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Hadyniak SE, Hagen JFD, Eldred KC, Brenerman B, Hussey KA, McCoy RC, Sauria MEG, Kuchenbecker JA, Reh T, Glass I, Neitz M, Neitz J, Taylor J, Johnston RJ. Retinoic acid signaling regulates spatiotemporal specification of human green and red cones. PLoS Biol 2024; 22:e3002464. [PMID: 38206904 PMCID: PMC10783767 DOI: 10.1371/journal.pbio.3002464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024] Open
Abstract
Trichromacy is unique to primates among placental mammals, enabled by blue (short/S), green (medium/M), and red (long/L) cones. In humans, great apes, and Old World monkeys, cones make a poorly understood choice between M and L cone subtype fates. To determine mechanisms specifying M and L cones, we developed an approach to visualize expression of the highly similar M- and L-opsin mRNAs. M-opsin was observed before L-opsin expression during early human eye development, suggesting that M cones are generated before L cones. In adult human tissue, the early-developing central retina contained a mix of M and L cones compared to the late-developing peripheral region, which contained a high proportion of L cones. Retinoic acid (RA)-synthesizing enzymes are highly expressed early in retinal development. High RA signaling early was sufficient to promote M cone fate and suppress L cone fate in retinal organoids. Across a human population sample, natural variation in the ratios of M and L cone subtypes was associated with a noncoding polymorphism in the NR2F2 gene, a mediator of RA signaling. Our data suggest that RA promotes M cone fate early in development to generate the pattern of M and L cones across the human retina.
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Affiliation(s)
- Sarah E. Hadyniak
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
| | - Joanna F. D. Hagen
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
| | - Kiara C. Eldred
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
- Department of Biological Structure, University of Washington, Seattle, Washington State, United States
| | - Boris Brenerman
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
| | - Katarzyna A. Hussey
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
| | - Michael E. G. Sauria
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
| | - James A. Kuchenbecker
- Department of Ophthalmology, University of Washington, Seattle, Washington State, United States
| | - Thomas Reh
- Department of Biological Structure, University of Washington, Seattle, Washington State, United States
| | - Ian Glass
- Department of Biological Structure, University of Washington, Seattle, Washington State, United States
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington, Seattle, Washington State, United States
| | - Jay Neitz
- Department of Ophthalmology, University of Washington, Seattle, Washington State, United States
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
| | - Robert J. Johnston
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States
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2
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Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YHH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. bioRxiv 2023:2023.09.26.559521. [PMID: 37808736 PMCID: PMC10557686 DOI: 10.1101/2023.09.26.559521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four 'omes' to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.
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Affiliation(s)
- Mitchell R. Vollger
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kiara C. Eldred
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Elliott Swanson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | - Yong-Han H. Cheng
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | - Jane Ranchalis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Yizi Mao
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Elizabeth E. Blue
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ulrike Schwarze
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Katherine M. Munson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | | | - Aimee Allworth
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sirisak Chanprasert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Ian Glass
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Martha Horike-Pyne
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kathleen A. Leppig
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | | | | | - Sam Sheppeard
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Stephanie M. Sherman
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Samuel Strohbehn
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Amy L. Yuen
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | - Thomas A. Reh
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Peter H. Byers
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Fuki M. Hisama
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gail P. Jarvik
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Yasemin Sancak
- University of Washington School of Medicine, Department of Pharmacology, Seattle, WA, USA
| | - Katrina M. Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Andrew B. Stergachis
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity. Cell Rep Methods 2023; 3:100548. [PMID: 37671011 PMCID: PMC10475847 DOI: 10.1016/j.crmeth.2023.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/16/2023] [Accepted: 07/14/2023] [Indexed: 09/07/2023]
Abstract
With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA sequencing (RNA-seq) multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10× methods produce highly concordant cell-class compositions and then expand sci-Plex to analyze the cell-class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to 6 weeks later. Our data show sci-Plex's potential to dramatically scale up the analysis of treatment conditions on relevant human models.
