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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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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.
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DDP321F5: 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.

Mentions: We designed 13 expression assays (Fig. 4) that targeted the majority of the TCF7L2 splicing forms, we observed in human tissues. Expression of these assays was quantified in samples from pancreas, pancreatic islets, colon, liver, monocytes, skeletal muscles, subcutaneous adipose tissue and lymphoblastoid cell lines. Expression of an alternative exon 13b (assay ‘ex13–13b’) was detected only in pancreatic islets, pancreas and colon and this assay was not used in the analysis that included all tissue samples. The expression of assay ‘ex4–4a’ was low in all tissues and was not studied further. Supplementary Material, Fig. S1 illustrates the diversity in expression of each assay in human tissues. We performed Principal Component Analysis (PCA) on samples from eight tissues using four sets of expression assays (Fig. 5A–D). We observed better discrimination between pancreatic islets and other tissues based on expression of assays for C-terminal alternative exons 12, 13, 13a and 14 of TCF7L2 (Fig. 5C) than those of assays detecting the N-terminal exons (Fig. 5A and B) or all expression assays together (Fig. 5D and Supplementary Material, Table S4 for relative expression of each splicing form in human tissues).


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)

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

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

DDP321F5: 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.
Mentions: We designed 13 expression assays (Fig. 4) that targeted the majority of the TCF7L2 splicing forms, we observed in human tissues. Expression of these assays was quantified in samples from pancreas, pancreatic islets, colon, liver, monocytes, skeletal muscles, subcutaneous adipose tissue and lymphoblastoid cell lines. Expression of an alternative exon 13b (assay ‘ex13–13b’) was detected only in pancreatic islets, pancreas and colon and this assay was not used in the analysis that included all tissue samples. The expression of assay ‘ex4–4a’ was low in all tissues and was not studied further. Supplementary Material, Fig. S1 illustrates the diversity in expression of each assay in human tissues. We performed Principal Component Analysis (PCA) on samples from eight tissues using four sets of expression assays (Fig. 5A–D). We observed better discrimination between pancreatic islets and other tissues based on expression of assays for C-terminal alternative exons 12, 13, 13a and 14 of TCF7L2 (Fig. 5C) than those of assays detecting the N-terminal exons (Fig. 5A and B) or all expression assays together (Fig. 5D and Supplementary Material, Table S4 for relative expression of each splicing form in human tissues).

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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Related in: MedlinePlus