A large-scale CRISPR screen reveals context-specific genetic regulation of retinal ganglion cell regeneration

• DOI: 10.1242/dev.202754
• Publication Date: 2024-07-15T10:57:40Z
• Authors: Kevin Emmerich; John Hageter; Thanh Hoang; Pin Lyu; Abigail V. Sharrock; Anneliese Ceisel; James Thierer; Zeeshaan Chunawala; Saumya Nimmagadda; Isabella Palazzo; Frazer Matthews; Liyun Zhang; David T. White; Catalina Rodriguez; Gianna Graziano; Patrick Marcos; Adam May; Tim Mulligan; Barak Reibman; Meera T. Saxena; David F. Ackerley; Jiang Qian; Seth Blackshaw; Eric Horstick; Jeff S. Mumm
• Keywords: Retinal Ganglion Cells; 0303 health sciences; Stem Cells; Zebrafish Proteins; Retina; Nerve Regeneration; Animals, Genetically Modified; 03 medical and health sciences; Basic Helix-Loop-Helix Transcription Factors; Animals; Regeneration; CRISPR-Cas Systems; Zebrafish; Research Article; Transcription Factors

ABSTRACT Many genes are known to regulate retinal regeneration after widespread tissue damage. Conversely, genes controlling regeneration after limited cell loss, as per degenerative diseases, are undefined. As stem/progenitor cell responses scale to injury levels, understanding how the extent and specificity of cell loss impact regenerative processes is important. Here, transgenic zebrafish enabling selective retinal ganglion cell (RGC) ablation were used to identify genes that regulate RGC regeneration. A single cell multiomics-informed screen of 100 genes identified seven knockouts that inhibited and 11 that promoted RGC regeneration. Surprisingly, 35 out of 36 genes known and/or implicated as being required for regeneration after widespread retinal damage were not required for RGC regeneration. The loss of seven even enhanced regeneration kinetics, including the proneural factors neurog1, olig2 and ascl1a. Mechanistic analyses revealed that ascl1a disruption increased the propensity of progenitor cells to produce RGCs, i.e. increased ‘fate bias’. These data demonstrate plasticity in the mechanism through which Müller glia convert to a stem-like state and context specificity in how genes function during regeneration. Increased understanding of how the regeneration of disease-relevant cell types is specifically controlled will support the development of disease-tailored regenerative therapeutics.