Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids

Abstract

Retinal organoids (ROs) derived from human induced pluripotent stem cells (hiPSCs) provide potential opportunities for studying human retinal development and disorders; however, to what extent ROs recapitulate the epigenetic features of human retinal development is unknown. In this study, we systematically profiled chromatin accessibility and transcriptional dynamics over long-term human retinal and RO development. Our results showed that ROs recapitulated the human retinogenesis to a great extent, but divergent chromatin features were also discovered. We further reconstructed the transcriptional regulatory network governing human and RO retinogenesis in vivo. Notably, NFIB and THRA were identified as regulators in human retinal development. The chromatin modifications between developing human and mouse retina were also cross-analyzed. Notably, we revealed an enriched bivalent modification of H3K4me3 and H3K27me3 in human but not in murine retinogenesis, suggesting a more dedicated epigenetic regulation on human genome.

Pluripotent stem cell-derived retinal organoids for disease modeling and development of therapies

“…Expression levels of retinal genes, however, varied considerably among retinal organoids from different iPSCs lines 23,36 . Transcriptional profiling alone 21,23,32,36 or in combination with open chromatin analysis 37 revealed similarities to human eye development with stage 1 showing early neurogenesis and retinal progenitor gene signatures, followed by interneuron and synaptogenesis‐related gene expression in stage 2 and, finally, photoreceptor differentiation and maturation prominent in stage 3. These studies highlighted broad similarities of organoids to developing native retina tissue, despite protocol differences, based on light microscopy and/or transcriptome‐based staging.…”

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

“…In 2018, scATAC-seq was applied to cluster cells at different stages of mouse forebrain development and used to identify key regulatory factors inferred from the accessible chromatin peaks [ 69 ]. Integrating ChIP-seq, ATAC-seq, and DNase-seq in organoid models [ 70 ] with transcriptomic data will help to reveal the developmental dynamics of specific cells, discover key transcriptional regulators, and identify disease susceptible cell populations [ 71 – 73 ]. Multi-omics integration of single-cell transcriptome and ATAC-seq in organ development can provide a robust foundation for the clinical treatment of diseases.…”

Engineered tissues and strategies to overcome challenges in drug development

“…For example, assayed features for tissue vascularization might look for immunohistochemical characterization of specific cadherins and tight junction proteins in the correct locations or functional assays such as barrier permeability or response to cytokines. Increasingly, cellular “omic” characterizations such as single-cell RNA and epigenetic sequencing methods are options for assaying morphogenesis in in vitro cultures [ 151 , 152 ]. Data dimensional reduction and comparison of the in vitro tissue to primary cells or tissue samples can help determine the degree of morphogenesis and maturation.…”