Polymorphisms within the Protein Tyrosine Phosphatase 1B (PTPN1) Gene Promoter: Functional Characterization and Association with Type 2 Diabetes and Related Metabolic Traits

Abstract

Abstract Background: Protein tyrosine phosphatase 1B (PTPN1) dephosphorylates insulin receptors and attenuates insulin signaling. Polymorphisms in the coding sequence of PTPN1 have been variably associated with type 2 diabetes (T2D). We hypothesized that variations within the PTPN1 promoter might contribute to the development of T2D and related metabolic traits. Methods: We screened 2.0 kb of PTPN1 promoter in 174 T2D patients and 412 controls using PCR and denaturing HPLC. Association analysis was performed between diabetes and related traits and single-nucleotide polymorphism genotypes. We functionally tested 2 variants (−1023C>A and −51delA) by measuring their influence on luciferase activity in HepG2 cells and performing the electrophoretic mobility shift assay (EMSA). Results: One common (−1023C>A) and 6 rare (−51delA, −451A>G, −467T>C, −1045G>A, −1286-3bp-del, and −1291-9bp-del) variants were identified in the PTPN1 promoter. The −1023(C) allele had significant association with T2D that disappeared after we adjusted for established diabetes risk factors. The alleles of −1023C>A and −51delA variants did not show significant effects on the biochemical markers after adjustment for established diabetes risk factors in the nondiabetic and diabetic groups separately. The −51delA variant decreased luciferase gene expression in HepG2 cells by 2-fold. EMSA revealed a weaker binding of −51delA to specific protein family proteins compared with the A allele. The −1023C>A variant had no influence in either experiment. Conclusions: The PTPN1 promoter variants −1023C>A and −51delA (which appears to be functional) were not associated with T2D or related traits in this study but must be investigated in a larger population to reveal any potential metabolic association.