Association of SUMO4, as a Candidate Gene for IDDM5, with Susceptibility to Type 1 Diabetes in Asian Populations

Polymorphism M55V in gene encoding small ubiquitin-like modifier 4 (SUMO4) protein associates with susceptibility to type 1 (and type 2) diabetes

BACKGROUND

The association between small ubiquitin-like modifier 4 (SUMO4) gene polymorphism and type 1 diabetes mellitus (T1DM) or type 2 diabetes mellitus (T2DM) has been investigated in several studies. We conducted a meta-analysis to evaluate the association of SUMO4 gene polymorphism with T1DM and T2DM susceptibility.

METHODS

A meta-analysis was performed on the published studies before August 2011. The association of SUMO4 M55V polymorphism with T1DM and T2DM was evaluated. Meta-analysis was performed for genotypes AA versus GG, AA versus AG, AA versus AG + GG and A allele versus G allele in a fixed/random effect model. The combined odds ratio (OR) with 95% confidence interval (95% CI) was calculated to estimate the strength of the association.

RESULTS

Sixteen case-control studies including 9190 cases and 10 456 healthy controls were included. T1DM patients were divided into Asian and Caucasian subgroup. We detected a significant association of SUMO4 M55V polymorphism with T1DM in Asian population (A versus G: OR = 0.79, 95%CI = 0.72-0.86, p = 0.000) and a significant association of SUMO4 M55V polymorphism with T1DM in Caucasian population (A versus G: OR = 0.84, 95%CI = 0.73-0.97, p = 0.007). Included T2DM patients were all Asian. Meanwhile, a significant association of SUMO4 M55V polymorphism with T2DM was also found (A versus G: OR = 0.86, 95%CI = 0.79-0.94, p = 0.001).

CONCLUSIONS

Our study demonstrates significant associations of SUMO4 M55V polymorphism with T1DM in Asian and Caucasian population and with T2DM in Asian population.

Association between the SUMO4 M55V (A163G) polymorphism and susceptibility to type 1 diabetes: a meta-analysis

OBJECTIVE

The aim of this study was to determine whether the SUMO4 M55V (A163G) polymorphism confers susceptibility to type 1 diabetes (T1D).

METHODS

A meta-analysis was conducted on the association between the SUMO4 M55V polymorphism and T1D using; (1) allelic contrast (G vs. A), and the (2) recessive (GG vs. GA+AA), (3) dominant (GG+GA vs. AA), and (4) additive models (GG vs. AA).

RESULTS

Thirteen separate studies were considered in the meta-analysis, which in total included 5915 patients and 6660 controls, and five European and eight Asian sample populations. Europeans had a higher prevalence of the G allele than Asians (50.4% vs. 30.2%). Meta-analysis of the SUMO4 M55V polymorphism showed an association between T1D and the SUMO4 G allele in all study subjects (OR=1.236, 95% CI=1.112-1.373, p=7.9×10(-6)), and stratification by ethnicity indicated a highly significant association between the SUMO4 G allele and T1D in Asians (OR=1.303, 95% CI=1.169-1.452, p=1.78×10(-7)) and a marginal association with T1D in Europeans (OR=1.177, 95% CI=1.000-1.386, p=0.050). Furthermore, significant associations were found between the SUMO4 M55V polymorphism and T1D and all study subjects, Europeans, and Asians using the dominant model (OR=1.239, 95% CI=1.144-1.342, p=1.4×10(-8); OR=1.156, 95% CI=1.051-1.271, p=0.003; OR=1.461, 95% CI=1.262-1.691, p=3.8×10(-8), respectively).

CONCLUSIONS

This meta-analysis indicates that the SUMO4 M55V polymorphism confers susceptibility to T1D in Asians and Europeans.

