Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids.
Melissa K JonesDevansh AgarwalKevin W MazoManan ChopraShawna L JurlinaNicholas DashQianlan XuAnna R OgataMelissa ChowAlex D HillNetra K KambliGuorong XuRoman SasikAmanda BirminghamKathleen M FischRobert N WeinrebRay A EnkeDorota Skowronska-KrawczykKarl J WahlinPublished in: Cells (2022)
Retinogenesis involves the specification of retinal cell types during early vertebrate development. While model organisms have been critical for determining the role of dynamic chromatin and cell-type specific transcriptional networks during this process, an enhanced understanding of the developing human retina has been more elusive due to the requirement for human fetal tissue. Pluripotent stem cell (PSC) derived retinal organoids offer an experimentally accessible solution for investigating the developing human retina. To investigate cellular and molecular changes in developing early retinal organoids, we developed SIX6-GFP and VSX2-tdTomato (or VSX2-h2b-mRuby3) dual fluorescent reporters. When differentiated as 3D organoids these expressed GFP at day 15 and tdTomato (or mRuby3) at day 25, respectively. This enabled us to explore transcriptional and chromatin related changes using RNA-seq and ATAC-seq from pluripotency through early retina specification. Pathway analysis of developing organoids revealed a stepwise loss of pluripotency, while optic vesicle and retina pathways became progressively more prevalent. Correlating gene transcription with chromatin accessibility in early eye field development showed that retinal cells underwent a clear change in chromatin landscape, as well as gene expression profiles. While each dataset alone provided valuable information, considering both in parallel provided an informative glimpse into the molecular nature eye development.
Keyphrases
- diabetic retinopathy
- induced pluripotent stem cells
- optic nerve
- transcription factor
- gene expression
- optical coherence tomography
- genome wide
- single cell
- endothelial cells
- rna seq
- stem cells
- dna damage
- early stage
- pluripotent stem cells
- dna methylation
- healthcare
- single molecule
- mesenchymal stem cells
- squamous cell carcinoma
- induced apoptosis
- copy number
- oxidative stress
- signaling pathway
- multidrug resistant
- cell death
- heat shock
- social media
- cell fate
- quantum dots