1
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Pan D, Zhang X, Jin K, Jin ZB. CRX haploinsufficiency compromises photoreceptor precursor translocation and differentiation in human retinal organoids. Stem Cell Res Ther 2023; 14:346. [PMID: 38049871 PMCID: PMC10696917 DOI: 10.1186/s13287-023-03590-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND The CRX-associated autosomal dominant retinopathies suggest a possible pathogenic mechanism of gene haploinsufficiency. However, based on reported human patient cases and studies with mouse models, it is hard to confirm the specific weight of haploinsufficiency in pathogenesis due to the interspecies gaps between gene expression and function. METHODS We created monoallelic CRX by replacing one allele with tdTomato in human embryonic stem cells (hESCs) and subsequently dissect pathogenesis in hESCs-derived retinal organoids. We used transcriptome and immunofluorescence analyses to dissect phenotypic differences between CRX-monoallelic knockout and control wildtype organoids. For location analysis of CRX+ cells, a CRX-expression-tracing system was constructed in control hESCs. We implemented long-term live-cell imaging to describe the translocation of CRX+ cells between two groups in early organoid differentiation. The expression pattern of these dynamic differences was validated using RNA-seq and immunofluorescence assays. RESULTS We identified delayed differentiation of outer nuclear layer (ONL) stratification along with thinner ONL, serious loss of photoreceptor outer segments, as well as downregulated expression of gene for phototransduction and inner/outer segment formation. By live-cell imaging and immunostaining, we observed the overtension of actomyosin network and the arrested translocation of monoallelic CRX+ cells in the early stage of retinal differentiation. CONCLUSIONS We confirmed that gene haploinsufficiency is the mechanism for the dominant pathogenicity of CRX and discovered that CRX regulated postmitotic photoreceptor precursor translocation in addition to its specification of photoreceptor cell fates during human retinal development. These findings revealed a new underlying mechanism of CRX dominant pathogenesis and provided a new clue for the treatment of CRX-associated human retinopathies.
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Affiliation(s)
- Deng Pan
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
| | - Xiao Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Kangxin Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
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2
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Zhang X, Leavey P, Appel H, Makrides N, Blackshaw S. Molecular mechanisms controlling vertebrate retinal patterning, neurogenesis, and cell fate specification. Trends Genet 2023; 39:736-757. [PMID: 37423870 PMCID: PMC10529299 DOI: 10.1016/j.tig.2023.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023]
Abstract
This review covers recent advances in understanding the molecular mechanisms controlling neurogenesis and specification of the developing retina, with a focus on insights obtained from comparative single cell multiomic analysis. We discuss recent advances in understanding the mechanisms by which extrinsic factors trigger transcriptional changes that spatially pattern the optic cup (OC) and control the initiation and progression of retinal neurogenesis. We also discuss progress in unraveling the core evolutionarily conserved gene regulatory networks (GRNs) that specify early- and late-state retinal progenitor cells (RPCs) and neurogenic progenitors and that control the final steps in determining cell identity. Finally, we discuss findings that provide insight into regulation of species-specific aspects of retinal patterning and neurogenesis, including consideration of key outstanding questions in the field.
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Affiliation(s)
- Xin Zhang
- Department of Ophthalmology, Columbia University School of Medicine, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University School of Medicine, New York, NY, USA.
| | - Patrick Leavey
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Haley Appel
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neoklis Makrides
- Department of Ophthalmology, Columbia University School of Medicine, New York, NY, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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3
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Bonezzi PJ, Tarchick MJ, Moore BD, Renna JM. Light drives the developmental progression of outer retinal function. J Gen Physiol 2023; 155:e202213262. [PMID: 37432412 PMCID: PMC10336150 DOI: 10.1085/jgp.202213262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/24/2023] [Accepted: 06/08/2023] [Indexed: 07/12/2023] Open
Abstract
The complex nature of rod and cone photoreceptors and the light-evoked responsivity of bipolar cells in the mature rodent retina have been well characterized. However, little is known about the emergent light-evoked response properties of the mouse retina and the role light plays in shaping these emergent responses. We have previously demonstrated that the outer retina is responsive to green light as early as postnatal day 8 (P8). Here, we characterize the progression of both photoreceptors (rods and cones) and bipolar cell responses during development and into adulthood using ex vivo electroretinogram recordings. Our data show that the majority of photoreceptor response at P8 originates from cones and that these outputs drive second-order bipolar cell responses as early as P9. We find that the magnitude of the photoresponse increases concurrently with each passing day of postnatal development and that many functional properties of these responses, as well as the relative rod/cone contributions to the total light-evoked response, are age dependent. We compare these responses at eye opening and maturity to age-matched animals raised in darkness and found that the absence of light diminishes emergent and mature cone-to-bipolar cell signaling. Furthermore, we found cone-evoked responses to be significantly slower in dark-reared retinas. Together, this work characterizes the developmental photoresponsivity of the mouse retina while highlighting the importance of properly timed sensory input for the maturation of the first visual system synapse.
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Affiliation(s)
- Paul J. Bonezzi
- Department of Biology, The University of Akron, Akron, OH, USA
| | | | | | - Jordan M. Renna
- Department of Biology, The University of Akron, Akron, OH, USA
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4
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Interaction of human CRX and NRL in live HEK293T cells measured using fluorescence resonance energy transfer (FRET). Sci Rep 2022; 12:6937. [PMID: 35484285 PMCID: PMC9050680 DOI: 10.1038/s41598-022-10689-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/11/2022] [Indexed: 12/04/2022] Open
Abstract
CRX and NRL are retina-specific transcription factors that control rod photoreceptor differentiation and synergistically activate rod phototransduction gene expression. Previous experiments showed they interact in vitro and in yeast two-hybrid assays. Here, we examined CRX-NRL interaction in live HEK293T cells using two fluorescence resonance energy transfer (FRET) approaches: confocal microscopy and flow cytometry (FC-FRET). FC-FRET can provide measurements from many cells having wide donor–acceptor expression ranges. FRET efficiencies were calibrated with a series of donor (EGFP)-acceptor (mCherry) fusion proteins separated with linkers between 6–45 amino acids. CRX and NRL were fused at either terminus with EGFP or mCherry to create fluorescent proteins, and all combinations were tested in transiently transfected cells. FRET signals between CRX or NRL homo-pairs were highest with both fluorophores fused to the DNA binding domains (DBD), lower with both fused to the activation domains (AD), and not significant when fused on opposite termini. NRL had stronger FRET signals than CRX. A significant FRET signal between CRX and NRL hetero-pairs was detected when donor was fused to the CRX DNA binding domain and the acceptor fused to the NRL activation domain. FRET signals increased with CRX or NRL expression levels at a rate much higher than expected for collisional FRET alone. Together, our results show the formation of CRX-NRL complexes in live HEK293T cells that are close enough for FRET.
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5
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Lewandowski D, Foik AT, Smidak R, Choi EH, Zhang J, Hoang T, Tworak A, Suh S, Leinonen H, Dong Z, Pinto AF, Tom E, Luu JC, Lee JY, Ma X, Bieberich E, Blackshaw S, Saghatelian A, Lyon DC, Skowronska-Krawczyk D, Tabaka M, Palczewski K. Inhibition of ceramide accumulation in AdipoR1-/- mice increases photoreceptor survival and improves vision. JCI Insight 2022; 7:156301. [PMID: 35015730 PMCID: PMC8876453 DOI: 10.1172/jci.insight.156301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Adiponectin receptor 1 (ADIPOR1) is a lipid and glucose metabolism regulator that possesses intrinsic ceramidase activity. Mutations of the ADIPOR1 gene have been associated with nonsyndromic and syndromic retinitis pigmentosa. Here, we show that the absence of AdipoR1 in mice leads to progressive photoreceptor degeneration, significant reduction of electroretinogram amplitudes, decreased retinoid content in the retina, and reduced cone opsin expression. Single-cell RNA-Seq results indicate that ADIPOR1 encoded the most abundantly expressed ceramidase in mice and one of the 2 most highly expressed ceramidases in the human retina, next to acid ceramidase ASAH1. We discovered an accumulation of ceramides in the AdipoR1–/– retina, likely due to insufficient ceramidase activity for healthy retina function, resulting in photoreceptor death. Combined treatment with desipramine/L-cycloserine (DC) lowered ceramide levels and exerted a protective effect on photoreceptors in AdipoR1–/– mice. Moreover, we observed improvement in cone-mediated retinal function in the DC-treated animals. Lastly, we found that prolonged DC treatment corrected the electrical responses of the primary visual cortex to visual stimuli, approaching near-normal levels for some parameters. These results highlight the importance of ADIPOR1 ceramidase in the retina and show that pharmacological inhibition of ceramide generation can provide a therapeutic strategy for ADIPOR1-related retinopathy.
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Affiliation(s)
- Dominik Lewandowski
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Andrzej T Foik
- International Center for Translational Eye Research, Institute of Physical Chemistry PAS, Warsaw, Poland
| | - Roman Smidak
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Elliot H Choi
- Department of Pharmacology, Case Western Reserve University, Cleveland, United States of America
| | - Jianye Zhang
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Aleksander Tworak
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Susie Suh
- Department of Pharmacology, Case Western Reserve University, Cleveland, United States of America
| | - Henri Leinonen
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Zhiqian Dong
- Department of Medical Devices, Polgenix Inc., Cleveland, United States of America
| | - Antonio Fm Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, United States of America
| | - Emily Tom
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Jennings C Luu
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
| | - Joan Y Lee
- MetroHealth Medical Center, Case Western Reserve University, Cleveland, United States of America
| | - Xiuli Ma
- Department of Medical Devices, Polgenix Inc, Cleveland, United States of America
| | - Erhard Bieberich
- Department of Physiology, University of Kentucky, Lexington, United States of America
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, John Hopkins School of Medicine, Baltimore, United States of America
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, United States of America
| | - David C Lyon
- Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, United States of America
| | | | - Marcin Tabaka
- International Center for Translational Eye Research, Institute of Physical Chemistry PAS, Warsaw, Poland
| | - Krzysztof Palczewski
- Department of Ophthalmology, University of California, Irvine, Irvine, United States of America
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6
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Lovera M, Lüders J. The ciliary impact of nonciliary gene mutations. Trends Cell Biol 2021; 31:876-887. [PMID: 34183231 DOI: 10.1016/j.tcb.2021.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 01/15/2023]
Abstract
Mutations in genes encoding centriolar or ciliary proteins cause diseases collectively known as 'ciliopathies'. Interestingly, the Human Phenotype Ontology database lists numerous disorders that display clinical features reminiscent of ciliopathies but do not involve defects in the centriole-cilium proteome. Instead, defects in different cellular compartments may impair cilia indirectly and cause additional, nonciliopathy phenotypes. This phenotypic heterogeneity, perhaps combined with the field's centriole-cilium-centric view, may have hindered the recognition of ciliary contributions. Identifying these diseases and dissecting how the underlying gene mutations impair cilia not only will add to our understanding of cilium assembly and function but also may open up new therapeutic avenues.
