Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-<i>cis</i> retinal

Kaya, Koray Dogan; Chen, Holly Y.; Brooks, Matthew; Kelley, Ryan A.; Shimada, Hiroko; Nagashima, Kunio; Val, Natalia de; Drinnan, Charles T.; Gieser, Linn; Kruczek, Kamil; Erceg, Slaven; Li, Tiansen; Lukovic, Dunja; Adlakha, Yogita K.; Welby, Emily; Swaroop, Anand

doi:10.1101/733071

Cited by 49 publications

(79 citation statements)

References 68 publications

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“…Retinal cell specification occurs in AIPL1-LCA and control ROs. We next explored molecular aspects of retinal cell specification in differentiating ROs from the AIPL1-LCA patient hiPSC line and from the two control hiPSC lines (combined as one control because of similar gene expression profiles as described previously 33 ), by analyzing transcriptome profiles at four different time points (day (D) 25, D60, D88, and D123 corresponding to W4, W9, W13, and W18, respectively). These time points span retinal organoid formation before the appearance of apical protrusions from ROs.…”

Section: Resultsmentioning

confidence: 99%

Retinal Organoids derived from hiPSCs of an AIPL1-LCA Patient Maintain Cytoarchitecture despite Reduced levels of Mutant AIPL1

Lukovic

Castro

Kaya

et al. 2020

Sci Rep

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Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) is a photoreceptor-specific chaperone that stabilizes the effector enzyme of phototransduction, cGMP phosphodiesterase 6 (PDE6). Mutations in the AIPL1 gene cause a severe inherited retinal dystrophy, Leber congenital amaurosis type 4 (LCA4), that manifests as the loss of vision during the first year of life. In this study, we generated three-dimensional (3D) retinal organoids (ROs) from human induced pluripotent stem cells (hiPSCs) derived from an LCA4 patient carrying a Cys89Arg mutation in AIPL1. This study aimed to (i) explore whether the patient hiPSC-derived ROs recapitulate LCA4 disease phenotype, and (ii) generate a clinically relevant resource to investigate the molecular mechanism of disease and safely test novel therapies for LCA4 in vitro. We demonstrate reduced levels of the mutant AIPL1 and PDE6 proteins in patient organoids, corroborating the findings in animal models; however, patient-derived organoids maintained retinal cell cytoarchitecture despite significantly reduced levels of AIPL1. Hereditary retinal degenerations are clinically and genetically heterogeneous and constitute a major cause of incurable visual impairment in working age adults. Unfortunately, this group of diseases currently lacks effective treatment options. Among the divergent clinical phenotypes, Leber congenital amaurosis (LCA) accounts for ∼5% of all inherited retinopathies and is among the most severe, with patients exhibiting visual dysfunction and losing electroretinogram signals during the early years of age 1. Patients typically present nystagmus (repetitive, uncontrolled movements of the eyes), poor pupillary light response, and fundus abnormalities 2. Currently, as many as 25 genes have been identified as causing LCA (https://sph.uth.edu/retnet/) primarily in an autosomal recessive manner; however, genetic defects have not been identified in almost 30% of LCA patients 2. All known causative genes are expressed in photoreceptors and/or the retinal pigment epithelium (RPE) and associated with a wide range of functions, including phototransduction, retinoid cycling, protein trafficking, and ciliary transport. Mutations in the aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) gene lead to early onset retinal disease and account for up to 5-10% of all mutations causing LCA 3 resulting in a clinically severe form, LCA type 4 (LCA4, OMIM #604393) 4. The AIPL1 gene locates to chromosome 17, with 79 mutations identified to date as causing LCA (Human Genome Mutation Database). AIPL1 encodes a 384 amino acid protein expressed only in photoreceptors and the pineal gland 5. The protein has an FK506-binding protein (FKBP)-like domain within the N terminus, a tetratricopeptide (TPR) domain with three TPR repeats, and a primate unique proline-rich domain

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Section: Resultsmentioning

confidence: 99%

Retinal Organoids derived from hiPSCs of an AIPL1-LCA Patient Maintain Cytoarchitecture despite Reduced levels of Mutant AIPL1

Lukovic

Castro

Kaya

et al. 2020

Sci Rep

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“…In that direction, our studies provide a valuable framework and transcriptomic resource for modeling development and disease in mouse retinal organoids. We also note that transcriptome analyses of human retinal organoids has provided an objective system to evaluate their differentiation status and shown accelerated rod maturation by using 9- cis retinal (Kaya et al., 2019).…”

Section: Discussionmentioning

confidence: 99%

Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo

et al. 2019

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Stem cell-derived retinal organoids recapitulate many landmarks of in vivo differentiation but lack functional maturation of distinct cell types, especially photoreceptors. Using comprehensive temporal transcriptome analyses, we show that transcriptome shift from postnatal day 6 (P6) to P10, associated with morphogenesis and synapse formation during mouse retina development, was not evident in organoids, and co-expression clusters with similar patterns included different sets of genes. Furthermore, network analysis identified divergent regulatory dynamics between developing retina in vivo and in organoids, with temporal dysregulation of specific signaling pathways and delayed or reduced expression of genes involved in photoreceptor function(s) and survival. Accordingly, addition of docosahexaenoic acid and fibroblast growth factor 1 to organoid cultures specifically promoted the maturation of photoreceptors, including cones. Our study thus identifies regulatory signals deficient in developing retinal organoids and provides experimental validation by producing a more mature retina in vitro, thereby facilitating investigations in disease modeling and therapies.

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“…Another alternative is mixing hPSC clumps with Matrigel to form epithelialized cysts, which can be then plated, later followed by gentle lifting with dispase to form well‐laminated organoids 21,22 . Replacement of widely used all‐ trans retinoic acid with 9‐ cis retinal accelerates differentiation of rod photoreceptors in retinal organoids, 23 whereas signaling by thyroid hormone facilitates the specification of L/M cone subtypes, 24 consistent with S‐cones being the default fate of photoreceptors 25,26 . Interestingly, scraping of the adherent culture and selection of subsequently formed optic vesicles improves the yield and efficiency of generating retinal organoids 27 .…”

Section: Differentiation Methods and Staging Of Retinal Organoidsmentioning

confidence: 99%

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

Kruczek

Swaroop

2020

Stem Cells

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Retinal diseases constitute a genetically and phenotypically diverse group of clinical conditions leading to vision impairment or blindness with limited treatment options. Advances in reprogramming of somatic cells to induced pluripotent stem cells and generation of three-dimensional organoids resembling the native retina offer promising tools to interrogate disease mechanisms and evaluate potential therapies for currently incurable retinal neurodegeneration. Next-generation sequencing, singlecell analysis, advanced electrophysiology, and high-throughput screening approaches are expected to greatly expand the utility of stem cell-derived retinal cells and organoids for developing personalized treatments. In this review, we discuss the current status and future potential of combining retinal organoids as human models with recent technologies to advance the development of gene, cell, and drug therapies for retinopathies.

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Transcriptome-based molecular staging of human stem cell-derived retinal organoids uncovers accelerated photoreceptor differentiation by 9-cis retinal

Cited by 49 publications

References 68 publications

Retinal Organoids derived from hiPSCs of an AIPL1-LCA Patient Maintain Cytoarchitecture despite Reduced levels of Mutant AIPL1

Retinal Organoids derived from hiPSCs of an AIPL1-LCA Patient Maintain Cytoarchitecture despite Reduced levels of Mutant AIPL1

Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo

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

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