Tissue-specific alternative splicing of TCF7L2

Abstract

Common variants in the transcription factor 7-like 2 (TCF7L2) gene have been identified as the strongest genetic risk factors for type 2 diabetes (T2D). However, the mechanisms by which these non-coding variants increase risk for T2D are not well-established. We used 13 expression assays to survey mRNA expression of multiple TCF7L2 splicing forms in up to 380 samples from eight types of human tissue (pancreas, pancreatic islets, colon, liver, monocytes, skeletal muscle, subcutaneous adipose tissue and lymphoblastoid cell lines) and observed a tissue-specific pattern of alternative splicing. We tested whether the expression of TCF7L2 splicing forms was associated with single nucleotide polymorphisms (SNPs), rs7903146 and rs12255372, located within introns 3 and 4 of the gene and most strongly associated with T2D. Expression of two splicing forms was lower in pancreatic islets with increasing counts of T2D-associated alleles of the SNPs: a ubiquitous splicing form (P = 0.018 for rs7903146 and P = 0.020 for rs12255372) and a splicing form found in pancreatic islets, pancreas and colon but not in other tissues tested here (P = 0.009 for rs12255372 and P = 0.053 for rs7903146). Expression of this form in glucose-stimulated pancreatic islets correlated with expression of proinsulin (r(2) = 0.84-0.90, P < 0.00063). In summary, we identified a tissue-specific pattern of alternative splicing of TCF7L2. After adjustment for multiple tests, no association between expression of TCF7L2 in eight types of human tissue samples and T2D-associated genetic variants remained significant. Alternative splicing of TCF7L2 in pancreatic islets warrants future studies. GenBank Accession Numbers: FJ010164-FJ010174.

Figure 1.

Location of expression assay ‘ex7–8’ and associated LD block with SNPs rs7903146 and rs12255372 within TCF7L2 gene, exons are marked as black rectangles.

Figure 2.

Expression of assay ‘ex7–8’ of TCF7L2 in human tissues as fold difference compared with expression level in pancreas. TCF7L2 expression is normalized to the levels of endogenous controls B2M and GAPDH (Supplementary Material, Table S1). Each tissue is represented by 1 or 2–3 pooled samples.

Figure 3.

Structure of the N-terminal part of TCF7L2: location of the β-catenin binding domain encoded by exons 1 and 2, and a T2D-associated LD block with SNPs rs7903146 and rs12255372. Shown: constitutive exons—black rectangles, alternative exons—white rectangles; alternative transcription starts sites TSS1, TSS2 and TSS3—arrows, potential translation starts—‘ATG’.

Figure 4.

Location of TaqMan expression assays within TCF7L2 gene. Shown: constitutive exons—black rectangles, alternative exons—white rectangles, expression assays—connected arrows.

Figure 5.

PCA in 289 samples from 8 human tissues. (A) PCA based on three N-terminal expression assays of TCF7L2: ‘TSS1’, TSS2’ and ‘ex7–8’. (B) PCA based on five N-terminal expression assays for TCF7L2: ‘TSS1’, ‘TSS2’, ‘TSS3’, ‘ex3a’ and ‘ex7–8’. (C) PCA based on six C-terminal expression assays for TCF7L2: ‘ex11–13’, ‘ex11–13a’, ‘ex11–14’, ‘ex12–13’, ‘ex13–13a’ and ‘ex13–14’. (D) PCA based on all eleven expression assays for TCF7L2.

Figure 6.

Expression of assay ‘ex13–13b’ in human pancreatic islets by rs12255372 and rs7903146 genotypes. Normalized expression of assay ‘ex13–13b’ is shown in Log 2 scale relative to a mean value of the whole set. Association was tested with univariate linear regression under an additive genetic model for SNPs and with adjustment for two sample sets.