PTPN2 deficiency amplifies interferon signaling and impairs functional maturation of human stem cell-derived islets [ATAC-Seq]

Background: Protein tyrosine phosphatases (PTPs) play key roles in b-cell function and diabetes development. PTPN2 is a candidate gene for type 1 diabetes (T1D) that negatively regulates the JAK/STAT signaling. However, the impact of PTPN2 deficiency on the differentiation and functionality of human stem cell-derived somatic metabolic cells remains unclear. Methods: PTPN2 expression in b cells from T1D organ donors and during the differentiation of human stem cell-derived islets (SC-islets) was evaluated in single-cell RNA-Sequencing data. Moreover, we differentiated CRISPR-Cas12a genome-edited PTPN2-deficient H1 human embryonic stem cells (H1-hESCs) into SC-islets, and sc RNA-Seq was performed. The maturation and functionality PTPN2 deficient SC-islets were assessed by implantation under the kidney capsule of NOD-SCID mice. Results: scRNA-Seq analysis showed that PTPN2 expression was increased in b cells from recently diagnosed T1D and decreased in long-standing T1D organ donors, compared with controls. Conversely, we found that PTPN2 expression was decreased at early stages of SC-islet differentiation and reconstituted at later stages, suggesting a developmental dynamic. CRISPR/Cas12-mediated gene editing was used to generate PTPN2-knockout human embryonic stem cells. PTPN2 deficiency exacerbated interferon-induced inflammatory signaling in stem cells and differentiated somatic metabolic cells. Interestingly, PTPN2 deficiency increased hedgehog signaling and reduced SC-islet differentiation efficiency in vitro. In addition, PTPN2-knockout SC-islets exhibited reduced glycemic control after implantation in vivo, mediated by reduced cell endocrine identity and enhanced interferon signaling. Conclusions: Our study postulates a key role of PTPN2 in preserving b-cell function during inflammatory and metabolic stress in SC-islets.