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Affiliation(s)
- Amy Tresenrider
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Kiara C. Eldred
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Sophia Cuschieri
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Dawn Hoffer
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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4
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D'Souza SP, Upton BA, Eldred KC, Glass I, Grover K, Ahmed A, Ngyuen MT, Gamlin P, Lang RA. Developmental adaptation of rod photoreceptor number via photoreception in melanopsin (OPN4) retinal ganglion cells. bioRxiv 2023:2023.08.24.554675. [PMID: 37662196 PMCID: PMC10473760 DOI: 10.1101/2023.08.24.554675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Photoreception, a form of sensory experience, is essential for normal development of the mammalian visual system. Detecting photons during development is a prerequisite for visual system function - from vision's first synapse at the cone pedicle and maturation of retinal vascular networks, to transcriptional establishment and maturation of cell types within the visual cortex. Consistent with this theme, we find that the lighting environment regulates developmental rod photoreceptor apoptosis via OPN4-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs). Using a combination of genetics, sensory environment manipulations, and computational approaches, we establish a molecular pathway in which light-dependent glutamate release from ipRGCs is detected via a transiently expressed kainate receptor (GRIK3) in immature rods localized to the inner retina. Communication between ipRGCs and nascent inner retinal rods appears to be mediated by unusual hybrid neurites projecting from ipRGCs that sense light before eye-opening. These structures, previously referred to as outer retinal dendrites (ORDs), span the ipRGC-immature rod distance over the first postnatal week and contain the machinery for sensory detection (melanopsin, OPN4) and axonal/anterograde neurotransmitter release (Synaptophysin, and VGLUT2). Histological and computational assessment of human mid-gestation development reveal conservation of several hallmarks of an ipRGC-to-immature rod pathway, including displaced immature rods, transient GRIK3 expression in the rod lineage, and the presence of ipRGCs with putative neurites projecting deep into the developing retina. Thus, this analysis defines a retinal retrograde signaling pathway that links the sensory environment to immature rods via ipRGC photoreceptors, allowing the visual system to adapt to distinct lighting environments priory to eye-opening.
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5
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Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity. bioRxiv 2023:2023.05.31.543087. [PMID: 37398481 PMCID: PMC10312535 DOI: 10.1101/2023.05.31.543087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA-seq multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10x methods produce highly concordant cell class compositions and then expand sci-Plex to analyze the cell class composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell classes up to six weeks later. Our data show sci-Plex's potential to dramatically scale-up the analysis of treatment conditions on relevant human models.
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Affiliation(s)
- Amy Tresenrider
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Kiara C. Eldred
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Sophia Cuschieri
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Dawn Hoffer
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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Wahlin KJ, Cheng J, Jurlina SL, Jones MK, Dash NR, Ogata A, Kibria N, Ray S, Eldred KC, Kim C, Heng JS, Phillips J, Johnston RJ, Gamm DM, Berlinicke C, Zack DJ. CRISPR Generated SIX6 and POU4F2 Reporters Allow Identification of Brain and Optic Transcriptional Differences in Human PSC-Derived Organoids. Front Cell Dev Biol 2021; 9:764725. [PMID: 34869356 PMCID: PMC8635054 DOI: 10.3389/fcell.2021.764725] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/11/2021] [Indexed: 01/29/2023] Open
Abstract
Human pluripotent stem cells (PSCs) represent a powerful tool to investigate human eye development and disease. When grown in 3D, they can self-assemble into laminar organized retinas; however, variation in the size, shape and composition of individual organoids exists. Neither the microenvironment nor the timing of critical growth factors driving retinogenesis are fully understood. To explore early retinal development, we developed a SIX6-GFP reporter that enabled the systematic optimization of conditions that promote optic vesicle formation. We demonstrated that early hypoxic growth conditions enhanced SIX6 expression and promoted eye formation. SIX6 expression was further enhanced by sequential inhibition of Wnt and activation of sonic hedgehog signaling. SIX6 + optic vesicles showed RNA expression profiles that were consistent with a retinal identity; however, ventral diencephalic markers were also present. To demonstrate that optic vesicles lead to bona fide "retina-like" structures we generated a SIX6-GFP/POU4F2-tdTomato dual reporter line that labeled the entire developing retina and retinal ganglion cells, respectively. Additional brain regions, including the hypothalamus and midbrain-hindbrain (MBHB) territories were identified by harvesting SIX6 + /POU4F2- and SIX6- organoids, respectively. Using RNAseq to study transcriptional profiles we demonstrated that SIX6-GFP and POU4F2-tdTomato reporters provided a reliable readout for developing human retina, hypothalamus, and midbrain/hindbrain organoids.
