Evidence map›Paper›PMID 36359808›Full record

ArticleCells2022

Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids.

Melissa K Jones, Devansh Agarwal, Kevin W Mazo, Manan Chopra, Shawna L Jurlina, Nicholas Dash, Qianlan Xu, Anna R Ogata, Melissa Chow, Alex D Hill and 9 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cells, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
0.6field-weighted citation impact, top 35% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed, 7 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Toward Retinal Organoids in High-Throughput.Cold Spring Harbor perspectives in medicine · 2024
    Review
  5. Article
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors at 4 institutions in 1 country.

Melissa K JonesViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.
Devansh AgarwalViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0001-8342-6119
Kevin W MazoViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0003-4094-034X
Manan ChopraViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0001-8928-2275
Shawna L JurlinaViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.
Nicholas DashViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.
Qianlan XuCenter for Translational Vision Research, University of California Irvine, Irvine, CA 92617, USA.
Anna R OgataViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.
Melissa ChowViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0002-6501-3991
Alex D HillViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.
Netra K KambliViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.
Guorong XuCenter for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA.
Roman SasikCenter for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0002-9266-8993
Amanda BirminghamCenter for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA.
Kathleen M FischCenter for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA.
Robert N WeinrebViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.ORCID 0000-0001-9553-3202
Ray A EnkeDepartment of Biology, James Madison University, Harrisonburg, VA 22807, USA.ORCID 0000-0002-3605-2107
Dorota Skowronska-KrawczykCenter for Translational Vision Research, University of California Irvine, Irvine, CA 92617, USA.ORCID 0000-0002-5758-4225
Karl J WahlinViterbi Family Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093, USA.
University of California San Diego · USUniversity of California, Irvine · USCalifornia State University, Channel Islands · USJames Madison University · US

Funding

UC San Diego Clinical and Translational Research InstituteUL1TR001442 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S, HOGARTH, MICHAEL · 2015 to 2024
$88.3M
Vision BiostatisticsP30EY022589 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Radha Ayyagari · 2012 to 2026
$10.3M
Pluripotent Stem Cell Derived 3D Retinas for Studies of Early Onset Retinal DegenerationR01EY031318 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WAHLIN, KARL J · 2020 to 2024
$2.4M
Transfer: Molecular Mechanisms of GlaucomaR01EY027011 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SKOWRONSKA-KRAWCZYK, DOROTA · 2017 to 2022
$2.3M
Translational Vision Research Training at UCSDT32EY026590 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZANGWILL, LINDA M · 2016 to 2025
$854k
Modeling Photoreceptor Development and Disease Using Human Pluripotent Stem CellsR00EY024648 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WAHLIN, KARL J · 2016 to 2018
$778k
Dissecting the biochemical role of epigenetically modified regulatory sequences within the genomes of retinal neurons (A1)R15EY028725 · NEI · JAMES MADISON UNIVERSITY · PI ENKE, RAYMOND · 2018 to 2018
$464k
A stem cell based optic nerve model for studies of axon guidance and regenerationR21EY031122 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHEN, SHAOCHEN, WAHLIN, KARL J · 2019 to 2019
$299k
Modeling Photoreceptor Development and Disease Using Human Pluripotent Stem CellsK99EY024648 · NEI · JOHNS HOPKINS UNIVERSITY · PI WAHLIN, KARL J · 2014 to 2015
$180k
NCATS NIH HHS UL1 TR001442NEI NIH HHS EY024648NEI NIH HHS EY026590NEI NIH HHS EY027011NEI NIH HHS EY031122NEI NIH HHS EY031318NEI NIH HHS K99 EY024648NEI NIH HHS P30 EY022589NEI NIH HHS P30EY022589NEI NIH HHS R00 EY024648NEI NIH HHS R01 EY027011NEI NIH HHS R01 EY031318NEI NIH HHS R15 EY028725NEI NIH HHS R15EY028725NEI NIH HHS R21 EY031122NEI NIH HHS T32 EY026590
6 · The paper itself

Abstract

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.

Indexed as

OrganoidsPluripotent Stem CellsCell DifferentiationChromatinHumansRetinaChromatinATAC-seqchromatinCRISPRgene-editingorganoidsretinaRNA-seqSIX6transcriptionVSX2

Identifiers

PMID36359808
PMCPMC9657268
OpenAlexW4308122661

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.