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Affiliation(s)
- Marta Lovera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jens Lüders
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
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Simna SP, Han Z. Prospects Of Non-Coding Elements In Genomic Dna Based Gene Therapy. Curr Gene Ther 2021; 22:89-103. [PMID: 33874871 DOI: 10.2174/1566523221666210419090357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/22/2022]
Abstract
Gene therapy has made significant development since the commencement of the first clinical trials a few decades ago and has remained a dynamic area of research regardless of obstacles such as immune response and insertional mutagenesis. Progression in various technologies like next-generation sequencing (NGS) and nanotechnology has established the importance of non-coding segments of a genome, thereby taking gene therapy to the next level. In this review, we have summarized the importance of non-coding elements, highlighting the advantages of using full-length genomic DNA loci (gDNA) compared to complementary DNA (cDNA) or minigene, currently used in gene therapy. The focus of this review is to provide an overview of the advances and the future of potential use of gDNA loci in gene therapy, expanding the therapeutic repertoire in molecular medicine.
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Affiliation(s)
- S P Simna
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
| | - Zongchao Han
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
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8
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O'Hara-Wright M, Gonzalez-Cordero A. Retinal organoids: a window into human retinal development. Development 2020; 147:147/24/dev189746. [PMID: 33361444 PMCID: PMC7774906 DOI: 10.1242/dev.189746] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinal development and maturation are orchestrated by a series of interacting signalling networks that drive the morphogenetic transformation of the anterior developing brain. Studies in model organisms continue to elucidate these complex series of events. However, the human retina shows many differences from that of other organisms and the investigation of human eye development now benefits from stem cell-derived organoids. Retinal differentiation methods have progressed from simple 2D adherent cultures to self-organising micro-physiological systems. As models of development, these have collectively offered new insights into the previously unexplored early development of the human retina and informed our knowledge of the key cell fate decisions that govern the specification of light-sensitive photoreceptors. Although the developmental trajectories of other retinal cell types remain more elusive, the collation of omics datasets, combined with advanced culture methodology, will enable modelling of the intricate process of human retinogenesis and retinal disease in vitro. Summary: Retinal organoid systems derived from human pluripotent stem cells are micro-physiological systems that offer new insights into previously unexplored human retina development.
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Affiliation(s)
- Michelle O'Hara-Wright
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, 2145, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, 2145, NSW, Australia .,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
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9
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Waldner DM, Ito K, Chen LL, Nguyen L, Chow RL, Lee A, Rancourt DE, Tremblay F, Stell WK, Bech-Hansen NT. Transgenic Expression of Cacna1f Rescues Vision and Retinal Morphology in a Mouse Model of Congenital Stationary Night Blindness 2A (CSNB2A). Transl Vis Sci Technol 2020; 9:19. [PMID: 33117610 PMCID: PMC7571326 DOI: 10.1167/tvst.9.11.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Purpose Congenital stationary night blindness 2A (CSNB2A) is a genetic retinal disorder characterized by poor visual acuity, nystagmus, strabismus, and other signs of retinal dysfunction resulting from mutations in Cacna1f -the gene coding for the pore-forming subunit of the calcium channel CaV1.4. Mouse models of CSNB2A have shown that mutations causing the disease deleteriously affect photoreceptors and their synapses with second-order neurons. This study was undertaken to evaluate whether transgenic expression of Cacna1f could rescue morphology and visual function in a Cacna1f-KO model of CSNB2A. Methods Strategic creation, breeding and use of transgenic mouse lines allowed for Cre-driven retina-specific expression of Cacna1f in a CSNB2A model. Transgene expression and retinal morphology were investigated with immunohistochemistry in retinal wholemounts or cross-sections. Visual function was assessed by optokinetic response (OKR) analysis and electroretinography (ERG). Results Mosaic, prenatal expression of Cacna1f in the otherwise Cacna1f-KO retina was sufficient to rescue some visual function. Immunohistochemical analyses demonstrated wild-type-like photoreceptor and synaptic morphology in sections with transgenic expression of Cacna1f. Conclusions This report describes a novel system for Cre-inducible expression of Cacna1f in a Cacna1f-KO mouse model of CSNB2A and provides preclinical evidence for the potential use of gene therapy in the treatment of CSNB2A. Translational Relevance These data have relevance in the treatment of CSNB2A and in understanding how photoreceptor integration might be achieved in retinas in which photoreceptors have been lost, such as retinitis pigmentosa, age-related macular degeneration, and other degenerative conditions.
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Affiliation(s)
- Derek M Waldner
- Graduate Department of Neuroscience, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kenichi Ito
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Li-Li Chen
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Lisa Nguyen
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Robert L Chow
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Amy Lee
- Department of Molecular Physiology and Biophysics, Department of Otolaryngology Head-Neck Surgery and Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Derrick E Rancourt
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Francois Tremblay
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine, and Clinical Vision Sciences Program, Faculty of Health Dalhousie University, NS, Canada
| | - William K Stell
- Department of Cell Biology and Anatomy and Department of Surgery, Hotchkiss Brain Institute, and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - N Torben Bech-Hansen
- Department of Medical Genetics, and Department of Surgery, Alberta Children's Hospital Research Institute, and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Hassall MM, McClements ME, Barnard AR, Patrício MI, Aslam SA, Maclaren RE. Analysis of Early Cone Dysfunction in an In Vivo Model of Rod-Cone Dystrophy. Int J Mol Sci 2020; 21:ijms21176055. [PMID: 32842706 PMCID: PMC7503557 DOI: 10.3390/ijms21176055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 08/20/2020] [Indexed: 01/12/2023] Open
Abstract
Retinitis pigmentosa (RP) is a generic term for a group of genetic diseases characterized by loss of rod and cone photoreceptor cells. Although the genetic causes of RP frequently only affect the rod photoreceptor cells, cone photoreceptors become stressed in the absence of rods and undergo a secondary degeneration. Changes in the gene expression profile of cone photoreceptor cells are likely to occur prior to observable physiological changes. To this end, we sought to achieve greater understanding of the changes in cone photoreceptor cells early in the degeneration process of the Rho−/− mouse model. To account for gene expression changes attributed to loss of cone photoreceptor cells, we normalized PCR in the remaining number of cones to a cone cell reporter (OPN1-GFP). Gene expression profiles of key components involved in the cone phototransduction cascade were correlated with tests of retinal cone function prior to cell loss. A significant downregulation of the photoreceptor transcription factor Crx was observed, which preceded a significant downregulation in cone opsin transcripts that coincided with declining cone function. Our data add to the growing understanding of molecular changes that occur prior to cone dysfunction in a model of rod-cone dystrophy. It is of interest that gene supplementation of CRX by adeno-associated viral vector delivery prior to cone cell loss did not prevent cone photoreceptor degeneration in this mouse model.
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Affiliation(s)
- Mark M. Hassall
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK; (M.E.M.); (A.R.B.); (M.I.P.); (S.A.A.); (R.E.M.)
- Correspondence: ; Tel.: +61-426-732-991
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK; (M.E.M.); (A.R.B.); (M.I.P.); (S.A.A.); (R.E.M.)
| | - Alun R. Barnard
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK; (M.E.M.); (A.R.B.); (M.I.P.); (S.A.A.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Maria I. Patrício
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK; (M.E.M.); (A.R.B.); (M.I.P.); (S.A.A.); (R.E.M.)
| | - Sher A. Aslam
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK; (M.E.M.); (A.R.B.); (M.I.P.); (S.A.A.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Robert E. Maclaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK; (M.E.M.); (A.R.B.); (M.I.P.); (S.A.A.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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11
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Gan L, Yang C, Shu Y, Liu F, Sun R, Deng B, Xu J, Huang G, Qu C, Gong B, Li J. Identification of a novel homozygous nonsense mutation in the CDHR1 gene in a Chinese family with autosomal recessive retinitis pigmentosa. Clin Chim Acta 2020; 507:17-22. [PMID: 32277948 DOI: 10.1016/j.cca.2020.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/07/2020] [Accepted: 04/07/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Retinitis pigmentosa (RP) is a group of hereditary retinal diseases that often lead to blindness. Although 80 genes associated with RP have been observed, the genetic mechanism of approximately 40% RP cases remains unknown. This study was to investigate the disease-causing gene in a Han Chinese family with autosomal recessive RP (arRP). METHODS A Chinese arRP family (RP-2373), consisting of three affected siblings and eight unaffected family members, was recruited in this study. All participants underwent complete ophthalmic examinations, including visual field testing, best-corrected visual acuity, fundus photography and electroretinography. Whole exome sequencing was performed on the three patients and Sanger sequencing was utilized to confirm the mutations identified in all family members and 2010 unrelated controls. RESULTS A novel homozygous nonsense mutation, c.1231C > T (p.Q411X) in the Cadherin-Related Family Member 1 (CDHR1) gene was identified in the RP-2373 family. The proband and her two affected sisters were found to carry a homozygous mutation that led to a substitution of Glutamine to a stop codon. Other unaffected members and 2010 ethnic-matched controls lacked this mutation. These data showed a complete co-segregation of the CDHR1 mutation with arRP in this family. The p.Q411X mutation was observed to affect highly conserved amino acid residue of CHDR1. CONCLUSION Our study expanded the CDHR1 mutation spectrum of RP in the Chinese population, which might help to better understand RP molecular pathogenesis.
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Affiliation(s)
- Li Gan
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chen Yang
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yi Shu
- School of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Fang Liu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ruiting Sun
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Bolin Deng
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Jiaxin Xu
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Guo Huang
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chao Qu
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Bo Gong
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China; Institute of Chengdu Biology, Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu 610072, China.
| | - Jing Li
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China.
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12
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Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ. Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species. Cell Syst 2020; 8:395-411.e8. [PMID: 31121116 DOI: 10.1016/j.cels.2019.04.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/24/2019] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
Analysis of gene expression in single cells allows for decomposition of cellular states as low-dimensional latent spaces. However, the interpretation and validation of these spaces remains a challenge. Here, we present scCoGAPS, which defines latent spaces from a source single-cell RNA-sequencing (scRNA-seq) dataset, and projectR, which evaluates these latent spaces in independent target datasets via transfer learning. Application of developing mouse retina to scRNA-Seq reveals intrinsic relationships across biological contexts and assays while avoiding batch effects and other technical features. We compare the dimensions learned in this source dataset to adult mouse retina, a time-course of human retinal development, select scRNA-seq datasets from developing brain, chromatin accessibility data, and a murine-cell type atlas to identify shared biological features. These tools lay the groundwork for exploratory analysis of scRNA-seq data via latent space representations, enabling a shift in how we compare and identify cells beyond reliance on marker genes or ensemble molecular identity.
