map (580 markers) across the linked region, one of the two strongest associations observed in Utah Caucasians was at marker rs1503814 (P < 0.00001 in pools, P < 0.004 in individuals). Based on this association, we typed additional markers and screened for sequence variation in the nearby DUSP12 gene. The strongest associations mapped to a highly conserved nongenic sequence just telomeric to rs1503814 and extended 10 kb telomeric through the DUSP12 gene and into the 5' end of the adjacent ATF6 gene. No coding variant could explain the association in the DUSP12 gene. An extended haplotype encompassing markers from -8,379 to +10,309 bp relative to the ATG start was more common in Caucasian case (0.381) than control subjects (0.285, P = 0.005) and was uniquely tagged by a 194-bp allele at either of two simple tandem repeat variants or by the T allele at marker +7,580. Markers -8,379 and +7,580 were nominally associated with type 2 diabetes in African-American subjects (P < 0.05), but with different alleles. Marker rs1503814 was strongly associated with postchallenge insulin levels among family members (P = 0.000002), but sequence variation in this region was not associated with type 2 diabetes in three other populations of European ancestry. Our data suggest that sequences in or upstream of DUSP12 may contribute to type 2 diabetes susceptibility, but the lack of replication suggests a small effect size.

The Genetic Basis of Type 2 Diabetes

Type 2 Diabetes results from a complex physiologic process that includes the pancreatic beta cells, peripheral glucose uptake in muscle, the secretion of multiple cytokines and hormone-like molecules from adipocytes, hepatic glucose production, and likely the central nervous system. Consistent with the complex web of physiologic defects, the emerging picture of the genetics will involve a large number of risk susceptibility genes, each individually with relatively small effect (odds ratios below 1.2 in most cases). The challenge for the future will include cataloging and confirming the genetic risk factors, and understanding how these risk factors interact with each other and with the known environmental and lifestyle risk factors that increase the propensity to type 2 diabetes.

The human obesity gene map: the 2005 update

This paper presents the 12th update of the human obesity gene map, which incorporates published results up to the end of October 2005. Evidence from single-gene mutation obesity cases, Mendelian disorders exhibiting obesity as a clinical feature, transgenic and knockout murine models relevant to obesity, quantitative trait loci (QTL) from animal cross-breeding experiments, association studies with candidate genes, and linkages from genome scans is reviewed. As of October 2005, 176 human obesity cases due to single-gene mutations in 11 different genes have been reported, 50 loci related to Mendelian syndromes relevant to human obesity have been mapped to a genomic region, and causal genes or strong candidates have been identified for most of these syndromes. There are 244 genes that, when mutated or expressed as transgenes in the mouse, result in phenotypes that affect body weight and adiposity. The number of QTLs reported from animal models currently reaches 408. The number of human obesity QTLs derived from genome scans continues to grow, and we now have 253 QTLs for obesity-related phenotypes from 61 genome-wide scans. A total of 52 genomic regions harbor QTLs supported by two or more studies. The number of studies reporting associations between DNA sequence variation in specific genes and obesity phenotypes has also increased considerably, with 426 findings of positive associations with 127 candidate genes. A promising observation is that 22 genes are each supported by at least five positive studies. The obesity gene map shows putative loci on all chromosomes except Y. The electronic version of the map with links to useful publications and relevant sites can be found at http://obesitygene.pbrc.edu.

Genetic variation in adiponectin receptor 1 and adiponectin receptor 2 is associated with type 2 diabetes in the Old Order Amish

