Single-Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [RNA-Seq]

Retinal ganglion cells (RGCs) are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not regenerate after injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC survival after injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals, zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection (ONT) using isl2b:eGFP transgenic fish line, single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3, a cell population having progenitor and regenerative identity. Nine bulk RNA-seq libraries were prepared from FACS-purified retinal ganglion cells (RGC) from pooled tissue from nine sets of adult zebrafish: three libraries from injured tissue after optic nerve transection at each of 3 timepoints: 1, 5, and 7 days post-injury (dpi), and three from uninjured tissue on the same days.