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Affiliation(s)
- Genevieve L Stein-O'Brien
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA
| | - Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Thomas Sherman
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Qiwen Hu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Sheng Liu
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
| | - Carlo Colantuoni
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA; Center for Human Systems Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA; Mathematical Institute for Data Science, Johns Hopkins University, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering and Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA.
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13
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Buono L, Martinez-Morales JR. Retina Development in Vertebrates: Systems Biology Approaches to Understanding Genetic Programs: On the Contribution of Next-Generation Sequencing Methods to the Characterization of the Regulatory Networks Controlling Vertebrate Eye Development. Bioessays 2020; 42:e1900187. [PMID: 31997389 DOI: 10.1002/bies.201900187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/16/2020] [Indexed: 12/18/2022]
Abstract
The ontogeny of the vertebrate retina has been a topic of interest to developmental biologists and human geneticists for many decades. Understanding the unfolding of the genetic program that transforms a field of progenitors cells into a functionally complex and multi-layered sensory organ is a formidable challenge. Although classical genetic studies succeeded in identifying the key regulators of retina specification, understanding the architecture of their gene network and predicting their behavior are still a distant hope. The emergence of next-generation sequencing platforms revolutionized the field unlocking the access to genome-wide datasets. Emerging techniques such as RNA-seq, ChIP-seq, ATAC-seq, or single cell RNA-seq are used to characterize eye developmental programs. These studies provide valuable information on the transcriptional and cis-regulatory profiles of precursors and differentiated cells, outlining the trajectories that connect each intermediate state. Here, recent systems biology efforts are reviewed to understand the genetic programs shaping the vertebrate retina.
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Affiliation(s)
- Lorena Buono
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA) , Seville, 41013 , Spain
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14
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Albrecht NE, Alevy J, Jiang D, Burger CA, Liu BI, Li F, Wang J, Kim SY, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gaspero A, Justice MJ, Westenskow PD, Yamamoto S, Seavitt JR, Beaudet AL, Dickinson ME, Samuel MA. Rapid and Integrative Discovery of Retina Regulatory Molecules. Cell Rep 2020; 24:2506-2519. [PMID: 30157441 DOI: 10.1016/j.celrep.2018.07.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/15/2018] [Accepted: 07/27/2018] [Indexed: 12/26/2022] Open
Abstract
Retinal function relies on precisely organized neurons and synapses and a properly patterned vasculature to support them. Alterations in these features can result in vision loss. However, our understanding of retinal organization pathways remains incomplete because of a lack of methods to rapidly identify neuron and vasculature regulators in mammals. Here we developed a pipeline for the identification of neural and synaptic integrity genes by high-throughput retinal screening (INSiGHT) that analyzes candidate expression, vascular patterning, cellular organization, and synaptic arrangement. Using this system, we examined 102 mutant mouse lines and identified 16 unique retinal regulatory genes. Fifteen of these candidates are identified as novel retina regulators, and many (9 of 16) are associated with human neural diseases. These results expand the genetic landscape involved in retinal circuit organization and provide a road map for continued discovery of mammalian retinal regulators and disease-causing alleles.
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Affiliation(s)
- Nicholas E Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan Alevy
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney A Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian I Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fenge Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julia Wang
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angelina Gaspero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica J Justice
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Peter D Westenskow
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary E Dickinson
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie A Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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15
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Lukowski SW, Lo CY, Sharov AA, Nguyen Q, Fang L, Hung SS, Zhu L, Zhang T, Grünert U, Nguyen T, Senabouth A, Jabbari JS, Welby E, Sowden JC, Waugh HS, Mackey A, Pollock G, Lamb TD, Wang PY, Hewitt AW, Gillies MC, Powell JE, Wong RC. A single-cell transcriptome atlas of the adult human retina. EMBO J 2019; 38:e100811. [PMID: 31436334 DOI: 10.15252/embj.2018100811] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 01/12/2023] Open
Abstract
The retina is a specialized neural tissue that senses light and initiates image processing. Although the functional organization of specific retina cells has been well studied, the molecular profile of many cell types remains unclear in humans. To comprehensively profile the human retina, we performed single-cell RNA sequencing on 20,009 cells from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct cell populations representing all known neural retinal cells: rod photoreceptors, cone photoreceptors, Müller glia, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, astrocytes, and microglia. Our data captured molecular profiles for healthy and putative early degenerating rod photoreceptors, and revealed the loss of MALAT1 expression with longer post-mortem time, which potentially suggested a novel role of MALAT1 in rod photoreceptor degeneration. We have demonstrated the use of this retina transcriptome atlas to benchmark pluripotent stem cell-derived cone photoreceptors and an adult Müller glia cell line. This work provides an important reference with unprecedented insights into the transcriptional landscape of human retinal cells, which is fundamental to understanding retinal biology and disease.
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Affiliation(s)
- Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
| | - Camden Y Lo
- Monash University, Melbourne, Vic., Australia
| | - Alexei A Sharov
- National Institute for Aging, National Institutes of Health, Baltimore, MD, USA
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
| | - Lyujie Fang
- Centre for Eye Research Australia, Melbourne, Vic., Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Vic., Australia.,Jinan University, Guangzhou, China
| | - Sandy Sc Hung
- Centre for Eye Research Australia, Melbourne, Vic., Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Vic., Australia
| | - Ling Zhu
- The University of Sydney, Faculty of Medicine, Save Sight Institute, Sydney, NSW, Australia
| | - Ting Zhang
- The University of Sydney, Faculty of Medicine, Save Sight Institute, Sydney, NSW, Australia
| | - Ulrike Grünert
- The University of Sydney, Faculty of Medicine, Save Sight Institute, Sydney, NSW, Australia
| | - Tu Nguyen
- Centre for Eye Research Australia, Melbourne, Vic., Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Vic., Australia
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jafar S Jabbari
- Australian Genome Research Facility, Melbourne, Vic., Australia
| | - Emily Welby
- Stem Cells and Regenerative Medicine Section, NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Jane C Sowden
- Stem Cells and Regenerative Medicine Section, NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | | | | | - Trevor D Lamb
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Peng-Yuan Wang
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Melbourne, Vic., Australia.,Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Science, Shenzhen, China
| | - Alex W Hewitt
- Centre for Eye Research Australia, Melbourne, Vic., Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Vic., Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Tas., Australia
| | - Mark C Gillies
- The University of Sydney, Faculty of Medicine, Save Sight Institute, Sydney, NSW, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia
| | - Raymond Cb Wong
- Centre for Eye Research Australia, Melbourne, Vic., Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Vic., Australia.,Shenzhen Eye Hospital, Shenzhen University School of Medicine, Shenzhen, China
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16
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Clark BS, Stein-O'Brien GL, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S. Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification. Neuron 2019; 102:1111-1126.e5. [PMID: 31128945 PMCID: PMC6768831 DOI: 10.1016/j.neuron.2019.04.010] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/07/2019] [Accepted: 04/03/2019] [Indexed: 12/26/2022]
Abstract
Precise temporal control of gene expression in neuronal progenitors is necessary for correct regulation of neurogenesis and cell fate specification. However, the cellular heterogeneity of the developing CNS has posed a major obstacle to identifying the gene regulatory networks that control these processes. To address this, we used single-cell RNA sequencing to profile ten developmental stages encompassing the full course of retinal neurogenesis. This allowed us to comprehensively characterize changes in gene expression that occur during initiation of neurogenesis, changes in developmental competence, and specification and differentiation of each major retinal cell type. We identify the NFI transcription factors (Nfia, Nfib, and Nfix) as selectively expressed in late retinal progenitor cells and show that they control bipolar interneuron and Müller glia cell fate specification and promote proliferative quiescence.
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Affiliation(s)
- Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Genevieve L Stein-O'Brien
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fion Shiau
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gabrielle H Cannon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily Davis-Marcisak
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas Sherman
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thanh V Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fatemeh Rajaii
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rebecca E James-Esposito
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Richard M Gronostajski
- Department of Biochemistry, Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Computational Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Mathematical Institute for Data Science, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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17
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Alevy J, Burger CA, Albrecht NE, Jiang D, Samuel MA. Progressive myoclonic epilepsy-associated gene Kctd7 regulates retinal neurovascular patterning and function. Neurochem Int 2019; 129:104486. [PMID: 31175897 DOI: 10.1016/j.neuint.2019.104486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 12/28/2022]
Abstract
Neuron function relies on and instructs the development and precise organization of neurovascular units that in turn support circuit activity. However, our understanding of the molecular cues that regulate this relationship remains sparse. Using a high-throughput screening pipeline, we recently identified several new regulators of vascular patterning. Among these was the potassium channel tetramerization domain-containing protein 7 (KCTD7). Mutations in KCTD7 are associated with progressive myoclonic epilepsy, but how KCTD7 regulates neural development and function remains poorly understood. To begin to identify such mechanisms, we focus on mouse retina, a tractable part of the central nervous system that contains precisely ordered neuron subtypes supported by a trilaminar vascular network. We find that deletion of Kctd7 induces defective patterning of the adult retina vascular network, resulting in increased branching, vessel length, and lacunarity. These alterations reflect early and specific defects in vessel development, as emergence of the superficial and deep vascular layers were delayed. These defects are likely due to a role for Kctd7 in inner retina neurons. Kctd7 is absent from vessels but present in neurons in the inner retina, and its deletion resulted in a corresponding increase in the number of bipolar cells in development and increased vessel branching in adults. These alterations were accompanied by retinal function deficits. Together, these data suggest that neuronal Kctd7 drives growth and patterning of the vasculature and that neurovascular interactions may participate in the pathogenesis of KCTD7-related human diseases.
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Affiliation(s)
- Jonathan Alevy
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Courtney A Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas E Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Melanie A Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA.
