Multimodal Spatiotemporal Phenotyping of Human Retinal Organoid Development

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2023 May 8

PMID 37156914

Authors

Philipp Wahle

Giovanna Brancati

Christoph Harmel

Zhisong He

Gabriele Gut

Jacobo Sarabia Del Castillo

Aline Xavier da Silveira Dos Santos

Qianhui Yu

Pascal Noser

Jonas Simon Fleck

Bruno Gjeta

Dinko Pavlinic

Simone Picelli

Max Hess

Gregor W Schmidt

Tom T A Lummen

Yanyan Hou

Patricia Galliker

David Goldblum

Marton Balogh

Cameron S Cowan

Hendrik P N Scholl

Botond Roska

Magdalena Renner

Lucas Pelkmans

Barbara Treutlein

J Gray Camp

Affiliations

Soon will be listed here.

Abstract

Organoids generated from human pluripotent stem cells provide experimental systems to study development and disease, but quantitative measurements across different spatial scales and molecular modalities are lacking. In this study, we generated multiplexed protein maps over a retinal organoid time course and primary adult human retinal tissue. We developed a toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components and global patterning in each organoid and primary tissue. In addition, we generated a single-cell transcriptome and chromatin accessibility timecourse dataset and inferred a gene regulatory network underlying organoid development. We integrated genomic data with spatially segmented nuclei into a multimodal atlas to explore organoid patterning and retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death and showing that mosaic genetic perturbations in retinal organoids provide insight into cell fate regulation.

Citing Articles

Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development.

Zhang J, Wang J, Zhou Q, Chen Z, Zhuang J, Zhao X Nat Commun. 2025; 16(1):2307.

PMID: 40055379 PMC: 11889126. DOI: 10.1038/s41467-025-57625-9.

Generation of a Double Reporter mES Cell Line to Simultaneously Trace the Generation of Retinal Progenitors and Photoreceptors.

Zabiegalov O, Berger A, Kamdar D, Adamou K, Tian C, Mbefo M Cells. 2025; 14(4).

PMID: 39996725 PMC: 11854395. DOI: 10.3390/cells14040252.

Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells.

Blair J, Hartman A, Zenk F, Wahle P, Brancati G, Dalgarno C Nat Commun. 2025; 16(1):1346.

PMID: 39905064 PMC: 11794950. DOI: 10.1038/s41467-025-56590-7.

Single-cell sequencing in diabetic retinopathy: progress and prospects.

Yang T, Zhang N, Yang N J Transl Med. 2025; 23(1):49.

PMID: 39806376 PMC: 11727737. DOI: 10.1186/s12967-024-06066-x.

Optimized Prime Editing of Human Induced Pluripotent Stem Cells to Efficiently Generate Isogenic Models of Mendelian Diseases.

Cerna-Chavez R, Ortega-Gasco A, Azhar Baig H, Ehrenreich N, Metais T, Scandura M Int J Mol Sci. 2025; 26(1.

PMID: 39795970 PMC: 11719581. DOI: 10.3390/ijms26010114.

References

Schier A . Single-cell biology: beyond the sum of its parts. Nat Methods. 2020; 17(1):17-20. DOI: 10.1038/s41592-019-0693-3. View

Zhu C, Preissl S, Ren B . Single-cell multimodal omics: the power of many. Nat Methods. 2020; 17(1):11-14. DOI: 10.1038/s41592-019-0691-5. View

Hickey J, Neumann E, Radtke A, Camarillo J, Beuschel R, Albanese A . Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods. 2021; 19(3):284-295. PMC: 9264278. DOI: 10.1038/s41592-021-01316-y. View

Chiaradia I, Lancaster M . Brain organoids for the study of human neurobiology at the interface of in vitro and in vivo. Nat Neurosci. 2020; 23(12):1496-1508. DOI: 10.1038/s41593-020-00730-3. View

Takebe T, Wells J . Organoids by design. Science. 2019; 364(6444):956-959. PMC: 8212787. DOI: 10.1126/science.aaw7567. View

