Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition

Finkbeiner, Connor; Ortuño‐Lizarán, Isabel; Sridhar, Akshayalakshmi; Hooper, Marcus; Petter, Sidnee; Reh, Thomas A.

doi:10.1016/j.celrep.2021.110294

Cited by 54 publications

(46 citation statements)

References 49 publications

(78 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our findings build upon recent works that used primarily fetal tissue and stem cell-derived organoids to map cell type-specific chromatin accessibility in the human retina 29,42 . Datasets from these studies offer a rich resource for decoding retinal development, but might not fully recapitulate the biology of the mature retina, making them potentially less suitable for studying eye disorders that present later in life.…”

Section: Discussionsupporting

confidence: 73%

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

Wang

Nair

et al. 2022

Preprint

View full text Add to dashboard Cite

Genome-wide association studies (GWAS) of eye disorders have identified hundreds of genetic variants associated with ocular disease. However, the vast majority of these variants are noncoding, making it challenging to interpret their function. Here, we present a joint single-cell atlas of gene expression and chromatin accessibility of the adult human retina with >50,000 cells, which we used to analyze noncoding single-nucleotide polymorphisms (SNPs) implicated by GWAS of age-related macular degeneration, glaucoma, diabetic retinopathy, myopia, and type 2 macular telangiectasia. We integrate this atlas with a HiChIP enhancer connectome, expression quantitative trait loci (eQTL) data, and base-resolution deep learning models to predict noncoding SNPs with causal roles in eye disease, assess SNP impact on transcription factor binding, and define their known and novel target genes. Our efforts nominate pathogenic SNP-target gene interactions for multiple vision disorders and provide a potentially powerful resource for interpreting noncoding variation in the eye.

show abstract

Section: Discussionsupporting

confidence: 73%

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

Wang

Nair

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“… 18 Recently, a single cell ATAC-seq analysis of PF treatment of human fetal tissue showed a decrease in accessibility of regions bearing the RBPJ motif (Notch effector) and an increase in accessible regions with an OTX2 motif. 19 Because we know approximately when each of the retinal cell types are born from birth dating studies, we hypothesized that targeting the differentiation of specific cell types by using PF would generate an enriched pool of targeted cell types. These cells could then be used for transplantation or for studying molecular pathways that guide RPC differentiation.…”

mentioning

confidence: 99%

Timed Notch Inhibition Drives Photoreceptor Fate Specification in Human Retinal Organoids

Chew

Martinez

Chirco

et al. 2022

Invest. Ophthalmol. Vis. Sci.

View full text Add to dashboard Cite

Purpose Transplanting photoreceptors from human pluripotent stem cell–derived retinal organoids have the potential to reverse vision loss in affected individuals. However, transplantable photoreceptors are only a subset of all cells in the organoids. Hence, the goal of our current study was to accelerate and synchronize photoreceptor differentiation in retinal organoids by inhibiting the Notch signaling pathway at different developmental time-points using a small molecule, PF-03084014 (PF). Methods Human induced pluripotent stem cell– and human embryonic stem cells–derived retinal organoids were treated with 10 µM PF for 3 days starting at day 45 (D45), D60, D90, and D120 of differentiation. Organoids were collected at post-treatment days 14, 28, and 42 and analyzed for progenitor and photoreceptor markers and Notch pathway inhibition by immunohistochemistry (IHC), quantitative PCR, and bulk RNA sequencing ( n = 3–5 organoids from three independent experiments). Results Retinal organoids collected after treatment showed a decrease in progenitor markers (KI67, VSX2, PAX6, and LHX2) and an increase in differentiated pan-photoreceptor markers (OTX2, CRX, and RCVRN) at all organoid stages except D120. PF-treated organoids at D45 and D60 exhibited an increase in cone photoreceptor markers (RXRG and ARR3). PF treatment at D90 revealed an increase in cone and rod photoreceptors markers (ARR3, NRL, and NR2E3). Bulk RNA sequencing analysis mirrored the immunohistochemistry data and quantitative PCR confirmed Notch effector inhibition. Conclusions Timing the Notch pathway inhibition in human retinal organoids to align with progenitor competency stages can yield an enriched population of early cone or rod photoreceptors.

show abstract

“…The copyright holder for this preprint this version posted March 6, 2022. ; https://doi.org/10.1101/2022.03.05.483140 doi: bioRxiv preprint characteristic of this state is the activation of enhancers containing E box motifs, which are recognized by bHLH transcription factors including Atoh7. As suggested by extensive previous studies [93][94][95][96][97][98][99][100][101] , interactions between the Notch pathway and the bHLH transcription factors likely are the major underlying mechanism for this epigenetic change; downregulation of the Notch pathway by lateral inhibition is critical for activation of the bHLH genes and retinal cell differentiation, whereas bHLH transcription factors activate the Notch ligand genes, which in turn activate the pathway in nRPCs to promote proliferation and inhibit differentiation 87,88,91,94,102,103 . Our finding that Atoh7 regulates multiple component genes of the Notch pathway fits this model.…”

Section: Discussionmentioning

confidence: 99%

Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation

Cheng

Nan

et al. 2022

Preprint

View full text Add to dashboard Cite

During development, all retinal cell types emerge from multipotent retinal progenitor cells (RPCs) following distinct trajectories. Each lineage is subject to regulation by multiple intrinsic and extrinsic factors, which converge onto the epigenetic landscape to dictate the collective gene expression profile and thereby the phenotypes of individual cell states/types. Recent scRNA-seq studies have further delineated these trajectories, providing a general picture of the relationships between the different cell states/types and revealing a transitional RPC state shared by all the early lineages. Nevertheless, how the epigenetic landscape shifts along individual trajectories is only beginning to be disseminated, and the roles of key transcription factors in these shifts are not known. In this study, we dissect the changes of the epigenetic landscape along these trajectories in the early developing retina by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages, with a focus on retinal ganglion cells (RGCs). Using CUT&Tag-seq, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2, and Isl1, and uncover their roles in shaping the epigenetic landscape to control gene expression in a sequential and combinatorial fashion during RGC genesis. These results provide experimental support for a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from the multipotent transitional RPCs.

show abstract

Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition

Abstract: Highlights d Chromatin accessibility of human fetal retina reveals transcription factor cascades d Accessible chromatin of hESC-derived retinal organoids shows conserved development d Retinal organoids and fetal retina show differences in Notch signaling

Cited by 54 publications

References 49 publications

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

Timed Notch Inhibition Drives Photoreceptor Fate Specification in Human Retinal Organoids

Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation

Contact Info

Product

Resources

About