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18
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Kaufman ML, Park KU, Goodson NB, Chew S, Bersie S, Jones KL, Lamba DA, Brzezinski JA. Transcriptional profiling of murine retinas undergoing semi-synchronous cone photoreceptor differentiation. Dev Biol 2019; 453:155-167. [PMID: 31163126 DOI: 10.1016/j.ydbio.2019.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/24/2019] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Uncovering the gene regulatory networks that control cone photoreceptor formation has been hindered because cones only make up a few percent of the retina and form asynchronously during development. To overcome these limitations, we used a γ-secretase inhibitor, DAPT, to disrupt Notch signaling and force proliferating retinal progenitor cells to rapidly adopt neuronal identity. We treated mouse retinal explants at the peak of cone genesis with DAPT and examined tissues at several time-points by histology and bulk RNA-sequencing. We found that this treatment caused supernumerary cone formation in an overwhelmingly synchronized fashion. This analysis revealed several categorical patterns of gene expression changes over time relative to DMSO treated control explants. These were placed in the temporal context of the activation of Otx2, a transcription factor that is expressed at the onset of photoreceptor development and that is required for both rod and cone formation. One group of interest had genes, such as Mybl1, Ascl1, Neurog2, and Olig2, that became upregulated by DAPT treatment before Otx2. Two other groups showed upregulated gene expression shortly after Otx2, either transiently or permanently. This included genes such as Mybl1, Meis2, and Podxl. Our data provide a developmental timeline of the gene expression events that underlie the initial steps of cone genesis and maturation. Applying this strategy to human retinal organoid cultures was also sufficient to induce a massive increase in cone genesis. Taken together, our results provide a temporal framework that can be used to elucidate the gene regulatory logic controlling cone photoreceptor development.
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Affiliation(s)
- Michael L Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Noah B Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shereen Chew
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Stephanie Bersie
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deepak A Lamba
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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19
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Getter T, Suh S, Hoang T, Handa JT, Dong Z, Ma X, Chen Y, Blackshaw S, Palczewski K. The selective estrogen receptor modulator raloxifene mitigates the effect of all- trans-retinal toxicity in photoreceptor degeneration. J Biol Chem 2019; 294:9461-9475. [PMID: 31073029 DOI: 10.1074/jbc.ra119.008697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/08/2019] [Indexed: 12/19/2022] Open
Abstract
The retinoid cycle is a metabolic process in the vertebrate retina that continuously regenerates 11-cis-retinal (11-cisRAL) from the all-trans-retinal (atRAL) isomer. atRAL accumulation can cause photoreceptor degeneration and irreversible visual dysfunction associated with incurable blinding retinal diseases, such as Stargardt disease, retinitis pigmentosa (RP), and atrophic age-related macular degeneration (AMD). The underlying cellular mechanisms leading to retinal degeneration remain uncertain, although previous studies have shown that atRAL promotes calcium influx associated with cell apoptosis. To identify compounds that mitigate the effects of atRAL toxicity, here we developed an unbiased and robust image-based assay that can detect changes in intracellular calcium levels in U2OS cells. Using our assay in a high-throughput screen of 2,400 compounds, we noted that selective estrogen receptor modulators (SERMs) potently stabilize intracellular calcium and thereby counteract atRAL-induced toxicity. In a light-induced retinal degeneration mouse model (Abca4 -/- Rdh8 -/-), raloxifene (a benzothiophene-type scaffold SERM) prevented the onset of photoreceptor apoptosis and thus protected the retina from degeneration. The minor structural differences between raloxifene and one of its derivatives (Y 134) had a major impact on calcium homeostasis after atRAL exposure in vitro, and we verified this differential impact in vivo In summary, the SERM raloxifene has structural and functional neuroprotective effects in the retina. We propose that the highly sensitive image-based assay developed here could be applied for the discovery of additional drug candidates preventing photoreceptor degeneration.
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Affiliation(s)
- Tamar Getter
- From the Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697, .,the Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Susie Suh
- From the Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697.,the Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Thanh Hoang
- the Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - James T Handa
- the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | | | - Xiuli Ma
- Polgenix Inc., Irvine, California 92617
| | - Yuanyuan Chen
- the Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, and.,the McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Seth Blackshaw
- the Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Krzysztof Palczewski
- From the Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, California 92697, .,the Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
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20
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Rohde K, Hertz H, Rath MF. Homeobox genes in melatonin-producing pinealocytes: Otx2 and Crx act to promote hormone synthesis in the mature rat pineal gland. J Pineal Res 2019; 66:e12567. [PMID: 30803008 DOI: 10.1111/jpi.12567] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 02/03/2023]
Abstract
Homeobox genes encode transcription factors that regulate developmental processes; however, in the pineal gland, a neuroendocrine organ responsible for nocturnal melatonin synthesis, expression of the homeobox genes Otx2 (orthodenticle homeobox 2) and Crx (cone-rod homeobox) persists postnatally. We here show that OTX2 and CRX are exclusively present in melatonin-producing pinealocytes of the rat pineal gland. To understand the roles of Otx2 and Crx in the mature pineal gland, we used siRNA technology in cultured rat pinealocytes with the nocturnal situation mimicked by adding norepinephrine to the culture media. siRNA-induced knockdown of Otx2 was found to reduce expression levels of the enzymes involved in melatonin synthesis at both transcript and protein levels. Similar results were obtained when knocking down Crx. Knocking down Otx2 and Crx simultaneously produced an even larger reduction in both transcript and protein levels of the melatonin-producing enzymes and also reduced the levels of melatonin released to the culture media. These results suggest that Otx2 and Crx, both alone and in combination, act to control pineal melatonin synthesis.
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Affiliation(s)
- Kristian Rohde
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Hertz
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin F Rath
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Tan L, Xing D, Daley N, Xie XS. Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems. Nat Struct Mol Biol 2019; 26:297-307. [PMID: 30936528 DOI: 10.1038/s41594-019-0205-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/20/2019] [Indexed: 11/09/2022]
Abstract
Sensory neurons in the mouse eye and nose have unusual chromatin organization. Here we report their three-dimensional (3D) genome structure at 20-kilobase (kb) resolution, achieved by applying our recently developed diploid chromatin conformation capture (Dip-C) method to 409 single cells from the retina and the main olfactory epithelium of adult and newborn mice. The 3D genome of rod photoreceptors exhibited inverted radial distribution of euchromatin and heterochromatin compared with that of other cell types, whose nuclear periphery is mainly heterochromatin. Such genome-wide inversion is not observed in olfactory sensory neurons (OSNs). However, OSNs exhibited an interior bias for olfactory receptor (OR) genes and enhancers, in clear contrast to non-neuronal cells. Each OSN harbored multiple aggregates of OR genes and enhancers from different chromosomes. We also observed structural heterogeneity of the protocadherin gene cluster. This type of genome organization may provide the structural basis of the 'one-neuron, one-receptor' rule of olfaction.
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Affiliation(s)
- Longzhi Tan
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Dong Xing
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nicholas Daley
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA.,Belmont Hill School, Belmont, MA, USA
| | - X Sunney Xie
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA. .,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China. .,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.
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22
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New Thiol-Sensitive Dye Application for Measuring Oxidative Stress in Cell Cultures. Sci Rep 2019; 9:1659. [PMID: 30733499 PMCID: PMC6367440 DOI: 10.1038/s41598-018-38132-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/12/2018] [Indexed: 11/13/2022] Open
Abstract
A xanthene derivative, Granada Green dinitrobenzene sulfonate (GGDNBS), has been synthesized to assay cellular oxidative stress based on changes in the concentration of biothiols. The dye is able to react with biological thiols by a thiolysis reaction that promotes a change in fluorescence intensity. To demonstrate the usefulness of GGDNBS for in vivo oxidative stress measurements, 661 W photoreceptor-derived cells were exposed to light to induce ROS generation, and changes in GGDNBS fluorescence were measured. In these cells, GGDNBS fluorescence was correlated with the biothiol levels measured by an enzymatic method. Therefore, GGDNBS allows us to monitor changes in the levels of biothiols associated with ROS generation via single-cell bioimaging.
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23
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Zheng C, Jin FQ, Trippe BL, Wu J, Chalfie M. Inhibition of cell fate repressors secures the differentiation of the touch receptor neurons of Caenorhabditis elegans. Development 2018; 145:dev.168096. [PMID: 30291162 DOI: 10.1242/dev.168096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
Abstract
Terminal differentiation generates the specialized features and functions that allow postmitotic cells to acquire their distinguishing characteristics. This process is thought to be controlled by transcription factors called 'terminal selectors' that directly activate a set of downstream effector genes. In Caenorhabditis elegans, the differentiation of both the mechanosensory touch receptor neurons (TRNs) and the multidendritic nociceptor FLP neurons uses the terminal selectors UNC-86 and MEC-3. The FLP neurons fail to activate TRN genes, however, because a complex of two transcriptional repressors (EGL-44/EGL-46) prevents their expression. Here, we show that the ZEB family transcriptional factor ZAG-1 promotes TRN differentiation not by activating TRN genes but by preventing the expression of EGL-44/EGL-46. As EGL-44/EGL-46 also inhibits the production of ZAG-1, these proteins form a bistable, negative-feedback loop that regulates the choice between the two neuronal fates.
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Affiliation(s)
- Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Felix Qiaochu Jin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brian Loeber Trippe
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ji Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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24
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Anand D, Kakrana A, Siddam AD, Huang H, Saadi I, Lachke SA. RNA sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery. Hum Genet 2018; 137:941-954. [PMID: 30417254 DOI: 10.1007/s00439-018-1958-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/07/2018] [Indexed: 12/21/2022]
Abstract
Isolated or syndromic congenital cataracts are heterogeneous developmental defects, making the identification of the associated genes challenging. In the past, mouse lens expression microarrays have been successfully applied in bioinformatics tools (e.g., iSyTE) to facilitate human cataract-associated gene discovery. To develop a new resource for geneticists, we report high-throughput RNA sequencing (RNA-seq) profiles of mouse lens at key embryonic stages (E)10.5 (lens pit), E12.5 (primary fiber cell differentiation), E14.5 and E16.5 (secondary fiber cell differentiation). These stages capture important events as the lens develops from an invaginating placode into a transparent tissue. Previously, in silico whole-embryo body (WB)-subtraction-based "lens-enriched" expression has been effective in prioritizing cataract-linked genes. To apply an analogous approach, we generated new mouse WB RNA-seq datasets and show that in silico WB subtraction of lens RNA-seq datasets successfully identifies key genes based on lens-enriched expression. At ≥2 counts-per-million expression, ≥1.5 log2 fold-enrichment (p < 0.05) cutoff, E10.5 lens exhibits 1401 enriched genes (17% lens-expressed genes), E12.5 lens exhibits 1937 enriched genes (22% lens-expressed genes), E14.5 lens exhibits 2514 enriched genes (31% lens-expressed genes), and E16.5 lens exhibits 2745 enriched genes (34% lens-expressed genes). Biological pathway analysis identified genes associated with lens development, transcription regulation and signaling pathways, among other functional groups. Furthermore, these new RNA-seq data confirmed high expression of established cataract-linked genes and identified new potential regulators in the lens. Finally, we developed new lens stage-specific UCSC Genome Brower annotation tracks and made these publicly accessible through iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ) for user-friendly visualization of lens gene expression/enrichment to prioritize genes from high-throughput data from cataract cases.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA
| | - Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, 19716, USA. .,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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25
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Brandebura AN, Morehead M, Heller DT, Holcomb P, Kolson DR, Jones G, Mathers PH, Spirou GA. Glial Cell Expansion Coincides with Neural Circuit Formation in the Developing Auditory Brainstem. Dev Neurobiol 2018; 78:1097-1116. [PMID: 30136399 DOI: 10.1002/dneu.22633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/24/2018] [Accepted: 07/24/2018] [Indexed: 02/01/2023]
Abstract
Neural circuit formation involves maturation of neuronal, glial and vascular cells, as well as cell proliferation and cell death. A fundamental understanding of cellular mechanisms is enhanced by quantification of cell types during key events in synapse formation and pruning and possessing qualified genetic tools for cell type-specific manipulation. Acquiring this information in turn requires validated cell markers and genetic tools. We quantified changing proportions of neurons, astrocytes, oligodendrocytes, and microglia in the medial nucleus of the trapezoid body (MNTB) during neural circuit development. Cell type-specific markers, light microscopy and 3D virtual reality software, the latter developed in our laboratory, were used to count cells within distinct cell populations at postnatal days (P)3 and P6, bracketing the period of nerve terminal growth and pruning in this system. These data revealed a change from roughly equal numbers of neurons and glia at P3 to a 1.5:1 ratio of glia to neurons at P6. PCNA and PH3 labeling revealed that proliferation of oligodendrocytes contributed to the increase in glial cell number during this timeframe. We next evaluated Cre driver lines for selectivity in labeling cell populations. En1-Cre was specific for MNTB neurons. PDGFRα-Cre and Aldh1L1-Cre, thought to be mostly specific for oligodendrocyte lineage cells and astrocytes, respectively, both labeled significant numbers of neurons, oligodendrocytes, and astrocytes and are non-specific genetic tools in this neural system.