Rood J, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A . Toward a Common Coordinate Framework for the Human Body. Cell. 2019; 179(7):1455-1467. PMC: 6934046. DOI: 10.1016/j.cell.2019.11.019. View

Camp J, Platt R, Treutlein B . Mapping human cell phenotypes to genotypes with single-cell genomics. Science. 2019; 365(6460):1401-1405. DOI: 10.1126/science.aax6648. View

Hao Y, Hao S, Andersen-Nissen E, Mauck 3rd W, Zheng S, Butler A . Integrated analysis of multimodal single-cell data. Cell. 2021; 184(13):3573-3587.e29. PMC: 8238499. DOI: 10.1016/j.cell.2021.04.048. View

Brancati G, Treutlein B, Camp J . Resolving Neurodevelopmental and Vision Disorders Using Organoid Single-Cell Multi-omics. Neuron. 2020; 107(6):1000-1013. DOI: 10.1016/j.neuron.2020.09.001. View

10.

Sasai Y . Cytosystems dynamics in self-organization of tissue architecture. Nature. 2013; 493(7432):318-26. DOI: 10.1038/nature11859. View

11.

Nakano T, Ando S, Takata N, Kawada M, Muguruma K, Sekiguchi K . Self-formation of optic cups and storable stratified neural retina from human ESCs. Cell Stem Cell. 2012; 10(6):771-785. DOI: 10.1016/j.stem.2012.05.009. View

12.

Eiraku M, Takata N, Ishibashi H, Kawada M, Sakakura E, Okuda S . Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature. 2011; 472(7341):51-6. DOI: 10.1038/nature09941. View

13.

Zhong X, Gutierrez C, Xue T, Hampton C, Vergara M, Cao L . Generation of three-dimensional retinal tissue with functional photoreceptors from human iPSCs. Nat Commun. 2014; 5:4047. PMC: 4370190. DOI: 10.1038/ncomms5047. View

14.

Cowan C, Renner M, De Gennaro M, Gross-Scherf B, Goldblum D, Hou Y . Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution. Cell. 2020; 182(6):1623-1640.e34. PMC: 7505495. DOI: 10.1016/j.cell.2020.08.013. View

15.

Afanasyeva T, Corral-Serrano J, Garanto A, Roepman R, Cheetham M, Collin R . A look into retinal organoids: methods, analytical techniques, and applications. Cell Mol Life Sci. 2021; 78(19-20):6505-6532. PMC: 8558279. DOI: 10.1007/s00018-021-03917-4. View

16.

Sridhar A, Hoshino A, Finkbeiner C, Chitsazan A, Dai L, Haugan A . Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures. Cell Rep. 2020; 30(5):1644-1659.e4. PMC: 7901645. DOI: 10.1016/j.celrep.2020.01.007. View

17.

Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson J . Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. Dev Cell. 2020; 53(4):473-491.e9. PMC: 8015270. DOI: 10.1016/j.devcel.2020.04.009. View

18.

Parfitt D, Lane A, Ramsden C, Carr A, Munro P, Jovanovic K . Identification and Correction of Mechanisms Underlying Inherited Blindness in Human iPSC-Derived Optic Cups. Cell Stem Cell. 2016; 18(6):769-781. PMC: 4899423. DOI: 10.1016/j.stem.2016.03.021. View

19.

Khan M, Arno G, Fakin A, Parfitt D, Dhooge P, Albert S . Detailed Phenotyping and Therapeutic Strategies for Intronic ABCA4 Variants in Stargardt Disease. Mol Ther Nucleic Acids. 2020; 21:412-427. PMC: 7352060. DOI: 10.1016/j.omtn.2020.06.007. View

20.

Dulla K, Aguila M, Lane A, Jovanovic K, Parfitt D, Schulkens I . Splice-Modulating Oligonucleotide QR-110 Restores CEP290 mRNA and Function in Human c.2991+1655A>G LCA10 Models. Mol Ther Nucleic Acids. 2018; 12:730-740. PMC: 6092551. DOI: 10.1016/j.omtn.2018.07.010. View