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

¹ Department of Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, I.R. Iran.
² Division of Clinical Biochemistry, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, University of Toronto, Ontario, Canada.
³ Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modarres University, Tehran, I.R. Iran.
⁴ Program in Genetics and Genomic Biology, Hospital for Sick Children, University of Toronto, Ontario, Canada.
⁵ Endocrinology and Metabolism Research Centre, Shariati Hospital, Tehran University of Medical Sciences, Tehran, I.R. Iran.
⁶ Department of Biochemistry, Institute Pasteur of Iran, Tehran, I.R. Iran.
⁷ Robarts Research Institute and University of Western Ontario, London, Ontario, Canada.

^aAddress correspondence to this author at: Division of Clinical Biochemistry, DPLM, Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8 Canada. Fax 416-813-6257; e-mail khosrow.adeli{at}sickkids.ca.

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.