TYK2 Promoter Variant and Diabetes Mellitus in the Japanese

BACKGROUND

Recently, natural mutation of Tyrosine kinase 2 (Tyk2) gene has been shown to determine susceptibility to murine virus-induced diabetes. In addition, a previous human genome-wide study suggested the type 1 diabetes (T1D) susceptibility region to be 19p13, where the human TYK2 gene is located (19p13.2).

METHODS

Polymorphisms of TYK2 gene at the promoter region and exons were studied among 331 healthy controls, and 302 patients with T1D and 314 with type 2 diabetes (T2D) in the Japanese.

FINDINGS

A TYK2 promoter haplotype with multiple genetic polymorphisms, which are in complete linkage disequilibrium, named TYK2 promoter variant, presenting decreased promoter activity, is associated with an increased risk of not only T1D (odds ratio (OR), 2.4; 95% confidence interval (CI), 1.2 to 4.6; P = 0.01), but also T2D (OR, 2.1; 95% CI, 1.1 to 4.1; P = 0.03). The risk is high in patients with T1D associated with flu-like syndrome at diabetes onset and also those without anti-glutamic acid decarboxylase autoantibody.

INTERPRETATION

The TYK2 promoter variant is associated with an overall risk for diabetes, serving a good candidate as a virus-induced diabetes susceptibility gene in humans.

FUNDING

Ministry of Education, Culture, Sports, Science and Technology and of Health, Labor and Welfare of Japan.

Genetic regulation of B cell receptor signaling pathway: Insights from expression quantitative trait locus analysis using a mixed model

The B cell receptor (BCR) signaling pathway regulates non-immune cellular response through various pathways like MAPK, NF-kB, and PI3K-Akt. This study aimed to identify expression quantitative trait loci (eQTL) and their regulatory functions on BCR signaling pathway genes. A mixed model was employed to analyze eQTL using RNA expression levels in lymphoblastoid from 376 Europeans in the GEUVADIS dataset. In total, 266 SNPs, including 115 cis-acting SNPs, were found for association with transcription of 13 genes (P < 5 × 10-8), revealing 19 independent signals for five genes through linkage disequilibrium analysis. Functional analysis, aligning them with DNase sensitive sites, transcription factor binding sites, histone modification, promoters/enhancers, CpG islands, and ChIA-PET, identified regulatory variants targeting SYK, VAV2, and PLCG2. Notably, rs2562397 was validated as a SYK promoter variant, and rs694505, rs636667, and rs4889409 were confirmed as enhancer variants for VAV2 and PLCG2. Their allelic differences in gene expression were also confirmed using ENCODE ChIP-seq and Sei neural network prediction. Persistent differential expression of these genes by alleles might impact the adaptive immune system, vascular development, and/or relevant diseases that have been previously associated with other variants of the genes. Comprehensive genetic architecture studies of the BCR signaling pathway, along with experiments demonstrating related mechanisms, will greatly contribute to understanding the underlying mechanisms of relevant disease development and implementing precision medicine.

Sequence analysis of the 5' region of the chymotrypsin C (CTRC) gene in chronic pancreatitis

BACKGROUND/OBJECTIVES

Loss-of-function chymotrypsin C (CTRC) variants increase the risk for chronic pancreatitis (CP) by reducing protective pancreatic CTRC activity. Variants in the 5' upstream region that includes the promoter might affect CTRC expression but have not been investigated to date. The aim of the present study was to address this knowledge gap.

METHODS

We analyzed ∼1.4 kb of the 5' region of the CTRC gene in 293 patients with chronic pancreatitis of alcoholic and non-alcoholic etiology and 402 controls from the Hungarian National Pancreas Registry by direct Sanger sequencing.

RESULTS

We identified 14 gene variants, which included 11 novel variants and 3 previously reported variants. When allele frequencies were considered, none of the variants were significantly overrepresented in CP cases or controls. Genotype distribution of the frequently occurring variant c.-913A>G showed a statistically significant enrichment of the homozygous GG genotype (versus the AA genotype) in CP cases versus controls (OR 1.67, 95 % CI 1.2-2.4, P 0.0053). However, the disease association was driven by the linkage disequilibrium with the known CTRC risk variant c.180C>T.

CONCLUSIONS

We found no significant association between variants in the 5' region of the CTRC gene and CP risk.