Adiponectin receptor 1 (ADIPOR1) and adiponectin receptor 2 (ADIPOR2) are newly identified receptors for adiponectin, an adipocytokine with anti-inflammatory and insulin-sensitizing properties. We screened for polymorphisms by performing sequence analysis on all eight exons, splice junctions, and approximately 2 kb of the 5' flanking regions of each receptor. We detected 5 single nucleotide polymorphisms (SNPs) in ADIPOR1 and 16 SNPs in ADIPOR2. We genotyped these SNPs in Amish subjects with type 2 diabetes (n = 137), impaired glucose tolerance (IGT) (n = 139), and normal glucose tolerance (n = 342) to test for association with type 2 diabetes. Three intronic SNPs in ADIPOR1 were significantly associated with type 2 diabetes (P = 0.014-0.007; odds ratio [OR] 1.61-1.65) and in high linkage disequilibrium (r2 = 0.97-1.0). In ADIPOR2, we found that five SNPs delineated one large haplotype block (r2= 0.9-1.0) spanning >98 kb of the gene and promoter region, which was strongly associated with the combined type 2 diabetes/IGT trait (P < or = 0.001; OR 1.64-1.71). To our knowledge, these data provide the first evidence for association between variation in the adiponectin receptors and type 2 diabetes.

Polymorphism in the calsequestrin 1 (CASQ1) gene on chromosome 1q21 is associated with type 2 diabetes in the old order Amish

Calsequestrin (CASQ)1 is involved in intracellular storage and release of calcium, a process that has been shown to mediate glucose transport in muscle. Its gene, CASQ1, is encoded on chromosome 1q21, a region that has been linked to type 2 diabetes in the Amish and several other populations. We screened all 11 exons, exon-intron junctions, and the proximal regulatory region of CASQ1 for mutations. We detected four novel single nucleotide polymorphisms (SNPs) (-1470C-->T, -1456delG, -1366insG, and 593C-->T). Ten informative SNPs within CASQ1 were genotyped in Amish subjects with type 2 diabetes (n = 145), impaired glucose tolerance (n = 148), and normal glucose tolerance (n = 358). Rs2275703 and rs617698 in introns 4 and 2 were significantly associated with type 2 diabetes (P = 0.008 and 0.04, respectively); three other SNPs showed borderline evidence for association to type 2 diabetes (P = 0.076-0.093). Furthermore, in nondiabetic subjects (n = 754), both rs2275703 and rs617698 were significantly associated with glucose area under the curve during an oral glucose tolerance test (P = 0.035 and 0.013, respectively). Haplotype analysis suggested that no haplotype could explain these associations better than rs2275703. These findings, coupled with similar findings in Utah Caucasians, suggest that sequence variation in CASQ1 may influence risk of type 2 diabetes.

Calsquestrin 1 (CASQ1) gene polymorphisms under chromosome 1q21 linkage peak are associated with type 2 diabetes in Northern European Caucasians

Genome-wide scans in multiple populations have identified chromosome 1q21-q24 as one susceptibility region for type 2 diabetes. To map the susceptibility genes, we first placed a dense single nucleotide polymorphism (SNP) map across the linked region. We identified two SNPs that showed strong associations, and both mapped to within intron 2 of the calsequestrin 1 (CASQ1) gene. We tested the hypothesis that sequence variation in or near CASQ1 contributed to type 2 diabetes susceptibility in Northern European Caucasians by identifying additional SNPs from the public database and by screening the CASQ1 gene for additional variation. In addition to 15 known SNPs in this region, we found 8 new SNPs, 3 of which were in exons. A single rare nonsynonymous SNP in exon 11 (A348V) was not associated with type 2 diabetes. The associated SNPs were localized to the region between -1,404 in the 5' flanking region and 2,949 in intron 2 (P = 0.002 to P = 0.034). No SNP 3' to intron 2, including the adjacent gene PEA15, showed an association. The strongest associations were restricted to individuals of Northern European ancestry ascertained in Utah. A six-marker haplotype was also associated with type 2 diabetes (P = 0.008), but neither transmission disequilibrium test nor family-based association studies were significant for the most strongly associated SNP in intron 2 (SNP CASQ2312). An independent association of SNPs in introns 2 and 4 with type 2 diabetes is reported in Amish families with linkage to chromosome 1q21-q24. Our findings suggest that noncoding SNPs in CASQ1 alter diabetes susceptibility, either by a direct effect on CASQ1 gene expression or perhaps by regulating a nearby gene such as PEA15.