Transcriptomic profiling of human iPSC-derived Schwann-like cells reveals NF2-regulated gene regulatory networks

Abstract

Schwann cells are vital to development and maintenance of the peripheral nervous system, and their dysfunction has been implicated in a range of neurological and neoplastic disorders, including NF2 -related schwannomatosis ( NF2 -SWN). We have developed a human induced pluripotent stem cells (hiPSCs) model for the study of Schwann-like cell differentiation in health and disease. We performed sequence-based transcriptomics, immunofluorescence-based morphological analysis, and CRISPR-Cas9-based validation of differentiation from hiPSCs derived Schwann cell precursors (SCPs) to terminally differentiated Schwann-like cells (SLCs) representing 6 distinct stages of development across a period of 31 days. To further validate our findings, we performed integrated, cross-species analyses at bulk and single cell resolution. Our hiPSCs model of Schwann cell development shared overlapping gene expression signatures with human amniotic mesenchymal stem cell (hAMSCs) derived SLCs and in vivo mouse models but also revealed unique features that may reflect species-specific aspects of Schwann cell biology. Moreover, we have identified gene co-expression modules that are dynamically regulated during hiPSCs to SLCs differentiation associated with ear and neural development, cell fate determination, the NF2 gene, and extracellular matrix (ECM) organization. Through integrated analysis of multiple datasets and genetic disruption of NF2 via CRISPR-Cas9 gene editing in hiPSC derived SCPs, we have identified transcriptomic signatures suggesting a series of novel ECM associated genes potentially regulated by Merlin, providing a hypothesis-generating framework for future functional studies. The hiPSC model generated in this study further provides a system for studying NF2-regulated gene expression throughout Schwann-like cell development in the context of widely available data on iPSC Schwann cells and rare diseases that lack effective treatments such as NF2 -SWN.