Improving power of genome-wide association studies with weighted false discovery rate control and prioritized subset analysis

The issue of large-scale testing has caught much attention with the advent of high-throughput technologies. In genomic studies, researchers are often confronted with a large number of tests. To make simultaneous inference for the many tests, the false discovery rate (FDR) control provides a practical balance between the number of true positives and the number of false positives. However, when few hypotheses are truly non-null, controlling the FDR may not provide additional advantages over controlling the family-wise error rate (e.g., the Bonferroni correction). To facilitate discoveries from a study, weighting tests according to prior information is a promising strategy. A 'weighted FDR control' (WEI) and a 'prioritized subset analysis' (PSA) have caught much attention. In this work, we compare the two weighting schemes with systematic simulation studies and demonstrate their use with a genome-wide association study (GWAS) on type 1 diabetes provided by the Wellcome Trust Case Control Consortium. The PSA and the WEI both can increase power when the prior is informative. With accurate and precise prioritization, the PSA can especially create substantial power improvements over the commonly-used whole-genome single-step FDR adjustment (i.e., the traditional un-weighted FDR control). When the prior is uninformative (true disease susceptibility regions are not prioritized), the power loss of the PSA and the WEI is almost negligible. However, a caution is that the overall FDR of the PSA can be slightly inflated if the prioritization is not accurate and precise. Our study highlights the merits of using information from mounting genetic studies, and provides insights to choose an appropriate weighting scheme to FDR control on GWAS.

Approaches in type 1 diabetes research: A status report

Type 1 diabetes is a multifactorial disease with an early age of onset, in which the insulin producing beta cell of the pancreas are destroyed because of autoimmunity. It is the second most common chronic disease in children and account for 5% to 10% of all diagnosed cases of diabetes. India is having an incidence of 10.6 cases/year/100,000, and recent studies indicate that the prevalence of type 1 diabetes in India is increasing. However in view of poor health care network, there is no monitoring system in the country. Of the 18 genomic intervals implicated for the risk to develop type 1 diabetes, the major histocompatibility complex (MHC) region on chromosome 6p21.31 has been the major contributor estimated to account for 40-50%, followed by 10% frequency of INS-VNTR at 5' flanking region of the insulin gene on chromosome 11p15.5. However, population studies suggest that > 95% of type 1 diabetes have HLA-DR3 or DR4, or both, and in family studies, sibling pairs affected with type 1 diabetes have a non-random distribution of shared HLA haplotypes. As predisposing genetic factors such as HLA alleles are known, immunological interventions to prevent type 1 diabetes are of great interest. In the present study we have reviewed the status of molecular genetics of the disease and the approaches that need to be adopted in terms of developing patient and suitable control cohorts in the country.

Polymorphisms in the ADRB2 gene and Graves disease: a case-control study and a meta-analysis of available evidence

Background

The beta-2-Adrenergic receptor (ADRB2) gene on chromosome 5q33.1 is an important immunoregulatory factor. We and others have previously implicated chromosomal region 5q31-33 for contribution to the genetic susceptibility to Graves disease (GD) in East-Asian populations. Two recent studies showed associations between the single nucleotide polymorphism (SNP) rs1042714 in the ADRB2 gene and GD. In this study, we aimed to fully investigate whether the ADRB2 gene conferred susceptibility to GD in Chinese population, and to perform a meta-analysis of association between ADRB2 and GD.

Methods

Approximately 1 kb upstream the transcription start site and the entire coding regions of the ADRB2 gene were resequenced in 48 Han Chinese individuals to determine the linkage disequilibrium (LD) patterns. Tag SNPs were selected and genotyped in a case-control collection of 1,118 South Han Chinese subjects, which included 428 GD patients and 690 control subjects. A meta-analysis was performed with the data obtained in the present samples and those available from prior studies.

Results

Fifteen SNPs in the ADRB2 gene were identified by resequencing and one SNP was novel. Ten tag SNPs were investigated further to assess association of ADRB2 in the case-control collection. Neither individual tag SNP nor haplotypes showed association with GD in Han Chinese population (P > 0.05). Our meta-analysis of the ADRB2 SNP rs1042714 measured heterogeneity between the ethnic groups (I² = 53.1%) and no association to GD was observed in the overall three studies with a random effects model (OR = 1.13, 95% CI, 0.95 to 1.36; P = 0.18). However, significant association was found from the combined data of Caucasian population with a fixed effects model (OR = 1.18, 95% CI, 1.06 to 1.32; P = 0.002; I² = 5.9%).