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Affiliation(s)
- Karl J. Wahlin
- Shiley Eye Institute, University of California, San Diego, San Diego, CA, United States,*Correspondence: Karl J. Wahlin,
| | - Jie Cheng
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Shawna L. Jurlina
- Shiley Eye Institute, University of California, San Diego, San Diego, CA, United States
| | - Melissa K. Jones
- Shiley Eye Institute, University of California, San Diego, San Diego, CA, United States
| | - Nicholas R. Dash
- Shiley Eye Institute, University of California, San Diego, San Diego, CA, United States
| | - Anna Ogata
- Shiley Eye Institute, University of California, San Diego, San Diego, CA, United States
| | - Nawal Kibria
- Shiley Eye Institute, University of California, San Diego, San Diego, CA, United States
| | - Sunayan Ray
- Shiley Eye Institute, University of California, San Diego, San Diego, CA, United States
| | - Kiara C. Eldred
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Catherine Kim
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jacob S. Heng
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, United States
| | - Jenny Phillips
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Robert J. Johnston
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David M. Gamm
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States,Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States,McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Cynthia Berlinicke
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Donald J. Zack
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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7
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Eldred KC, Reh TA. Human retinal model systems: Strengths, weaknesses, and future directions. Dev Biol 2021; 480:114-122. [PMID: 34529997 DOI: 10.1016/j.ydbio.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The retina is a complex neuronal structure that converts light energy into visual perception. Many specialized aspects of the primate retina, including a cone rich macula for high acuity vision, ocular size, and cell type diversity are not found in other animal models. In addition, the unique morphologies and distinct laminar positions of cell types found in the retina make this model system ideal for the study of neuronal cell fate specification. Many key early events of human retinal development are inaccessible to investigation as they occur during gestation. For these reasons, it has been necessary to develop retinal model systems to gain insight into human-specific retinal development and disease. Recent advances in culturing retinal tissue have generated new systems for retinal research and have moved us closer to generating effective regenerative therapies for vision loss. Here, we describe the strengths, weaknesses, and future directions for different human retinal model systems including dissociated primary tissue, explanted primary tissue, retinospheres, and stem cell-derived retinal organoids.
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Affiliation(s)
- Kiara C Eldred
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Thomas A Reh
- Department of Biological Structure, Institute for Stem Cells and Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
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Eldred KC, Avelis C, Johnston RJ, Roberts E. Modeling binary and graded cone cell fate patterning in the mouse retina. PLoS Comput Biol 2020; 16:e1007691. [PMID: 32150546 PMCID: PMC7082072 DOI: 10.1371/journal.pcbi.1007691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/19/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
Nervous systems are incredibly diverse, with myriad neuronal subtypes defined by gene expression. How binary and graded fate characteristics are patterned across tissues is poorly understood. Expression of opsin photopigments in the cone photoreceptors of the mouse retina provides an excellent model to address this question. Individual cones express S-opsin only, M-opsin only, or both S-opsin and M-opsin. These cell populations are patterned along the dorsal-ventral axis, with greater M-opsin expression in the dorsal region and greater S-opsin expression in the ventral region. Thyroid hormone signaling plays a critical role in activating M-opsin and repressing S-opsin. Here, we developed an image analysis approach to identify individual cone cells and evaluate their opsin expression from immunofluorescence imaging tiles spanning roughly 6 mm along the D-V axis of the mouse retina. From analyzing the opsin expression of ~250,000 cells, we found that cones make a binary decision between S-opsin only and co-expression competent fates. Co-expression competent cells express graded levels of S- and M-opsins, depending nonlinearly on their position in the dorsal-ventral axis. M- and S-opsin expression display differential, inverse patterns. Using these single-cell data, we developed a quantitative, probabilistic model of cone cell decisions in the retinal tissue based on thyroid hormone signaling activity. The model recovers the probability distribution for cone fate patterning in the mouse retina and describes a minimal set of interactions that are necessary to reproduce the observed cell fates. Our study provides a paradigm describing how differential responses to regulatory inputs generate complex patterns of binary and graded cell fates. The development of a cell in a mammalian tissue is governed by a complex regulatory network that responds to many input signals to give the cell a distinct identity, a process referred to as cell-fate specification. Some of these cell fates have binary on-or-off gene expression patterns, while others have graded gene expression that changes across the tissue. Differentiation of the photoreceptor cells that sense light in the mouse retina provides a good example of this process. Here, we explore how complex patterns of cell fates are specified in the mouse retina by building a computational model based on analysis of a large number of photoreceptor cells from microscopy images of whole retinas. We use the data and the model to study what exactly it means for a cell to have a binary or graded cell fate and how these cell fates can be distinguished from each other. Our study shows how tens-of-thousands of individual photoreceptor cells can be patterned across a complex tissue by a regulatory network, creating a different outcome depending upon the received inputs.
