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Tissue-specific alternative splicing of TCF7L2.

Prokunina-Olsson L, Welch C, Hansson O, Adhikari N, Scott LJ, Usher N, Tong M, Sprau A, Swift A, Bonnycastle LL, Erdos MR, He Z, Saxena R, Harmon B, Kotova O, Hoffman EP, Altshuler D, Groop L, Boehnke M, Collins FS, Hall JL - Hum. Mol. Genet. (2009)

Bottom Line: 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).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.GenBank Accession Numbers: FJ010164-FJ010174.

View Article: PubMed Central - PubMed

Affiliation: Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA. prokuninal@mail.nih.gov

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.

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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.
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DDP321F2: 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.

Mentions: First, we measured the mRNA expression of TCF7L2 using an assay that targeted exons 7 and 8 of the gene (assay ‘ex7–8’, Fig. 1), and detected signals in all human tissues tested (Supplementary Material, Table S1). When normalized to expression of two housekeeping genes, β2 microglobulin (B2M) and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), the highest levels of expression were found in pancreas, colon, brain, small intestine and peripheral blood monocytes. The lowest levels of expression were found in resting and activated peripheral blood T and B cells and lymphoblastoid cell lines (Fig. 2 and Supplementary Material, Table S1). Expression of TCF7L2, measured with the assay ‘ex7–8’ in 311 samples of pancreas, pancreatic islets, colon, liver, monocytes and subcutaneous adipose tissue from individuals without T2D, was not associated with genotypes of the two most strongly T2D-associated SNPs, rs7903146 and rs12255372 (Table 1). On the basis of the number of samples and standard deviation in expression of assays in each tissue tested, we estimated the detectable fold difference between the groups of samples carrying the risk and non-risk alleles (Table 1). In this analysis, we had 80% power (with a type I error rate of 5%) to detect a 1.13-fold difference in expression in colon, a 1.33-fold difference in liver, a 1.37-fold difference in monocytes, 2.06-fold in skeletal muscle, a 2.34-fold difference in pancreatic islets and a 2.87-fold difference in adipose tissue (Table 1).


Tissue-specific alternative splicing of TCF7L2.

Prokunina-Olsson L, Welch C, Hansson O, Adhikari N, Scott LJ, Usher N, Tong M, Sprau A, Swift A, Bonnycastle LL, Erdos MR, He Z, Saxena R, Harmon B, Kotova O, Hoffman EP, Altshuler D, Groop L, Boehnke M, Collins FS, Hall JL - Hum. Mol. Genet. (2009)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2748888&req=5

DDP321F2: 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.
Mentions: First, we measured the mRNA expression of TCF7L2 using an assay that targeted exons 7 and 8 of the gene (assay ‘ex7–8’, Fig. 1), and detected signals in all human tissues tested (Supplementary Material, Table S1). When normalized to expression of two housekeeping genes, β2 microglobulin (B2M) and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), the highest levels of expression were found in pancreas, colon, brain, small intestine and peripheral blood monocytes. The lowest levels of expression were found in resting and activated peripheral blood T and B cells and lymphoblastoid cell lines (Fig. 2 and Supplementary Material, Table S1). Expression of TCF7L2, measured with the assay ‘ex7–8’ in 311 samples of pancreas, pancreatic islets, colon, liver, monocytes and subcutaneous adipose tissue from individuals without T2D, was not associated with genotypes of the two most strongly T2D-associated SNPs, rs7903146 and rs12255372 (Table 1). On the basis of the number of samples and standard deviation in expression of assays in each tissue tested, we estimated the detectable fold difference between the groups of samples carrying the risk and non-risk alleles (Table 1). In this analysis, we had 80% power (with a type I error rate of 5%) to detect a 1.13-fold difference in expression in colon, a 1.33-fold difference in liver, a 1.37-fold difference in monocytes, 2.06-fold in skeletal muscle, a 2.34-fold difference in pancreatic islets and a 2.87-fold difference in adipose tissue (Table 1).

Bottom Line: 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).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.GenBank Accession Numbers: FJ010164-FJ010174.

View Article: PubMed Central - PubMed

Affiliation: Genome Technology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA. prokuninal@mail.nih.gov

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.

Show MeSH
Related in: MedlinePlus