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Affiliation(s)
- Ashley N Brandebura
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia.,Graduate program in Biochemistry and Molecular Biology, West Virginia University, Morgantown, West Virginia.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia
| | - Michael Morehead
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia.,Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, West Virginia
| | - Daniel T Heller
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia
| | - Paul Holcomb
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia
| | - Douglas R Kolson
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia
| | - Garrett Jones
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia
| | - Peter H Mathers
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia.,Department of Biochemistry, West Virginia University, Morgantown, West Virginia.,Department of Otolaryngology HNS, West Virginia University, Morgantown, West Virginia.,Department of Ophthalmology, West Virginia University, Morgantown, West Virginia
| | - George A Spirou
- Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia.,Sensory Neuroscience Research Center, West Virginia University, Morgantown, West Virginia.,Department of Otolaryngology HNS, West Virginia University, Morgantown, West Virginia
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26
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Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs SL, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. Nat Commun 2018; 9:1364. [PMID: 29636475 PMCID: PMC5893535 DOI: 10.1038/s41467-018-03856-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Age-related macular degeneration (AMD) is a significant cause of vision loss in the elderly. The extent to which epigenetic changes regulate AMD progression is unclear. Here we globally profile chromatin accessibility using ATAC-Seq in the retina and retinal pigmented epithelium (RPE) from AMD and control patients. Global decreases in chromatin accessibility occur in the RPE with early AMD, and in the retina of advanced disease, suggesting that dysfunction in the RPE drives disease onset. Footprints of photoreceptor and RPE-specific transcription factors are enriched in differentially accessible regions (DARs). Genes associated with DARs show altered expression in AMD. Cigarette smoke treatment of RPE cells recapitulates chromatin accessibility changes seen in AMD, providing an epigenetic link between a known risk factor for AMD and AMD pathology. Finally, overexpression of HDAC11 is partially responsible for the observed reduction in chromatin accessibility, suggesting that HDAC11 may be a potential new therapeutic target for AMD.
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Affiliation(s)
- Jie Wang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Peng Shang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Srinivasa R Sripathi
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pingwu Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Marisol Cano
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shuli Xia
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Hugo W Moser Research Institute at Kennedy Krieger, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Shannath L Merbs
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Donald J Zack
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James T Handa
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Debasish Sinha
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Ophthalmology, Cell Biology and Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15224, USA
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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27
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A Red-Emitting, Multidimensional Sensor for the Simultaneous Cellular Imaging of Biothiols and Phosphate Ions. SENSORS 2018; 18:s18010161. [PMID: 29315248 PMCID: PMC5795539 DOI: 10.3390/s18010161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/21/2017] [Accepted: 01/02/2018] [Indexed: 01/12/2023]
Abstract
The development of new fluorescent probes for cellular imaging is currently a very active field because of the large potential in understanding cell physiology, especially targeting anomalous behaviours due to disease. In particular, red-emitting dyes are keenly sought, as the light in this spectral region presents lower interferences and a deeper depth of penetration in tissues. In this work, we have synthesized a red-emitting, dual probe for the multiplexed intracellular detection of biothiols and phosphate ions. We have prepared a fluorogenic construct involving a silicon-substituted fluorescein for red emission. The fluorogenic reaction is selectively started by the presence of biothiols. In addition, the released fluorescent moiety undergoes an excited-state proton transfer reaction promoted by the presence of phosphate ions, which modulates its fluorescence lifetime, τ, with the total phosphate concentration. Therefore, in a multidimensional approach, the intracellular levels of biothiols and phosphate can be detected simultaneously using a single fluorophore and with spectral clearing of cell autofluorescence interferences. We have applied this concept to different cell lines, including photoreceptor cells, whose levels of biothiols are importantly altered by light irradiation and other oxidants.
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28
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Garcia AL, Udeh A, Kalahasty K, Hackam AS. A growing field: The regulation of axonal regeneration by Wnt signaling. Neural Regen Res 2018; 13:43-52. [PMID: 29451203 PMCID: PMC5840987 DOI: 10.4103/1673-5374.224359] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The canonical Wnt/β-catenin pathway is a highly conserved signaling cascade that plays critical roles during embryogenesis. Wnt ligands regulate axonal extension, growth cone guidance and synaptogenesis throughout the developing central nervous system (CNS). Recently, studies in mammalian and fish model systems have demonstrated that Wnt/β-catenin signaling also promotes axonal regeneration in the adult optic nerve and spinal cord after injury, raising the possibility that Wnt could be developed as a therapeutic strategy. In this review, we summarize experimental evidence that reveals novel roles for Wnt signaling in the injured CNS, and discuss possible mechanisms by which Wnt ligands could overcome molecular barriers inhibiting axonal growth to promote regeneration. A central challenge in the neuroscience field is developing therapeutic strategies that induce robust axonal regeneration. Although adult axons have the capacity to respond to axonal guidance molecules after injury, there are several major obstacles for axonal growth, including extensive neuronal death, glial scars at the injury site, and lack of axonal guidance signals. Research in rodents demonstrated that activation of Wnt/β-catenin signaling in retinal neurons and radial glia induced neuronal survival and axonal growth, but that activation within reactive glia at the injury site promoted proliferation and glial scar formation. Studies in zebrafish spinal cord injury models confirm an axonal regenerative role for Wnt/β-catenin signaling and identified the cell types responsible. Additionally, in vitro and in vivo studies demonstrated that Wnt induces axonal and neurite growth through transcription-dependent effects of its central mediator β-catenin, potentially by inducing regeneration-promoting genes. Canonical Wnt signaling may also function through transcription-independent interactions of β-catenin with cytoskeletal elements, which could stabilize growing axons and control growth cone movement. Therefore, these studies suggest that Wnt-induced pathways responsible for regulating axonal growth during embryogenesis could be repurposed to promote axonal growth after injury.
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Affiliation(s)
- Armando L Garcia
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Adanna Udeh
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Karthik Kalahasty
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Abigail S Hackam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
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29
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Daum JM, Keles Ö, Holwerda SJ, Kohler H, Rijli FM, Stadler M, Roska B. The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch. eLife 2017; 6:31437. [PMID: 29106373 PMCID: PMC5685475 DOI: 10.7554/elife.31437] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/03/2017] [Indexed: 11/16/2022] Open
Abstract
High-resolution daylight vision is mediated by cone photoreceptors. The molecular program responsible for the formation of their light sensor, the outer segment, is not well understood. We correlated daily changes in ultrastructure and gene expression in postmitotic mouse cones, between birth and eye opening, using serial block-face electron microscopy (EM) and RNA sequencing. Outer segments appeared rapidly at postnatal day six and their appearance coincided with a switch in gene expression. The switch affected over 14% of all expressed genes. Genes that switched off were rich in transcription factors and neurogenic genes. Those that switched on contained genes relevant for cone function. Chromatin rearrangements in enhancer regions occurred before the switch was completed, but not after. We provide a resource comprised of correlated EM, RNAseq, and ATACseq data, showing that the growth of a key compartment of a postmitotic cell involves an extensive switch in gene expression and chromatin accessibility.
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Affiliation(s)
- Janine M Daum
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Özkan Keles
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sjoerd Jb Holwerda
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Michael Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Insitute of Bioinformatics, Basel, Switzerland
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
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30
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Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity. Proc Natl Acad Sci U S A 2017; 114:E8264-E8273. [PMID: 28900001 DOI: 10.1073/pnas.1707021114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Precise transcriptional regulation controlled by a transcription factor network is known to be crucial for establishing correct neuronal cell identities and functions in the CNS. In the retina, the expression of various cone and rod photoreceptor cell genes is regulated by multiple transcription factors; however, the role of epigenetic regulation in photoreceptor cell gene expression has been poorly understood. Here, we found that Samd7, a rod-enriched sterile alpha domain (SAM) domain protein, is essential for silencing nonrod gene expression through H3K27me3 regulation in rod photoreceptor cells. Samd7-null mutant mice showed ectopic expression of nonrod genes including S-opsin in rod photoreceptor cells and rod photoreceptor cell dysfunction. Samd7 physically interacts with Polyhomeotic homologs (Phc proteins), components of the Polycomb repressive complex 1 (PRC1), and colocalizes with Phc2 and Ring1B in Polycomb bodies. ChIP assays showed a significant decrease of H3K27me3 in the genes up-regulated in the Samd7-deficient retina, showing that Samd7 deficiency causes the derepression of nonrod gene expression in rod photoreceptor cells. The current study suggests that Samd7 is a cell type-specific PRC1 component epigenetically defining rod photoreceptor cell identity.