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Affiliation(s)
- Kiara C. Eldred
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Cameron Avelis
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Robert J. Johnston
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (RJJ); (ER)
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (RJJ); (ER)
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Eldred KC, Hadyniak SE, Hussey KA, Brenerman B, Zhang PW, Chamling X, Sluch VM, Welsbie DS, Hattar S, Taylor J, Wahlin K, Zack DJ, Johnston RJ. Thyroid hormone signaling specifies cone subtypes in human retinal organoids. Science 2018; 362:362/6411/eaau6348. [PMID: 30309916 PMCID: PMC6249681 DOI: 10.1126/science.aau6348] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 08/30/2018] [Indexed: 12/24/2022]
Abstract
INTRODUCTION: Cone photoreceptors in the human retina enable daytime, color, and high-acuity vision. The three subtypes of human cones are defined by the visual pigment that they express: blue-opsin (short wavelength; S), green-opsin (medium wavelength; M), or red-opsin (long wavelength; L). Mutations that affect opsin expression or function cause various forms of color blindness and retinal degeneration. RATIONALE: Our current understanding of the vertebrate eye has been derived primarily from the study of model organisms. We studied the human retina to understand the developmental mechanisms that generate the mosaic of mutually exclusive cone subtypes. Specification of human cones occurs in a two-step process. First, a decision occurs between S versus L/M cone fates. If the L/M fate is chosen, a subsequent choice is made between expression of L- or M-opsin. To determine the mechanism that controls the first decision between S and L/M cone fates, we studied human retinal organoids derived from stem cells. RESULTS: We found that human organoids and retinas have similar distributions, gene expression profiles, and morphologies of cone subtypes. During development, S cones are specified first, followed by L/M cones. This temporal switch from specification of S cones to generation of L/M cones is controlled by thyroid hormone (TH) signaling. In retinal organoids that lacked thyroid hormone receptor β (Thrβ), all cones developed into the S subtype. Thrβ binds with high affinity to triiodothyronine (T3), the more active form of TH, to regulate gene expression. We observed that addition of T3 early during development induced L/M fate in nearly all cones. Thus, TH signaling through Thrβ is necessary and sufficient to induce L/M cone fate and suppress S fate. TH exists largely in two states: thyroxine (T4), the most abundant circulating form of TH, and T3, which binds TH receptors with high affinity. We hypothesized that the retina itself could modulate TH levels to control subtype fates. We found that deiodinase 3 (DIO3), an enzyme that degrades both T3 and T4, was expressed early in organoid and retina development. Conversely, deiodinase 2 (DIO2), an enzyme that converts T4 to active T3, as well as TH carriers and transporters, were expressed later in development. Temporally dynamic expression of TH-degrading and -activating proteins supports a model in which the retina itself controls TH levels, ensuring low TH signaling early to specify S cones and high TH signaling later in development to produce L/M cones. CONCLUSION: Studies of model organisms and human epidemiology often generate hypotheses about human biology that cannot be studied in humans. Organoids provide a system to determine the mechanisms of human development, enabling direct testing of hypotheses in developing human tissue. Our studies identify temporal regulation of TH signaling as a mechanism that controls cone subtype specification in humans. Consistent with our findings, preterm human infants with low T3 and T4 have an increased incidence of color vision defects. Moreover, our identification of a mechanism that generates one cone subtype while suppressing the other, coupled with successful transplantation and incorporation of stem cell-derived photoreceptors in mice, suggests that the promise of therapies to treat human diseases such as color blindness, retinitis pigmentosa, and macular degeneration will be achieved in the near future. ■ The mechanisms underlying specification of neuronal subtypes within the human nervous system are largely unknown. The blue (S), green (M), and red (L) cones of the retina enable high-acuity daytime and color vision. To determine the mechanism that controls S versus L/M fates, we studied the differentiation of human retinal organoids. Organoids and retinas have similar distributions, expression profiles, and morphologies of cone subtypes. S cones are specified first, followed by L/M cones, and thyroid hormone signaling controls this temporal switch. Dynamic expression of thyroid hormone–degrading and –activating proteins within the retina ensures low signaling early to specify S cones and high signaling late to produce L/M cones. This work establishes organoids as a model for determining mechanisms of human development with promising utility for therapeutics and vision repair.
