Identification of potential transcription factors that enhance human iPSC generation

Nuha T Swaidan,Sara A Abdulla,Mohamed M Emara,Ahmed T Aboughalia,Abdul Haseeb S Wali,Khaoula Errafii,Nada H Soliman,Freshteh Palangi,Salam Salloum-Asfar

doi:10.1038/s41598-020-78932-9

Nuha T Swaidan, Sara A Abdulla + Show 7 more

Open Access

https://doi.org/10.1038/s41598-020-78932-9

Copy DOI

Abstract

Although many factors have been identified and used to enhance the iPSC reprogramming process, its efficiency remains quite low. In addition, reprogramming efficacy has been evidenced to be affected by disease mutations that are present in patient samples. In this study, using RNA-seq platform we have identified and validated the differential gene expression of five transcription factors (TFs) (GBX2, NANOGP8, SP8, PEG3, and ZIC1) that were associated with a remarkable increase in the number of iPSC colonies generated from a patient with Parkinson's disease. We have applied different bioinformatics tools (Gene ontology, protein–protein interaction, and signaling pathways analyses) to investigate the possible roles of these TFs in pluripotency and developmental process. Interestingly, GBX2, NANOGP8, SP8, PEG3, and ZIC1 were found to play a role in maintaining pluripotency, regulating self-renewal stages, and interacting with other factors that are involved in pluripotency regulation including OCT4, SOX2, NANOG, and KLF4. Therefore, the TFs identified in this study could be used as additional transcription factors that enhance reprogramming efficiency to boost iPSC generation technology.

Highlights

Parkinson’s diseases (PD), which is generated as a result of the abnormal aggregation of alpha synuclein (α-syn) protein[16]
As some mutations associated with human diseases have been found to affect reprogramming efficiency[15], we tested the effect of A53T PD mutation on induced pluripotent stem cells (iPSCs) reprogramming
All fibroblast samples were transduced with reprogramming vectors and the morphological changes associated with iPSC generation were assessed

Summary

Introduction

Parkinson’s diseases (PD), which is generated as a result of the abnormal aggregation of alpha synuclein (α-syn) protein[16]. Α-syn point mutation (A53T) is considered the most frequent (~ 85%) and wellstudied form, expressing high levels of pathogenicity and significantly increasing disease progression[17,18]. Beside these familial cases reported, sporadic ones that represent the majority of PD cases (90%)[19] and occur randomly without a clear or definite cause, have remarkably displayed the pathological forms of α-syn[16]. We report a set of genes that were differentially expressed in generated iPSCs despite the presence or absence of disease associated mutation. We provide evidence that those factors may be crucial in maintaining pluripotency and regulating self-renewal stages and could be used as pluripotency transcription factors for iPSC generation

Objectives

Methods

Results

Conclusion