The type 2 diabetes presumed causal variant within TCF7L2 resides in an element that controls the expression of ACSL5

Abstract

Aims/hypothesis One of the most strongly associated type 2 diabetes loci reported to date resides within the TCF7L2 gene. Previous studies point to the T allele of rs7903146 in intron 3 as the causal variant at this locus. We aimed to identify the actual gene(s) under the influence of this variant. Methods Using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease, we generated a 1.4 kb deletion of the genomic region harbouring rs7903146 in the HCT116 cell line, followed by global gene expression analysis. We then carried out a combination of circularised chromosome conformation capture (4C) and Capture C in cell lines, HCT116 and NCM460 in order to ascertain which promoters of these perturbed genes made consistent physical contact with this genomic region. Results We observed 99 genes with significant differential expression (false discovery rate [FDR] cut-off:10%) and an effect size of at least twofold. The subsequent promoter contact analyses revealed just one gene, ACSL5, which resides in the same topologically associating domain as TCF7L2. The generation of additional, smaller deletions (66 bp and 104 bp) comprising rs7903146 showed consistently reduced ACSL5 mRNA levels across all three deletions of up to 30-fold, with commensurate loss of acyl-CoA synthetase long-chain family member 5 (ACSL5) protein. Notably, the deletion of this single-nucleotide polymorphism region abolished significantly detectable chromatin contacts with the ACSL5 promoter. We went on to confirm that contacts between rs7903146 and the ACSL5 promoter regions were conserved in human colon tissue. ACSL5 encodes ACSL5, an enzyme with known roles in fatty acid metabolism. Conclusions/interpretation This 'variant to gene mapping' effort implicates the genomic location harbouring rs7903146 as a regulatory region for ACSL5.

An alternative effector gene at the type 2 diabetes-associated TCF7L2 locus?

“…Reported whole-body Acsl5 knockout mice show a consistent reduction in blood glucose levels [8,9] and improvements in insulin sensitivity [8]. In line with this, the study by Xia et al shows lower ACSL5 expression in the non-risk C allele compared with the type 2 diabetes risk-increasing T allele [6].These findings are also in agreement with previous observations in human islets, which demonstrate that the T allele confers greater enhancer activity at rs7903146 [10].…”

“…In the current issue of Diabetologia, Xia and colleagues [6] perform a series of state-of-the-art experiments to provide an alternative effector gene for the TCF7L2 locus, ACSL5. The authors deleted a 1.4 kb genomic region containing the variants most strongly associated with type 2 diabetes, in human intestinal epithelial cell lines.…”

“…Deleting the associated region resulted in a strong reduction of ACSL5 at both the mRNA and protein level, compared with control cells, and loss of enhancer-promoter interactions was detected in the chromatin capture assays. By generating two additional smaller CRISPR-Cas9-induced deletions, they went on to show that a 66 bp fragment, containing the most strongly associated variant (rs7903146) at the TCF7L2 locus, could recapitulate most of the regulatory effects observed within the 1.4 kb fragment [6].…”

Possible role of TCF7L2 in the pathogenesis of type 2 diabetes mellitus

“…Studies reported that better maintenance in glucose levels [20,21] and improvement in insulin sensitivity [20] in the whole-body ACSL5 knockout mice. Xia et al [22] found that a causal variant within TCF7L2 resides in an element that controls the expression of ACSL5 and speculated that TCF7L2 regulates ACSL5 expression. Given the correlation between ACSL5 and insulin sensitivity, inhibiting ACSL5 enzyme activity to treat T2DM could be promising.…”

Pharmacogenetics in type 2 diabetes: precision medicine or discovery tool?

“…Discovered in 2006 as a gene containing a common intronic variant with a relatively strong effect on type 2 diabetes risk [43], it was not until 2010 that fine-mapping and functional studies conclusively proved that the rs7903146 variant was causal in influencing TCF7L2 expression in islets [44], although a recent report suggests that it may act via another effector transcript [45]. Physiological studies in the DPP first demonstrated that this type 2 diabetes-associated variant diminishes beta cell function [46], but the precise molecular mechanisms by which the protein encoded by TCF7L2 (transcription factor 7-like 2 [TCF7L2]) does so have proven elusive.…”