Identification of candidate PAX2-regulated genes implicated in human kidney development

Yuta Yamamura,Shigeki Hirabayashi,Keisuke Okita,Yasuhiro Murakawa,Yasunori Iwata,Takashi Wada,Atsushi Tajima,Norihiko Sakai,Shuichi Kaneko,Shinji Kitajima,Kengo Furuichi,Masahito Yoshihara,Keisuke Sako,Kazuyoshi Hosomichi,Philip M Murphy,Kenji Osafune,Tadashi Toyama

doi:10.1038/s41598-021-88743-1

Abstract

PAX2 is a transcription factor essential for kidney development and the main causative gene for renal coloboma syndrome (RCS). The mechanisms of PAX2 action during kidney development have been evaluated in mice but not in humans. This is a critical gap in knowledge since important differences have been reported in kidney development in the two species. In the present study, we hypothesized that key human PAX2-dependent kidney development genes are differentially expressed in nephron progenitor cells from induced pluripotent stem cells (iPSCs) in patients with RCS relative to healthy individuals. Cap analysis of gene expression revealed 189 candidate promoters and 71 candidate enhancers that were differentially activated by PAX2 in this system in three patients with RCS with PAX2 mutations. By comparing this list with the list of candidate Pax2-regulated mouse kidney development genes obtained from the Functional Annotation of the Mouse/Mammalian (FANTOM) database, we prioritized 17 genes. Furthermore, we ranked three genes—PBX1, POSTN, and ITGA9—as the top candidates based on closely aligned expression kinetics with PAX2 in the iPSC culture system and susceptibility to suppression by a Pax2 inhibitor in cultured mouse embryonic kidney explants. Identification of these genes may provide important information to clarify the pathogenesis of RCS, human kidney development, and kidney regeneration.

Highlights

PAX2 is a transcription factor essential for kidney development and the main causative gene for renal coloboma syndrome (RCS)
PAX2 is one of the key disease genes that are defective in renal coloboma syndrome (RCS)[4,5], which is characterized by kidney hypoplasia or dysplasia and optic nerve dysplasia
To identify candidate genes regulated by PAX2 during human kidney development, we performed comprehensive transcriptome analysis of nephrons developing in vitro from induced pluripotent stem cells (iPSCs) from patients with RCS and healthy donors by cap analysis of gene expression (CAGE)

Summary

Introduction

PAX2 is a transcription factor essential for kidney development and the main causative gene for renal coloboma syndrome (RCS). We ranked three genes—PBX1, POSTN, and ITGA9— as the top candidates based on closely aligned expression kinetics with PAX2 in the iPSC culture system and susceptibility to suppression by a Pax[2] inhibitor in cultured mouse embryonic kidney explants Identification of these genes may provide important information to clarify the pathogenesis of RCS, human kidney development, and kidney regeneration. 189 promoters and 71 enhancers, especially three influential candidate genes, which are conserved in mice and humans, were detected This knowledge provides new clues for a deeper understanding of PAX2-associated biology in humans, including the molecular pathogenesis of RCS, and mechanisms of human kidney development and r egeneration[12,13]

Methods

Results

Conclusion