Single nucleotide polymorphism and promoter methylation analysis of protein tyrosine phosphatase 1B in patients with myeloproliferative neoplasms.

Abstract

Background: The recurrent somatic mutations in genes such as Janus kinase 2 (JAK2) lead to cytokine-independent activation of the JAK-signal transducer and activator of transcription (STAT) pathway, a crucial factor in the development of classic myeloproliferative neoplasms (cMPNs). Protein tyrosine phosphatase 1B (PTP1B) is a significant regulator in this pathway, while the single nucleotide polymorphism (SNP) and promoter methylation profiles of the PTP1B gene in cMPN patients have largely remained unexplored. Therefore, to further explore the SNP and promoter methylation profiles of the PTP1B gene in cMPNs, we conducted a comprehensive SNP analysis of the PTP1B gene as well as the methylation status detection of the PTP1B promoter between cMPN patients and healthy controls.

Methods: Bone marrow (BM) biopsies were collected from a cohort comprising 96 cMPN patients and 50 healthy controls. SNP-specific extension primers were utilized to facilitate single base extension at the SNP site. A MALDI-TOF mass spectrometer and MassARRAY Typer software were used to detected the SNP. The incidence of SNPs within PTP1B were calculated in cMPN patients and healthy controls. The promoter region of the PTP1B gene were amplified and methylation Bisulfite amplicon sequencing (BSAS) analysis were performed, MethylKIT software was utilized to analyzed the methylation levels at each CpG site of PTP1B. Visualization of data was facilitated using the Methylation Plotter software. Statistical analysis of methylation was performed using the Kruskal-Wallis test. Differences of methylation at PTP1B gene sites were analyzed by Kruskal-Wallis test. P values <0.05 were considered to be statistically significant.

Results: Our findings revealed seven coding-region SNPs, including a novel variant (g.50579818T>A). Additionally, we identified aberrant hypermethylation and hypomethylation of several CpG islands within the PTP1B gene. Notably, the incidence of SNPs was significantly different between cMPN patients and healthy controls, and the methylation level of the PTP1B promoter was markedly elevated in cMPN samples compared to healthy controls.

Conclusions: In this study, we identified a novel SNP and observed differences in the frequency of seven SNPs and hypermethylation of PTP1B promoters between cMPN patients and normal controls. These results suggest that the PTP1B gene might play a critical role in the pathogenesis of cMPNs. Further research exploring more mechanism and larger sample is warranted to fully elucidate the specific role of PTP1B in cMPNs.