Association of the Cytotoxic T Lymphocyte-Associated Antigen 4 Gene with Type 1 Diabetes: Evidence for Independent Effects of Two Polymorphisms on the Same Haplotype Block

• Published in: The journal of clinical endocrinology and metabolism 2004-12, Vol.89 (12), p.6257-6265
• Main Authors: Anjos, Suzana M., Tessier, Marie-Catherine, Polychronakos, Constantin
• Format: Article
• Language: English
• Subjects: Alleles; Antigens, CD; Antigens, Differentiation - genetics; Antigens, Differentiation - metabolism; Biological and medical sciences; Conserved Sequence; CTLA-4 Antigen; Diabetes Mellitus, Type 1 - genetics; DNA-Binding Proteins - genetics; Endocrinopathies; Fundamental and applied biological sciences. Psychology; Haplotypes; Heterozygote; Homozygote; Humans; Jurkat Cells; Linkage Disequilibrium; Lymphocytes - metabolism; Lymphoid Enhancer-Binding Factor 1; Medical sciences; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Promoter Regions, Genetic; Transcription Factors - genetics; Transcription, Genetic; Vertebrates: endocrinology
• ISSN: 0021-972X; 1945-7197
• DOI: 10.1210/jc.2004-0881

A recent study mapped the known association of type 1 diabetes with the cytotoxic T lymphocyte-associated antigen 4 gene to a polymorphism at the 3′end (+6230G>A), but could not rule out additional contribution from the 5′ end of the gene. To examine this possibility, we analyzed four polymorphisms at the 5′-flanking region for effects independent of +6230G>A. We confirm, by the transmission disequilibrium test, in 496 family trios overtransmission of the susceptibility allele (G) at +6230 (217/168; P = 0.013). Of the four promoter polymorphisms, one (−319C>T) showed overtransmission of the C allele (97/58; P = 0.0017). Because the undertransmitted T at the promoter is in linkage disequilibrium with the overtransmitted G at +6230G>A, the effect observed at the promoter cannot be accounted for by linkage disequilibrium with the +6230G>A. We confirm this by showing that parents heterozygous at the promoter but homozygous at +6230 overtransmit the C promoter allele even more significantly (53/24; P = 9 × 10−4). In vitro, the T promoter allele directs higher luciferase expression in Jurkat cells by 42% (P = 0.006), a difference also found in lymphocyte mRNA from eight individuals heterozygous at the promoter, but homozygous at +6230 (P = 1.3 × 10−4). Thus, the +6230G>A cannot be the sole functional variant. Either the two polymorphisms define a haplotype carrying the (yet unexamined) functional variant or the −319C>T contributes to the genetic association independently, a possibility suggested by the functional evidence we present.