Conclusion

Our study indicated that the ADRB2 gene did not exert a substantial influence on GD susceptibility in Han Chinese population, but contributed to a detectable GD risk in Caucasian population. This inconsistency resulted largely from between-ethnicity heterogeneity.

Characterization of a negative feedback network between SUMO4 expression and NFkappaB transcriptional activity

Previously, we have demonstrated evidence suggesting that SUMO4 negatively regulates NFkappaB transcriptional activity, probably through sumoylation of IkappaBalpha. Here, we present data indicating that SUMO4 possesses the capacity to conjugate to IkappaBalpha. Luciferase reporter assays in 3T3 cells deficient for IkappaBalpha further demonstrated that SUMO4 regulates NFkappaB signaling dependent on its sumoylation of IkappaBalpha. More importantly, a putative NFkappaB binding motif has been characterized within the SUMO4 promoter. Subsequent promoter reporter assays revealed that SUMO4 promoter with disrupted NFkappaB binding motif failed to response to NFkappaB specific IL-1beta stimulation. ChIP assays showed that NFkappaB binds to SUMO4 promoter and activates its transcription. Together, our data suggest that SUMO4 may act as a negative feedback regulator to prevent excessive activation of NFkappaB. Given the importance of NFkappaB signaling in immune response, SUMO4 could play a role to tightly control the potency of immune response to prevent autoimmunity.

Association of NFKB1 -94ins/del ATTG promoter polymorphism with susceptibility to and phenotype of Graves' disease

Recently, a functional polymorphism in the NFKB1 gene promoter (-94ins/del ATTG) has been identified and associated with chronic inflammatory diseases. The aim of this study was to analyze the association of NFKB1 polymorphism with susceptibility to and phenotype of Graves' disease (GD). The initial case-control association study, performed in a Polish-Warsaw cohort (388 GD patients and 688 controls), was followed by the two replication studies performed in Polish-Gliwice and Japanese-Kurume cohorts (198 GD patients and 194 controls, and 424 GD patients and 222 controls, respectively). The frequency of the -94del ATTG (D) allele was increased in GD compared to controls in Warsaw cohort. This finding was replicated in Gliwice cohort. Combining both Polish-Caucasian cohorts showed that the NFKB1 polymorphism was significantly associated with susceptibility to GD with a codominant mode of inheritance (P=0.00005; OR=1.37 (1.18-1.60)). No association with GD was found in Japanese cohort. However, subgroup analysis in Japanese GD patients revealed a correlation between the NFKB1genotype and the development of ophthalmopathy (P=0.009; OR=1.49 (1.10-2.01)), and the age of disease onset (P=0.009; OR=1.45 (1.09-1.91)). Our results suggest that NFKB1 -94ins/del ATTG polymorphism may be associated with susceptibility to and/or phenotype of GD.

Affinity chromatography of native SUMO proteins using His-tagged recombinant UBC9 bound to Co2+-charged talon resin

Four small ubiquitin-related modifier (SUMO) genes have been identified in humans. The recently identified SUMO4 was detected in mRNA transcripts from HEK293 cells, and human kidney and spleen tissue and may be involved in regulation of NF-kappaB and susceptibility to autoimmune diseases. However, identification and characterization of a native SUMO4 protein has not yet been reported. Here, we analyzed for the presence of native SUMO proteins in HEK293 cells and human kidney tissue using an affinity purification procedure using a UBC9 matrix followed by mass spectroscopy analyses for SUMO-specific peptides. Identification by mass spectroscopy of peptides generated by Trypsin and Lys-C digestion did reveal peptides unique to SUMO1 and SUMO2/3, but not SUMO4. In control experiments, SUMO4 prepared by recombinant methods was isolated and even enriched by our UBC9 affinity purification. Thus, SUMO4 protein appears to be either in extremely low abundance in human kidney or HEK293 cells or it is not present at all. It remains possible that SUMO4 protein is more abundant in other cell types or can be induced by hormonal or environmental challenges and the procedures reported here should be extremely useful for detecting native SUMO4. Furthermore, using His-tagged recombinant proteins bound to Co(2+)-charged Talon resin has general applicability to isolate native proteins that have strong non-covalent interactions with the resin-bound His-tagged proteins.