title: Association of two synonymous splicing-associated CpG single nucleotide polymorphisms in calpain 10 and solute carrier family 2 member 2 with type 2 diabetes.
abstract: Coding synonymous single nucleotide polymorphisms (SNPs) have attracted little attention until recently. However, such SNPs located in epigenetic, CpG sites modifying exonic splicing enhancers (ESEs) can be informative with regards to the recently verified association of intragenic methylation and splicing. The present study describes the association of type 2 diabetes (T2D) with the exonic, synonymous, epigenetic SNPs, rs3749166 in calpain 10 (CAPN10) glucose transporter (GLUT4) translocator and rs5404 in solute carrier family 2, member 2 (SLC2A2), also termed GLUT2, which, according to prior bioinformatic analysis, strongly modify the splicing potential of glucose transport-associated genes. Previous association studies reveal that only rs5404 exhibits a strong negative T2D association, while data on the CAPN10 polymorphism are contradictory. In the present study DNA from blood samples of 99 Greek non-diabetic control subjects and 71 T2D patients was analyzed. In addition, relevant publicly available cases (40) resulting from examination of 110 Personal Genome Project data files were analyzed. The frequency of the rs3749166 A allele, was similar in the patients and non-diabetic control subjects. However, AG heterozygotes were more frequent among patients (73.24% for Greek patients and 54.55% for corresponding non-diabetic control subjects; P=0.0262; total cases, 52.99 and 75.00%, respectively; P=0.0039). The rs5404 T allele was only observed in CT heterozygotes (Greek non-diabetic control subjects, 39.39% and Greek patients, 22.54%; P=0.0205; total cases, 34.69 and 21.28%, respectively; P=0.0258). Notably, only one genotype, heterozygous AG/CC, was T2D-associated (Greek non-diabetic control subjects, 29.29% and Greek patients, 56.33%; P=0.004; total cases, 32.84 and 56.58%, respectively; P=0.0008). Furthermore, AG/CC was strongly associated with very high (≥8.5%) glycosylated plasma hemoglobin levels among patients (P=0.0002 for all cases). These results reveal the complex heterozygotic SNP association with T2D, and indicate possible synergies of these epigenetic, splicing-regulatory, synonymous SNPs, which modify the splicing potential of two alternative glucose transport-associated genes.
authors.affiliation: Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; Department of Endocrinology, Diabetes and Metabolism, Panagia General Hospital, Thessaloniki 55132, Greece.
authors.forename: Maria
authors.initials: M
authors.lastname: Karambataki
authors.affiliation: Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
authors.forename: Andigoni
authors.initials: A
authors.lastname: Malousi
authors.affiliation: Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Tzimagiorgis
authors.affiliation: Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
authors.forename: Constantinos
authors.initials: C
authors.lastname: Haitoglou
authors.affiliation: Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
authors.forename: Aikaterini
authors.initials: A
authors.lastname: Fragou
authors.affiliation: Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
authors.forename: Elisavet
authors.initials: E
authors.lastname: Georgiou
authors.affiliation: Department of Endocrinology, Diabetes and Metabolism, Panagia General Hospital, Thessaloniki 55132, Greece.
authors.forename: Foteini
authors.initials: F
authors.lastname: Papadopoulou
authors.affiliation: Department of Endocrinology, Diabetes and Metabolism, Panagia General Hospital, Thessaloniki 55132, Greece.
authors.forename: Gerasimos E
authors.initials: GE
authors.lastname: Krassas
authors.affiliation: Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
authors.forename: Sofia
authors.initials: S
authors.lastname: Kouidou
keywords: CAPN10; HbA1c; SLC2A2; bioinformatics analysis; family history; heterozygosity; synonymous CpG polymorphisms