Single cell transcriptome profiling of developing chick retinal cells

Abstract

The vertebrate retina is a specialized photosensitive tissue comprised of six neuronal and one glial cell types, each of which develops in prescribed proportions at overlapping timepoints from a common progenitor pool. While each of these cells has a specific function contributing to proper vision in the mature animal, their differential representation in the retina as well as the presence of distinctive cellular subtypes makes identifying the transcriptomic signatures that lead to each retinal cell's fate determination and development challenging. We have analyzed transcriptomes from individual cells isolated from the chick retina throughout retinogenesis. While we focused our efforts on the retinal ganglion cells, our transcriptomes of developing chick cells also contained representation from multiple retinal cell types, including photoreceptors and interneurons at different stages of development. Most interesting was the identification of transcriptomes from individual mixed lineage progenitor cells in the chick as these cells offer a window into the cell fate decision-making process. Taken together, these data sets will enable us to uncover the most critical genes acting in the steps of cell fate determination and early differentiation of various retinal cell types.

Comprehensive analysis of retinal development at single cell resolution identifies NFI factors as essential for mitotic exit and specification of late-born cells

“…Previous large-scale expression profiling studies of retinal development have been limited in their scope owing to the use of bulk dissected material (Aldiri et al, 2017;Blackshaw et al, 2001;Blackshaw et al, 2004;Hoshino et al, 2017). Past single cell expression profiling studies in retina either analyzed only small numbers of cells (Laboissonniere et al, 2017;Mullally et al, 2016;Trimarchi et al, 2008), or profiled only mature cells in adult mice after fate specification (Macosko et al, 2015;Shekhar et al, 2016).…”

Reviewing guppy color vision: integrating the molecular and physiological variation in visual tuning of a classic system for sensory drive

“…Further work is needed to determine (1) which LWS opsin RH2-1 is co-expressed with (co-expression with LWS-3 would not change the cone λ max ), (2) whether there is co-expression of LWS-1 and LWS-3 , and (3) the frequency of cells co-expressing RH2-1 / LWS versus LWS-1 / LWS-3 opsins. In light of the limitations in distinguishing opsin alleles with FISH probes, we suggest future work use single cell based methods for quantifying gene expression in the retina, such as single cell qPCR or single cell transcriptomics ( Enright et al 2015a ; Macosko et al 2015 ; Laboissonniere et al 2017 ).…”

A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

“…The first studies to understand the gene expression profiles of individual retinal cells relied on manual isolation of individual cells and transcriptional profiling by qRT-PCR or microarray analysis ( Cherry et al, 2009 ; Kim et al, 2008 ; Laboissonniere et al, 2017a , 2019 ; Mizeracka et al, 2013 ; Mullally et al, 2016 ; Roesch et al, 2008 , 2012 , Trimarchi et al, 2007 , 2008 ). These studies provided the first comprehensive insights into the cellular specificity of gene expression.…”