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Affiliation(s)
- Kiara C Eldred
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Sarah E Hadyniak
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Katarzyna A Hussey
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Boris Brenerman
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Ping-Wu Zhang
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xitiz Chamling
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Valentin M Sluch
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Derek S Welsbie
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samer Hattar
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Taylor
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.,Department of Computer Science, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Karl Wahlin
- Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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Duboué ER, Hong E, Eldred KC, Halpern ME. Left Habenular Activity Attenuates Fear Responses in Larval Zebrafish. Curr Biol 2017; 27:2154-2162.e3. [PMID: 28712566 DOI: 10.1016/j.cub.2017.06.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/03/2017] [Accepted: 06/08/2017] [Indexed: 11/26/2022]
Abstract
Fear responses are defensive states that ensure survival of an organism in the presence of a threat. Perception of an aversive cue causes changes in behavior and physiology, such as freezing and elevated cortisol, followed by a return to the baseline state when the threat is evaded [1]. Neural systems that elicit fear behaviors include the amygdala, hippocampus, and medial prefrontal cortex. However, aside from a few examples, little is known about brain regions that promote recovery from an aversive event [2]. Previous studies had implicated the dorsal habenular nuclei in regulating fear responses and boldness in zebrafish [3-7]. We now show, through perturbation of its inherent left-right (L-R) asymmetry at larval stages, that the dorsal habenulo-interpeduncular (dHb-IPN) pathway expedites the return of locomotor activity following an unexpected negative stimulus, electric shock. Severing habenular efferents to the IPN, or only those from the left dHb, prolongs the freezing behavior that follows shock. Individuals with a symmetric, right-isomerized dHb also exhibit increased freezing. In contrast, larvae that have a symmetric, left-isomerized dHb, or in which just the left dHb-IPN projection is optogenetically activated, rapidly resume swimming post shock. In vivo calcium imaging reveals a neuronal subset, predominantly in the left dHb, whose activation is correlated with resumption of swimming. The results demonstrate functional specialization of the left dHb-IPN pathway in attenuating the response to fear.
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Affiliation(s)
- Erik R Duboué
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Elim Hong
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Kiara C Eldred
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Marnie E Halpern
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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11
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Moore SK, Bill BD, Hay LR, Emenegger J, Eldred KC, Greengrove CL, Masura JE, Anderson DM. Factors regulating excystment of Alexandrium in Puget Sound, WA, USA. Harmful Algae 2015; 43:103-110. [PMID: 26109923 PMCID: PMC4476272 DOI: 10.1016/j.hal.2015.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Factors regulating excystment of a toxic dinoflagellate in the genus Alexandrium were investigated in cysts from Puget Sound, Washington State, USA. Experiments were carried out in the laboratory using cysts collected from benthic seedbeds to determine if excystment is controlled by internal or environmental factors. The results suggest that the timing of germination is not tightly controlled by an endogenous clock, though there is a suggestion of a cyclical pattern. This was explored using cysts that had been stored under cold (4 °C), anoxic conditions in the dark and then incubated for 6 weeks at constant favorable environmental conditions. Excystment occurred during all months of the year, with variable excystment success ranging from 31-90%. When cysts were isolated directly from freshly collected sediments every month and incubated at the in situ bottom water temperature, a seasonal pattern in excystment was observed that was independent of temperature. This pattern may be consistent with secondary dormancy, an externally modulated pattern that prevents excystment during periods that are not favorable for sustained vegetative growth. However, observation over more annual cycles is required and the duration of the mandatory dormancy period of these cysts must be determined before the seasonality of germination can be fully characterized in Alexandrium from Puget Sound. Both temperature and light were found to be important environmental factors regulating excystment, with the highest rates of excystment observed for the warmest temperature treatment (20 °C) and in the light.