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31
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Aldiri I, Xu B, Wang L, Chen X, Hiler D, Griffiths L, Valentine M, Shirinifard A, Thiagarajan S, Sablauer A, Barabas ME, Zhang J, Johnson D, Frase S, Zhou X, Easton J, Zhang J, Mardis ER, Wilson RK, Downing JR, Dyer MA. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis. Neuron 2017; 94:550-568.e10. [PMID: 28472656 PMCID: PMC5508517 DOI: 10.1016/j.neuron.2017.04.022] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/15/2017] [Accepted: 04/14/2017] [Indexed: 12/21/2022]
Abstract
In the developing retina, multipotent neural progenitors undergo unidirectional differentiation in a precise spatiotemporal order. Here we profile the epigenetic and transcriptional changes that occur during retinogenesis in mice and humans. Although some progenitor genes and cell cycle genes were epigenetically silenced during retinogenesis, the most dramatic change was derepression of cell-type-specific differentiation programs. We identified developmental-stage-specific super-enhancers and showed that most epigenetic changes are conserved in humans and mice. To determine how the epigenome changes during tumorigenesis and reprogramming, we performed integrated epigenetic analysis of murine and human retinoblastomas and induced pluripotent stem cells (iPSCs) derived from murine rod photoreceptors. The retinoblastoma epigenome mapped to the developmental stage when retinal progenitors switch from neurogenic to terminal patterns of cell division. The epigenome of retinoblastomas was more similar to that of the normal retina than that of retina-derived iPSCs, and we identified retina-specific epigenetic memory.
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Affiliation(s)
- Issam Aldiri
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Lu Wang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Daniel Hiler
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Lyra Griffiths
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Marc Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Abbas Shirinifard
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Suresh Thiagarajan
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andras Sablauer
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Marie-Elizabeth Barabas
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jiakun Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Dianna Johnson
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Sharon Frase
- Cell and Tissue Imaging Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Elaine R Mardis
- Department of Genetics, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA; Department of Medicine, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA
| | - Richard K Wilson
- Department of Genetics, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA; Siteman Cancer Center, The Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63108, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA; Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
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Identification and prediction of alternative transcription start sites that generate rod photoreceptor-specific transcripts from ubiquitously expressed genes. PLoS One 2017. [PMID: 28640837 PMCID: PMC5480877 DOI: 10.1371/journal.pone.0179230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transcriptome complexity is substantially increased by the use of multiple transcription start sites for a given gene. By utilizing a rod photoreceptor-specific chromatin signature, and the RefSeq database of established transcription start sites, we have identified essentially all known rod photoreceptor genes as well as a group of novel genes that have a high probability of being expressed in rod photoreceptors. Approximately half of these novel rod genes are transcribed into multiple mRNA and/or protein isoforms through alternative transcriptional start sites (ATSS), only one of which has a rod-specific epigenetic signature and gives rise to a rod transcript. This suggests that, during retina development, some genes use ATSS to regulate cell type and temporal specificity, effectively generating a rod transcript from otherwise ubiquitously expressed genes. Biological confirmation of the relationship between epigenetic signatures and gene expression, as well as comparison of our genome-wide chromatin signature maps with available data sets for retina, namely a ChIP-on-Chip study of Polymerase-II (Pol-II) binding sites, ChIP-Seq studies for NRL- and CRX- binding sites and DHS (University of Washington data, available on UCSC mouse Genome Browser as a part of ENCODE project) fully support our hypothesis and together accurately identify and predict an array of new rod transcripts. The same approach was used to identify a number of TSS that are not currently in RefSeq. Biological conformation of the use of some of these TSS suggests that this method will be valuable for exploring the range of transcriptional complexity in many tissues. Comparison of mouse and human genome-wide data indicates that most of these alternate TSS appear to be present in both species, indicating that our approach can be useful for identification of regulatory regions that might play a role in human retinal disease.
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Occelli LM, Tran NM, Narfström K, Chen S, Petersen-Jones SM. CrxRdy Cat: A Large Animal Model for CRX-Associated Leber Congenital Amaurosis. Invest Ophthalmol Vis Sci 2017; 57:3780-92. [PMID: 27427859 PMCID: PMC4960999 DOI: 10.1167/iovs.16-19444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Purpose Mutations in the retinal transcription factor cone-rod homeobox (CRX) gene result in severe dominant retinopathies. A large animal model, the Rdy cat, carrying a spontaneous frameshift mutation in Crx, was reported previously. The present study aimed to further understand pathogenesis in this model by thoroughly characterizing the Rdy retina. Methods Structural and functional changes were found in a comparison between the retinas of CrxRdy/+ kittens and those of wild-type littermates and were determined at various ages by fundus examination, electroretinography (ERG), optical coherence tomography, and histologic analyses. RNA and protein expression changes of Crx and key target genes were analyzed using quantitative reverse-transcribed PCR, Western blot analysis, and immunohistochemistry. Transcription activity of the mutant Crx was measured by a dual-luciferase transactivation assay. Results CrxRdy/+ kittens had no recordable cone ERGs. Rod responses were delayed in development and markedly reduced at young ages and lost by 20 weeks. Photoreceptor outer segment development was incomplete and was followed by progressive outer retinal thinning starting in the cone-rich area centralis. Expression of cone and rod Crx target genes was significantly down-regulated. The mutant Crx allele was overexpressed, leading to high levels of the mutant protein lacking transactivation activity. Conclusions The CrxRdy mutation exerts a dominant negative effect on wild-type Crx by overexpressing mutant protein. These findings, consistent with those of studies in a mouse model, support a conserved pathogenic mechanism for CRX frameshift mutations. The similarities between the feline eye and the human eye with the presence of a central region of high cone density makes the CrxRdy/+ cat a valuable model for preclinical testing of therapies for dominant CRX diseases.
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Affiliation(s)
- Laurence M Occelli
- Small Animal Clinical Sciences Michigan State University, East Lansing, Michigan, United States
| | - Nicholas M Tran
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Kristina Narfström
- Department of Veterinary Medicine and Surgery, University of Missouri-Columbia, Columbia, Missouri, United States
| | - Shiming Chen
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Simon M Petersen-Jones
- Small Animal Clinical Sciences Michigan State University, East Lansing, Michigan, United States
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Chinchore Y, Begaj T, Wu D, Drokhlyansky E, Cepko CL. Glycolytic reliance promotes anabolism in photoreceptors. eLife 2017; 6. [PMID: 28598329 PMCID: PMC5499945 DOI: 10.7554/elife.25946] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
Vertebrate photoreceptors are among the most metabolically active cells, exhibiting a high rate of ATP consumption. This is coupled with a high anabolic demand, necessitated by the diurnal turnover of a specialized membrane-rich organelle, the outer segment, which is the primary site of phototransduction. How photoreceptors balance their catabolic and anabolic demands is poorly understood. Here, we show that rod photoreceptors in mice rely on glycolysis for their outer segment biogenesis. Genetic perturbations targeting allostery or key regulatory nodes in the glycolytic pathway impacted the size of the outer segments. Fibroblast growth factor signaling was found to regulate glycolysis, with antagonism of this pathway resulting in anabolic deficits. These data demonstrate the cell autonomous role of the glycolytic pathway in outer segment maintenance and provide evidence that aerobic glycolysis is part of a metabolic program that supports the biosynthetic needs of a normal neuronal cell type. DOI:http://dx.doi.org/10.7554/eLife.25946.001 Living cells need building materials and energy to grow and carry out their activities. Most cells in the body use sugars like glucose for these purposes. In a process known as glycolysis, cells break down glucose into molecules that are eventually converted to carbon dioxide and water to form the chemical ATP – the cellular currency for energy. Developing cells that have not yet fully specialized, and rapidly dividing cells, like cancer cells, consume large amounts of glucose via aerobic glycolysis (also known as the Warburg effect) as they require high levels of energy and building materials. As cells become more specialized and divide less often, they have a reduced need for building blocks, and adjust their consumption and breakdown of glucose accordingly. One exception is the photoreceptor cells, found in the light-sensitive part of our eyes. Although these specialized cells do not divide, they still need a lot of energy and building blocks to constantly renew their light-sensing and processing structures, and to capture and convert the information from the environment into signals. Previous research has shown that the eye also uses the Warburg effect. However, until now, it was not known whether the photoreceptors or other cells in the eye carry out this form of glycolysis. Using genetic tools, Chinchore et al. analysed how the photoreceptor cells in mice used glucose. The experiments demonstrated that the photoreceptors do indeed carry out the Warburg effect. Chinchore et al. further discovered that the Warburg effect is regulated by the same key enzymes and signalling molecules that cancer cells use. This indicates that specialized cells like photoreceptors might choose to retain certain metabolic features of their precursor cells, if they need to. These findings provide new insight into how photoreceptors use glucose. The next step will be to understand how aerobic glycolysis is regulated in healthy eyes as well as in eyes that are affected by degenerating diseases, which may ultimately lead to new ways of treating blindness. DOI:http://dx.doi.org/10.7554/eLife.25946.002
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Affiliation(s)
- Yashodhan Chinchore
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - Tedi Begaj
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - David Wu
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - Eugene Drokhlyansky
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - Constance L Cepko
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
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Broadgate S, Yu J, Downes SM, Halford S. Unravelling the genetics of inherited retinal dystrophies: Past, present and future. Prog Retin Eye Res 2017; 59:53-96. [PMID: 28363849 DOI: 10.1016/j.preteyeres.2017.03.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The identification of the genes underlying monogenic diseases has been of interest to clinicians and scientists for many years. Using inherited retinal dystrophies as an example of monogenic disease we describe the history of molecular genetic techniques that have been pivotal in the discovery of disease causing genes. The methods that were developed in the 1970's and 80's are still in use today but have been refined and improved. These techniques enabled the concept of the Human Genome Project to be envisaged and ultimately realised. When the successful conclusion of the project was announced in 2003 many new tools and, as importantly, many collaborations had been developed that facilitated a rapid identification of disease genes. In the post-human genome project era advances in computing power and the clever use of the properties of DNA replication has allowed the development of next-generation sequencing technologies. These methods have revolutionised the identification of disease genes because for the first time there is no need to define the position of the gene in the genome. The use of next generation sequencing in a diagnostic setting has allowed many more patients with an inherited retinal dystrophy to obtain a molecular diagnosis for their disease. The identification of novel genes that have a role in the development or maintenance of retinal function is opening up avenues of research which will lead to the development of new pharmacological and gene therapy approaches. Neither of which can be used unless the defective gene and protein is known. The continued development of sequencing technologies also holds great promise for the advent of truly personalised medicine.
