signature=26fcee8597bc04f12e7474ba8b9d4a54,Genetic variants at CDC123/CAMK1D and SPRY2 are associate...

In the present study, we identified significant associations between two variants (rs10906115 within CDC123/CAMK1D and rs1359790 near SPRY2) and susceptibility to type 2 diabetes in a Japanese population.

Recent advances in genotyping technology and accumulation of information about the human genome have facilitated GWAS worldwide, and nearly 40 susceptibility loci for type 2 diabetes have already been identified and confirmed in populations of European descent [1]. However, only ∼10% of type 2 diabetes heritability can be explained by those genetic loci [1]; thus, the majority of type 2 diabetes heritability genes remain unknown for these populations, and this applies even more so for populations not of European origin. By combining the present results with the original findings of Shu et al [9], rs10906115 and rs1359790 can now be considered to be convincing susceptibility loci for type 2 diabetes across different ethnic groups.

With regard to rs10906115 within the CDC123/CAMK1D locus, this SNP exists in the same linkage disequilibrium block as that for rs12779790, which was previously identified as a type 2 diabetes susceptibility SNP by European GWAS [16]. However, the linkage disequilibrium coefficient between rs10906115 and rs12779790 is low, as derived from genotype data from the present study (r

2 = 0.11), as well as from HapMap Japanese in Tokyo (JPT) (r

2 = 0.12), HapMap Han Chinese in Beijing, China (CHB) (r

2 = 0.05) and HapMap Centre d’Etude du Polymorphisme (Utah residents with northern and western European ancestry; CEU) (r

2 = 0.19) data (http://hapmap.ncbi.nlm.nih.gov/, accessed 22 June 2011). Using conditional analysis, we showed that rs10906115 was associated with type 2 diabetes independently of rs12779790, whereas the association between rs12779790 and type 2 diabetes (p = 0.036) was no longer significant after conditioning on rs10906115 in the present Japanese population; this confirms results previously reported by Shu et al. [9]. Thus, at least in East Asian populations, rs10906115 is likely to be linked more directly to true causal variation(s) involved in conferring susceptibility to type 2 diabetes.

However, in European populations rs10906115 did not show significant association with type 2 diabetes by itself (p = 0.11 in the Wellcome Trust Case Control Consortium/UK Type 2 Diabetes Genetics consortium [WTCCC/UKT2D][www.wtccc.org.uk/info/access_to_data_samples.shtml, accessed 14 December 2007], p = 0.5 in Diabetes Genetics Initiative [www.broadinstitute.org/diabetes/scandinavs/type2.html, accessed 27 January 2011]). Since conditional analysis for rs10906115 and rs12779790 has not been robustly performed in European populations, it is not clear whether the effects of these two SNPs on susceptibility to type 2 diabetes reflect the consequence of an identical causal variant, which is linked more closely to rs12779790 in European populations, or whether they are associated, independently of each other, with the disease. Fine-mapping of this locus among different ethnic groups including Asians and Europeans will be necessary to answer this question.

In the report by Shu et al., two additional SNPs showing modest associations with type 2 diabetes were identified, namely rs1436955 and rs10751301 (rs1436955 p = 7.14 × 10−7, rs10751301 p = 1.31 × 10−4) [9]. We therefore also examined the association between these two and type 2 diabetes in the Japanese. The variant rs1436955 is located in the C2CD4A/C2CD4B locus, which is a confirmed type 2 diabetes locus [4] and also associated with type 2 diabetes in the present Japanese population (OR 1.10, 95% CI 1.02, 1.19; p = 0.013 adjusted; Table 1). However, the association between rs1436955 and type 2 diabetes disappeared after conditioning on a previously reported variant, rs7172432 (p = 0.46; ESM Table 3). Since rs7172432 showed stronger association in the present population (p = 8.86 × 10−5; ESM Table 3) and the association remained significant even after conditioning on rs1436955, the association for rs1436955 is unlikely to be independent on the already confirmed signal. We did not observe a significant association between rs10751301 and type 2 diabetes in the Japanese population (OR 0.98, 95% CI 0.91, 1.05; p = 0.54 adjusted; Table 1). Although the present Japanese study had sufficient power to replicate the association reported previously (91% for α = 0.05), it cannot be completely ruled out that a small number of participants with impaired glucose tolerance were included in our control samples, as OGTTs were not always performed to select the control individuals, and this could have reduced the power of our study.

The mechanisms by which the variants evaluated contribute to susceptibility to type 2 diabetes are unknown. CDC123 and CAMK1D, both genes in the vicinity of rs10906115, encode a protein involved in cell cycle regulation [17] and a member of the Ca2+/calmodulin-dependent protein kinase 1 subfamily of serine threonine kinases [18], respectively. The variant rs1359790 is located 200 kb downstream of SPRY2, which encodes a protein belonging to the sprouty family and has been shown to inhibit growth factor-mediated, receptor tyrosine kinase-induced, mitogen-activated protein kinase signalling [19]. The roles of these genes in pancreatic beta cells or peripheral tissues involved in glucose metabolism have not yet been elucidated.

Impaired beta cell function in rs12779790 G allele carriers has been reported in European [20, 21] and Asian Indian populations. Grarup et al. reported that glucose-stimulated insulin secretion was decreased in homozygous carriers of rs12779790 G during OGTTs, without affecting fasting serum glucose or fasting serum insulin [20]. Simonis-Bik et al. also demonstrated a decreased second-phase insulin response in risk allele carriers during a 2-h hyperglycaemic clamp [21]. In Asian Indians, carriers of the rs12779790 G allele were shown to have decreased plasma insulin levels and lower HOMA-B [22], but these effects were more obvious in type 2 diabetes cases than in control participants.

We analysed the association of rs10906115 and rs1359790 with metabolic traits such as FPG, HOMA-IR and HOMA-B using control participants with no diabetes; however, we did not observe a significant correlation between the two variants and these metabolic traits, but our sample size might not have been large enough (ESM Table 5). Differences in study design and/or experimental procedures may underlie the discrepancy between the results of the present study and those of previous studies indicating an association between the CDC123/CAMK1D locus and quantitative traits related to glucose metabolism [20–22]. Further studies are required to clarify the precise mechanisms of how variants in these loci confer susceptibility to type 2 diabetes.

In conclusion, we identified a significant association of rs10906115 and rs1359790 with type 2 diabetes in a Japanese population, thus confirming a role for these loci in conferring susceptibility to type 2 diabetes across East Asian populations.