Cross-species transcriptomic and epigenomic analysis reveals key regulators of injury response and neuronal regeneration in vertebrate retinas

Abstract

Purpose : To comprehensively profile changes in transcriptomes and chromatin conformation associated with injury response and neuronal reprograming in Müller glia (MG) from species with dramatically different regenerative capacities.

Methods : We performed an integrated comparative analysis using bulk and single-cell RNA-Seq data in combination with bulk ATAC-Seq data in zebrafish, chick and mouse. We sequenced over 100 total RNA-Seq and 40 ATAC-Seq of Müller glia samples at multiple time points under two different retinal injury models (NMDA damage and light damage). In parallel, we conducted scRNA-Seq analysis of whole retinas for the same time points as used for the bulk RNA-Seq following either NMDA or light damage in zebrafish and mouse. In addition, we profiled multiple timepoints during zebrafish retinal development, P10 chick retina both before and at multiple time points after NMDA injury, and in zebrafish at multiple time points following treatment with TNFalpha and the gamma secretase inhibitor RO4929097,which induces MG reprogramming independent of neuronal injury. In total, we profiled 287,790 single cells across all these conditions.

Results : We found that MG in all three species pass through a state resembling reactive gliosis but differs considerably in its duration. Zebrafish MG undergo a very transient gliotic state and quickly move to neurogenesis after retinal damages, while these processes are relatively slower in chick MG. In contrast, mouse MG arrest in gliosis, before rapidly returning to a transcriptional state that closely resembles resting MG. Our integrated analysis identified evolutionarily conserved and species-specific gene regulatory networks that control glial quiescence, gliosis, proliferation and neurogenic competence in MG among the three species. In zebrafish and chick, transition from quiescence to gliosis is a critical stage in acquisition of retinal regeneration, while in mice a dedicated network suppresses this transition and rapidly restores quiescence. Selective disruption of NFI family transcription factors, which maintain and restore quiescence, enables Müller glia to proliferate and robustly generate neurons in adult mice following retinal injury.

Conclusions : These comprehensive resources and findings may facilitate the design of cell-based therapies aimed at restoring retinal neurons lost to degenerative disease.

This is a 2020 ARVO Annual Meeting abstract.