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Affiliation(s)
- Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
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Tamoxifen Provides Structural and Functional Rescue in Murine Models of Photoreceptor Degeneration. J Neurosci 2017; 37:3294-3310. [PMID: 28235894 DOI: 10.1523/jneurosci.2717-16.2017] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 02/05/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022] Open
Abstract
Photoreceptor degeneration is a cause of irreversible vision loss in incurable blinding retinal diseases including retinitis pigmentosa (RP) and atrophic age-related macular degeneration. We found in two separate mouse models of photoreceptor degeneration that tamoxifen, a selective estrogen receptor modulator and a drug previously linked with retinal toxicity, paradoxically provided potent neuroprotective effects. In a light-induced degeneration model, tamoxifen prevented onset of photoreceptor apoptosis and atrophy and maintained near-normal levels of electroretinographic responses. Rescue effects were correlated with decreased microglial activation and inflammatory cytokine production in the retina in vivo and a reduction of microglia-mediated toxicity to photoreceptors in vitro, indicating a microglia-mediated mechanism of rescue. Tamoxifen also rescued degeneration in a genetic (Pde6brd10) model of RP, significantly improving retinal structure, electrophysiological responses, and visual behavior. These prominent neuroprotective effects warrant the consideration of tamoxifen as a drug suitable for being repurposed to treat photoreceptor degenerative disease.SIGNIFICANCE STATEMENT Photoreceptor degeneration is a cause of irreversible blindness in a number of retinal diseases such as retinitis pigmentosa (RP) and atrophic age-related macular degeneration. Tamoxifen, a selective estrogen receptor modulator approved for the treatment of breast cancer and previously linked to a low incidence of retinal toxicity, was unexpectedly found to exert marked protective effects against photoreceptor degeneration. Structural and functional protective effects were found for an acute model of light-induced photoreceptor injury and for a genetic model for RP. The mechanism of protection involved the modulation of microglial activation and the production of inflammatory cytokines, highlighting the role of inflammatory mechanisms in photoreceptor degeneration. Tamoxifen may be suitable for clinical study as a potential treatment for diseases involving photoreceptor degeneration.
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Wolf A, Aslanidis A, Langmann T. Retinal expression and localization of Mef2c support its important role in photoreceptor gene expression. Biochem Biophys Res Commun 2016; 483:346-351. [PMID: 28017720 DOI: 10.1016/j.bbrc.2016.12.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
Abstract
Photoreceptor-specific gene expression is controlled by a hierarchical network of transcription factors, including the master regulators cone-rod homeobox (Crx) and neural retina leucine zipper (Nrl). Myocyte-enhancer factor 2c (Mef2c) is an ubiquitously expressed transcription factor with important functions in the cardiovascular system. Here, we performed a detailed analysis of Mef2c expression, localization and function in the retina to further elucidate its potential role for photoreceptor gene regulation. We showed that murine retinal Mef2c mRNA expression was high at birth and peaked at late postnatal developmental stages. Using immunohistochemistry and Western blot, Mef2c protein was detected in the outer nuclear layer of adult mouse and human retinas and localized to the nucleus of 661W photoreceptor-like cells. Mef2c knock-down in 661W cells reduced the expression of arrestin 3 (Arr3) and medium-wave-sensitive cone opsin (Opn1mw) but increased transcript levels of mitogen-activated protein kinase 15 (Mapk15) and phosphodiesterase 6h (Pde6h). In conclusion, Mef2c is highly expressed in the retina where it modulates photoreceptor-specific gene expression.
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Affiliation(s)
- Anne Wolf
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Alexander Aslanidis
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Thomas Langmann
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany.
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Abstract
Müller glia (MG) are the only glial cell type produced by the neuroepithelial progenitor cells that generate the vertebrate retina. MG are required to maintain retinal homeostasis and support the survival of retinal neurons. Furthermore, in certain vertebrate classes, MG function as adult stem cells, mediating retinal regeneration in response to injury. However, the mechanisms that regulate MG development are poorly understood because there is considerable overlap in gene expression between retinal progenitor cells and differentiated MG. We show that the LIM homeodomain transcription factor Lhx2 is required for the development of MG in the mouse retina. Temporally controlled knock-out studies reveal a requirement for Lhx2 during all stages of MG development, ranging from the proliferation of gliocompetent retinal progenitors, activation of Müller-specific gene expression, and terminal differentiation of MG morphological features. We show that Lhx2 regulates gliogenesis in part by regulating directly the expression of Notch pathway genes including Notch1, Dll1, and Dll3 and gliogenic transcription factors such as Hes1, Hes5, Sox8, and Rax. Conditional knock-out of Lhx2 resulted in a rapid downregulation of Notch pathway genes and loss of Notch signaling. We further demonstrate that Müller gliogenesis induced by misexpression of the potently gliogenic Notch pathway transcriptional effector Hes5 requires Lhx2 expression. These results indicate that Lhx2 not only directly regulates expression of Notch signaling pathway components, but also acts together with the gliogenic Notch pathway to drive MG specification and differentiation.
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Divekar SD, Tiek DM, Fernandez A, Riggins RB. Estrogen-related receptor β (ERRβ) - renaissance receptor or receptor renaissance? NUCLEAR RECEPTOR SIGNALING 2016; 14:e002. [PMID: 27507929 PMCID: PMC4978380 DOI: 10.1621/nrs.14002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/25/2016] [Indexed: 01/11/2023]
Abstract
Estrogen-related receptors (ERRs) are founding members of the orphan nuclear receptor (ONR) subgroup of the nuclear receptor superfamily. Twenty-seven years of study have yet to identify cognate ligands for the ERRs, though they have firmly placed ERRα and ERRγ at the intersection of cellular metabolism and oncogenesis. The pace of discovery for novel functions of ERRβ, however, has until recently been somewhat slower than that of its family members. ERRβ has also been largely ignored in summaries and perspectives of the ONR literature. Here, we provide an overview of established and emerging knowledge of ERRβ in mouse, man, and other species, highlighting unique aspects of ERRβ biology that set it apart from the other two estrogen-related receptors, with a focus on the impact of alternative splicing on the structure and function of this receptor.
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Affiliation(s)
- Shailaja D Divekar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
| | - Deanna M Tiek
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
| | - Aileen Fernandez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
| | - Rebecca B Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC (SDD, DMT, AF, RBR)
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Chaitankar V, Karakülah G, Ratnapriya R, Giuste FO, Brooks MJ, Swaroop A. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res 2016; 55:1-31. [PMID: 27297499 DOI: 10.1016/j.preteyeres.2016.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/06/2016] [Accepted: 06/08/2016] [Indexed: 02/08/2023]
Abstract
The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well.
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Affiliation(s)
- Vijender Chaitankar
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Gökhan Karakülah
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Felipe O Giuste
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Matthew J Brooks
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
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41
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Unachukwu UJ, Warren A, Li Z, Mishra S, Zhou J, Sauane M, Lim H, Vazquez M, Redenti S. Predicted molecular signaling guiding photoreceptor cell migration following transplantation into damaged retina. Sci Rep 2016; 6:22392. [PMID: 26935401 PMCID: PMC4776098 DOI: 10.1038/srep22392] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/11/2016] [Indexed: 12/18/2022] Open
Abstract
To replace photoreceptors lost to disease or trauma and restore vision, laboratories around the world are investigating photoreceptor replacement strategies using subretinal transplantation of photoreceptor precursor cells (PPCs) and retinal progenitor cells (RPCs). Significant obstacles to advancement of photoreceptor cell-replacement include low migration rates of transplanted cells into host retina and an absence of data describing chemotactic signaling guiding migration of transplanted cells in the damaged retinal microenvironment. To elucidate chemotactic signaling guiding transplanted cell migration, bioinformatics modeling of PPC transplantation into light-damaged retina was performed. The bioinformatics modeling analyzed whole-genome expression data and matched PPC chemotactic cell-surface receptors to cognate ligands expressed in the light-damaged retinal microenvironment. A library of significantly predicted chemotactic ligand-receptor pairs, as well as downstream signaling networks was generated. PPC and RPC migration in microfluidic ligand gradients were analyzed using a highly predicted ligand-receptor pair, SDF-1α – CXCR4, and both PPCs and RPCs exhibited significant chemotaxis. This work present a systems level model and begins to elucidate molecular mechanisms involved in PPC and RPC migration within the damaged retinal microenvironment.
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Affiliation(s)
- Uchenna John Unachukwu
- Biochemistry Doctoral Program, The Graduate School, City University of New York, New York, NY, USA.,Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, USA
| | - Alice Warren
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, USA
| | - Ze Li
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, USA
| | - Shawn Mishra
- Department of Biomedical Engineering, City College of New York, City University of New York, NY, USA
| | - Jing Zhou
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, USA.,Neuroscience Doctoral Program, The Graduate School, City University of New York, New York, NY, USA
| | - Moira Sauane
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, USA
| | - Hyungsik Lim
- Departments of Physics and Biology, Hunter College of the City University of New York, New York, NY USA
| | - Maribel Vazquez
- Department of Biomedical Engineering, City College of New York, City University of New York, NY, USA
| | - Stephen Redenti
- Biochemistry Doctoral Program, The Graduate School, City University of New York, New York, NY, USA.,Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, USA
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De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing. GENETICS RESEARCH INTERNATIONAL 2015; 2015:638679. [PMID: 26788372 PMCID: PMC4695645 DOI: 10.1155/2015/638679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/29/2023]
Abstract
We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.
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43
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Adachi H, Tominaga H, Maruyama Y, Yoneda K, Maruyama K, Yoshii K, Kinoshita S, Nakano M, Tashiro K. Stage-specific reference genes significant for quantitative PCR during mouse retinal development. Genes Cells 2015; 20:625-35. [PMID: 26059597 DOI: 10.1111/gtc.12254] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/27/2015] [Indexed: 11/26/2022]
Abstract
Developing mouse retina has been serving as an ideal model for investigating the molecular mechanism of neural development and angiogenesis, because several significant events associated with these physiological phenomena are drastically occurring in conjunction with retinal development. However, as many genes are influencing on each other to establish mature retina within 21 days from E10 to P12, we must carefully design the experiments, such as in the case of quantitating the amount of altered gene expression toward the establishment of retina by quantitative PCR. As we have seen considerable variations of quantitative results in different developmental stages of retina depending on the reference genes used for compensation, we here attempted to determine a reliable reference gene to accurately quantitate the target genes in each stage. According to the results of in silico prediction and comparison with a database of SAGE, we found that the most stable gene from early to late stages was Sdha, whereas one of the most popular housekeeping genes, Actb, was the one that could mislead the quantitative results even in the adult stage. Consequently, we pointed out the importance of selecting an appropriate reference gene, especially to quantitate the amount of gene expression in the developmental stages of a certain tissue.
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Affiliation(s)
- Hiroko Adachi
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Hiroyuki Tominaga
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yuko Maruyama
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kazuhito Yoneda
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kazuichi Maruyama
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kengo Yoshii
- Department of Medical Statistics, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Shigeru Kinoshita
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
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Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015; 46:1-30. [PMID: 25668385 PMCID: PMC4402139 DOI: 10.1016/j.preteyeres.2015.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/10/2023]
Abstract
Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.
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Affiliation(s)
- Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA.