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Affiliation(s)
- Stephanie K. Moore
- University Corporation for Atmospheric Research, Joint Office for Science Support, Visiting Scientist at Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Brian D. Bill
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Levi R. Hay
- University of Washigton, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Jennifer Emenegger
- University of Washigton, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Kiara C. Eldred
- University of Washigton, under contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, USA
| | - Cheryl L. Greengrove
- University of Washington Tacoma, Campus Box 358400, 1900 Commerce St., Tacoma, WA 98402, USA
| | - Julie E. Masura
- University of Washington Tacoma, Campus Box 358400, 1900 Commerce St., Tacoma, WA 98402, USA
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Eldred KC, Palmiter RD. Amphetamine-induced sensitization has little effect on multiple learning paradigms and fails to rescue mice with a striatal learning defect. PLoS One 2013; 8:e59964. [PMID: 23596507 PMCID: PMC3626598 DOI: 10.1371/journal.pone.0059964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 02/22/2013] [Indexed: 12/31/2022] Open
Abstract
Behavioral sensitization to psychostimulants such as amphetamine (AMPH) is associated with synaptic modifications that are thought to underlie learning and memory. Because AMPH enhances extracellular dopamine in the striatum where dopamine and glutamate signaling are essential for learning, one might expect that the molecular and morphological changes that occur in the striatum in response to AMPH, including changes in synaptic plasticity, would affect learning. To ascertain whether AMPH sensitization affects learning, we tested wild-type mice and mice lacking NMDA receptor signaling in striatal medium spiny neurons in several different learning tests (motor learning, Pavlovian association, U-maze escape test with strategy shifting) with or without prior sensitization to AMPH. Prior sensitization had minimal effect on learning in any of these paradigms in wild-type mice and failed to restore learning in mutant mice, despite the fact that the mutant mice became sensitized by the AMPH treatment. We conclude that the changes in synaptic plasticity and many other signaling events that occur in response to AMPH sensitization are dissociable from those involved in learning the tasks used in our experiments.
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Affiliation(s)
- Kiara C. Eldred
- Department of Biochemistry at the University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
| | - Richard D. Palmiter
- Department of Biochemistry at the University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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13
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Beutler LR, Eldred KC, Quintana A, Keene CD, Rose SE, Postupna N, Montine TJ, Palmiter RD. Severely impaired learning and altered neuronal morphology in mice lacking NMDA receptors in medium spiny neurons. PLoS One 2011; 6:e28168. [PMID: 22132236 PMCID: PMC3221701 DOI: 10.1371/journal.pone.0028168] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 11/02/2011] [Indexed: 12/11/2022] Open
Abstract
The striatum is composed predominantly of medium spiny neurons (MSNs) that integrate excitatory, glutamatergic inputs from the cortex and thalamus, and modulatory dopaminergic inputs from the ventral midbrain to influence behavior. Glutamatergic activation of AMPA, NMDA, and metabotropic receptors on MSNs is important for striatal development and function, but the roles of each of these receptor classes remain incompletely understood. Signaling through NMDA-type glutamate receptors (NMDARs) in the striatum has been implicated in various motor and appetitive learning paradigms. In addition, signaling through NMDARs influences neuronal morphology, which could underlie their role in mediating learned behaviors. To study the role of NMDARs on MSNs in learning and in morphological development, we generated mice lacking the essential NR1 subunit, encoded by the Grin1 gene, selectively in MSNs. Although these knockout mice appear normal and display normal 24-hour locomotion, they have severe deficits in motor learning, operant conditioning and active avoidance. In addition, the MSNs from these knockout mice have smaller cell bodies and decreased dendritic length compared to littermate controls. We conclude that NMDAR signaling in MSNs is critical for normal MSN morphology and many forms of learning.
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Affiliation(s)
- Lisa R. Beutler
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Kiara C. Eldred
- Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Albert Quintana
- Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Shannon E. Rose
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Thomas J. Montine
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Richard D. Palmiter
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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