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Karali M, Banfi S. Inherited Retinal Dystrophies: the role of gene expression regulators. Int J Biochem Cell Biol 2015; 61:115-9. [PMID: 25697419 DOI: 10.1016/j.biocel.2015.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 12/21/2022]
Abstract
Inherited Retinal Dystrophies (IRDs) are a clinically and genetically heterogeneous group of rare disorders characterized by a significant impairment in retinal function and vision. More than 150 genes have been associated with retinal dystrophies and the genetic overlap among different IRDs renders diagnosis and prognosis challenging. In this In Focus article, we give a summary on the pathogenic role of gene expression regulators in IRDs. Emphasis is given on key transcription factors that participate to regulatory gene networks controlling photoreceptor specification and maintenance, and their possible relevance as therapeutic targets. The increasing knowledge on the composition and function of these transcriptional regulatory networks indicates that intervening on transcription factors may be instrumental for a more effective treatment of some forms of IRDs, although the development of appropriate molecular tools to target them remains a formidable challenge.
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Affiliation(s)
- Marianthi Karali
- Telethon Institute for Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, NA, Italy
| | - Sandro Banfi
- Telethon Institute for Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, NA, Italy; Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples, Italy.
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46
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Patel AK, Surapaneni K, Yi H, Nakamura REI, Karli SZ, Syeda S, Lee T, Hackam AS. Activation of Wnt/β-catenin signaling in Muller glia protects photoreceptors in a mouse model of inherited retinal degeneration. Neuropharmacology 2014; 91:1-12. [PMID: 25486619 DOI: 10.1016/j.neuropharm.2014.11.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 11/13/2014] [Accepted: 11/19/2014] [Indexed: 11/18/2022]
Abstract
The canonical Wnt/β-catenin ("Wnt") pathway is an essential signaling cascade in the embryonic central nervous system (CNS) that regulates neuronal differentiation and survival. Loss of Wnt signaling in developing and adult tissue has been implicated in numerous CNS diseases, but the precise role of Wnt in regulating neuronal survival, and how its absence could lead to disease, is not understood. In this study, we investigated the effect of Wnt activation on neuronal survival in the adult retina, and identified cellular and molecular mediators. Pan-retinal Wnt signaling activation using Wnt3a induced functional and morphological rescue of photoreceptor neurons in the rd10 mouse model of retinal degeneration. Furthermore, Wnt activation using constitutively active β-catenin specifically targeted to Muller glia increased photoreceptor survival and reduced markers of glial and neuronal remodeling. Wnt-induced photoreceptor protection was associated with elevated levels of the prosurvival protein Stat3, and was reduced by shRNA-mediated knock-down of Stat3, indicating cross-talk between survival pathways. Therefore, these data increase our understanding of the role of Wnt signaling in the retina, and identify radial Muller glia as important cellular mediators of Wnt activity.
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Affiliation(s)
- Amit K Patel
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA
| | - Krishna Surapaneni
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA
| | - Hyun Yi
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA
| | - Rei E I Nakamura
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA
| | - Sapir Z Karli
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA
| | - Sarah Syeda
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA
| | - Tinthu Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA
| | - Abigail S Hackam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, USA.
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47
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Aslanidis A, Karlstetter M, Walczak Y, Jägle H, Langmann T. RETINA-specific expression of Kcnv2 is controlled by cone-rod homeobox (Crx) and neural retina leucine zipper (Nrl). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 801:31-41. [PMID: 24664678 DOI: 10.1007/978-1-4614-3209-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Cone dystrophy with supernormal rod response (CDSRR) is an autosomal recessive disorder that leads to progressive retinal degeneration with a distinct electroretinogram (ERG) phenotype. CDSRR patients show reduced sensitivity to dim light, augmented response to suprathreshold light and reduced response to flicker. The disorder is caused by mutations in the KCNV2 gene, which encodes the Kv11.1 subunit of a voltage-gated potassium channel. Here, we studied the retina-specific expression and cis-regulatory activity of the murine Kcnv2 gene using electroporation of explanted retinas. Using qRT-PCR profiling of early postnatal retinas, we showed that Kcnv2 expression increased towards P14, which marks the beginning of visual activity in mice. In vivo electroporation of GFP-Kcnv2 expressing plasmids revealed that Kv11.1 localizes to the inner segment membranes of adult P21 photoreceptors. Using bioinformatic prediction and chromatin immunoprecipitation (ChIP), we identified two Crx binding sites (CBS) and one Nrl binding site (NBS) in the Kcnv2 promoter. Reporter electroporation of the wild type promoter region induced strong DsRed expression, indicating high regulatory activity, whereas shRNA-mediated knockdown of Crx and Nrl resulted in reduced Kcnv2 promoter activity and low endogenous Kcnv2 mRNA expression in the retina. Site-directed mutagenesis of the CBS and NBS demonstrated that CBS2 is crucial for Kcnv2 promoter activity. We conclude that nucleotide changes in evolutionary conserved CBS could impact retina-specific expression levels of Kcnv2.
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Affiliation(s)
- Alexander Aslanidis
- Department of Ophthalmology, University of Cologne, Joseph-Stelzmann-Str. 9, 50931, Cologne, Germany
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Zagozewski JL, Zhang Q, Pinto VI, Wigle JT, Eisenstat DD. The role of homeobox genes in retinal development and disease. Dev Biol 2014; 393:195-208. [PMID: 25035933 DOI: 10.1016/j.ydbio.2014.07.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/02/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022]
Abstract
Homeobox genes are an evolutionarily conserved class of transcription factors that are critical for development of many organ systems, including the brain and eye. During retinogenesis, homeodomain-containing transcription factors, which are encoded by homeobox genes, play essential roles in the regionalization and patterning of the optic neuroepithelium, specification of retinal progenitors and differentiation of all seven of the retinal cell classes that derive from a common progenitor. Homeodomain transcription factors control retinal cell fate by regulating the expression of target genes required for retinal progenitor cell fate decisions and for terminal differentiation of specific retinal cell types. The essential role of homeobox genes during retinal development is demonstrated by the number of human eye diseases, including colobomas and anophthalmia, which are attributed to homeobox gene mutations. In the following review, we highlight the role of homeodomain transcription factors during retinogenesis and regulation of their gene targets. Understanding the complexities of vertebrate retina development will enhance our ability to drive differentiation of specific retinal cell types towards novel cell-based replacement therapies for retinal degenerative diseases.
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Affiliation(s)
- Jamie L Zagozewski
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Qi Zhang
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB, Canada R3E 0J9
| | - Vanessa I Pinto
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9
| | - Jeffrey T Wigle
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9; Institute of Cardiovascular Sciences, St. Boniface Hospital Research Institute, Winnipeg, MB, Canada R2H 2A6
| | - David D Eisenstat
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada T6G 2H7; Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada R3E 0J9; Department of Pediatrics, University of Alberta, Edmonton, AB, Canada T6G 1C9.
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Tran NM, Chen S. Mechanisms of blindness: animal models provide insight into distinct CRX-associated retinopathies. Dev Dyn 2014; 243:1153-66. [PMID: 24888636 DOI: 10.1002/dvdy.24151] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/24/2014] [Accepted: 05/10/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The homeodomain transcription factor CRX is a crucial regulator of mammalian photoreceptor gene expression. Mutations in the human CRX gene are associated with dominant inherited retinopathies Retinitis Pigmentosa (RP), Cone-Rod Dystrophy (CoRD), and Leber Congenital Amaurosis (LCA), of varying severity. In vitro and in vivo assessment of mutant CRX proteins have revealed pathogenic mechanisms for several mutations, but no comprehensive mutation-disease correlation has yet been reported. RESULTS Here we describe four different classes of disease-causing CRX mutations, characterized by mutation type, pathogenetic mechanism, and the molecular activity of the mutant protein: (1) hypomorphic missense mutations with reduced DNA binding, (2) antimorphic missense mutations with variable DNA binding, (3) antimorphic frameshift/nonsense mutations with intact DNA binding, and (4) antimorphic frameshift mutations with reduced DNA binding. Mammalian models representing three of these classes have been characterized. CONCLUSIONS Models carrying Class I mutations display a mild dominant retinal phenotype and recessive LCA, while models carrying Class III and IV mutations display characteristically distinct dominant LCA phenotypes. These animal models also reveal unexpected pathogenic mechanisms underlying CRX-associated retinopathies. The complexity of genotype-phenotype correlation for CRX-associated diseases highlights the value of developing comprehensive "true-to-disease" animal models for understanding pathologic mechanisms and testing novel therapeutic approaches.
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Affiliation(s)
- Nicholas M Tran
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, Missouri
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50
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Murali T, Pacifico S, Finley RL. Integrating the interactome and the transcriptome of Drosophila. BMC Bioinformatics 2014; 15:177. [PMID: 24913703 PMCID: PMC4229734 DOI: 10.1186/1471-2105-15-177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 05/28/2014] [Indexed: 12/29/2022] Open
Abstract
Background Networks of interacting genes and gene products mediate most cellular and developmental processes. High throughput screening methods combined with literature curation are identifying many of the protein-protein interactions (PPI) and protein-DNA interactions (PDI) that constitute these networks. Most of the detection methods, however, fail to identify the in vivo spatial or temporal context of the interactions. Thus, the interaction data are a composite of the individual networks that may operate in specific tissues or developmental stages. Genome-wide expression data may be useful for filtering interaction data to identify the subnetworks that operate in specific spatial or temporal contexts. Here we take advantage of the extensive interaction and expression data available for Drosophila to analyze how interaction networks may be unique to specific tissues and developmental stages. Results We ranked genes on a scale from ubiquitously expressed to tissue or stage specific and examined their interaction patterns. Interestingly, ubiquitously expressed genes have many more interactions among themselves than do non-ubiquitously expressed genes both in PPI and PDI networks. While the PDI network is enriched for interactions between tissue-specific transcription factors and their tissue-specific targets, a preponderance of the PDI interactions are between ubiquitous and non-ubiquitously expressed genes and proteins. In contrast to PDI, PPI networks are depleted for interactions among tissue- or stage- specific proteins, which instead interact primarily with widely expressed proteins. In light of these findings, we present an approach to filter interaction data based on gene expression levels normalized across tissues or developmental stages. We show that this filter (the percent maximum or pmax filter) can be used to identify subnetworks that function within individual tissues or developmental stages. Conclusions These observations suggest that protein networks are frequently organized into hubs of widely expressed proteins to which are attached various tissue- or stage-specific proteins. This is consistent with earlier analyses of human PPI data and suggests a similar organization of interaction networks across species. This organization implies that tissue or stage specific networks can be best identified from interactome data by using filters designed to include both ubiquitously expressed and specifically expressed genes and proteins.
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Affiliation(s)
| | | | - Russell L Finley
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA.
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