Single‐cell RNA sequencing: A new opportunity for retinal research

Overview

Dan Ji, Xiaobo Xia, Haibo Li, Zhou Zeng, Rong Rong, Mengling You

Published Online: Mar 22 2021

DOI: 10.1002/wrna.1652

Full article on Wiley Online Library: HTML PDF

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Abstract Single‐cell RNA sequencing (scRNA‐seq) is a technology for single‐cell transcriptome analysis that can be used to characterize complex dynamics of various retinal cell types. It provides deep scrutiny into the gene expression character of diverse cell types, lending insight into all the biological processes being carried out. The scRNA‐seq is an alternative to regular RNA‐seq, which does not achieve cellular heterogeneity. The retina, is a part of the central nervous system (CNS) and consists of six types of neurons and several types of glial cells. Studying retinal cell heterogeneity is important for understanding retinal diseases. Currently, scRNA‐seq is employed to assess retina development and retinal disease pathogenesis and has improved our understanding of the relationship between the retina, its visual pathways, and the brain. Moreover, this technology provides new ideas on the sensitivity and molecular mechanisms of cell subtypes involved in retinal‐related diseases. The application of scRNA‐seq technology has given us a deeper understanding of the latest advancements and challenges in retinal development and diseases. We advocate scRNA‐seq as one of the important tools for developing novel therapies for retinal diseases. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA in Disease and Development > RNA in Development RNA in Disease and Development > RNA in Disease

General workflow of scRNA‐seq. Organs and tissues are harvested and prepared as a single‐cell suspension. A suitable method is selected for single‐cell capture. After cell lysis, RNA is reverse transcribed to cDNA and amplified by PCR to generate a cDNA library for sequencing. The resulting sequence reads are assigned to cells via cell‐specific barcodes incorporated into the cDNA through the primers used for reverse transcription and are aligned to specific genes. Finally, specific analysis of the obtained data is carried out

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Data analysis process. (a) Flow chart of sequencing data analysis; (b1) single‐cell RNA sequencing; (b2) sequencing data; (b3) single‐cell expression profile obtained after quality control; (b4) cell assignment: this mainly includes cell trajectory analysis and cluster analysis; (b5) gene heat map that can be used to determine gene expression

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Single‐cell transcriptome atlas for the mammalian/human retina (a) structure of the retina; (b) mouse retina: Cluster of 44,808 mouse retinal single cells divided into 39 groups (Macosko et al., 2015); (c) human retina: 20,009 single cells from human retina divided into 18 clusters by t‐SNE (Lukowski et al., 2019); (d) BC: 27,499 bipolar cells divided into 26 clusters by t‐SNE (Shekhar et al., 2016); (e) photoreceptors: Photoreceptor cells from human retinal cells divided into 13 different clusters by t‐SNE (Lukowski et al., 2019); (f) RGC: 6225 RGCs divided into 40 subtypes by clustering (Rheaume et al., 2018); (g) AC: The 32,000 ACs from mice were divided into 63 types (Yan et al., 2020); (h,i) HCs (peripheral and foveal): The fovea and peripheral HC are mainly divided into two clusters (Peng et al., 2019); (j,k) non‐neuronal (peripheral and foveal): Four types of non‐neuronal cells were found in both the fovea and the periphery, including MG, pericytes, endothelial cells, and microglia (Peng et al., 2019)

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References

Armingol,, E., Officer,, A., Harismendy,, O., & Lewis,, N. E. (2021). Deciphering cell‐cell interactions and communication from gene expression. Nature Reviews. Genetics, 22, 71–88.
Benowitz,, L. I., He,, Z., & Goldberg,, J. L. (2017). Reaching the brain: Advances in optic nerve regeneration. Experimental Neurology, 287, 365–373.
Biswas,, S., Thomas,, A. A., Chen,, S., Aref‐Eshghi,, E., Feng,, B., Gonder,, J., Sadikovic,, B., & Chakrabarti,, S. (2018). MALAT1: An epigenetic regulator of inflammation in diabetic retinopathy. Scientific Reports, 8, 6526.
Blackshaw,, S., Harpavat,, S., Trimarchi,, J., Cai,, L., Huang,, H., Kuo,, W. P., Weber,, G., Lee,, K., Fraioli,, R. E., Cho,, S. H., Yung,, R., Asch,, E., Ohno‐Machado,, L., Wong,, W. H., & Cepko,, C. L. (2004). Genomic analysis of mouse retinal development. PLoS Biology, 2, E247.
Caprara,, C., & Grimm,, C. (2012). From oxygen to erythropoietin: Relevance of hypoxia for retinal development, health and disease. Progress in Retinal and Eye Research, 31, 89–119.
Cepko,, C. (2014). Intrinsically different retinal progenitor cells produce specific types of progeny. Nature Reviews. Neuroscience, 15, 615–627.
Chen,, R., Wu,, X., Jiang,, L., & Zhang,, Y. (2017). Single‐cell RNA‐Seq reveals hypothalamic cell diversity. Cell Reports, 18, 3227–3241.
Clark,, B. S., Stein‐O`Brien,, G. L., Shiau,, F., Cannon,, G. H., Davis‐Marcisak,, E., Sherman,, T., Santiago,, C. P., Hoang,, T. V., Rajaii,, F., James‐Esposito,, R. E., Gronostajski,, R. M., Fertig,, E. J., Goff,, L. A., & Blackshaw,, S. (2019). Single‐cell RNA‐Seq analysis of retinal development identifies NFI factors as regulating mitotic exit and late‐born cell specification. Neuron, 102, 1111–1126.
Collin,, J., Queen,, R., Zerti,, D., Dorgau,, B., Hussain,, R., Coxhead,, J., Cockell,, S., & Lako,, M. (2019). Deconstructing retinal organoids: Single cell RNA‐Seq reveals the cellular components of human pluripotent stem cell‐derived retina. Stem Cells, 37, 593–598.
Cowan,, C. S., Renner,, M., De Gennaro,, M., Gross‐Scherf,, B., Goldblum,, D., Hou,, Y., Munz,, M., Rodrigues,, T. M., Krol,, J., Szikra,, T., Cuttat,, R., Waldt,, A., Papasaikas,, P., Diggelmann,, R., Patino‐Alvarez,, C. P., Galliker,, P., Spirig,, S. E., Pavlinic,, D., Gerber‐Hollbach,, N., … Roska,, B. (2020). Cell types of the human retina and its organoids at single‐cell resolution. Cell, 182, 1623–1640.
Crow,, M., & Gillis,, J. (2019). Single cell RNA‐sequencing: Replicability of cell types. Current Opinion in Neurobiology, 56, 69–77.
Dowling,, J. (2012). The retina: An approachable part of the brain (Revised ed.). Belknap Press, Harvard University Press.
Euler,, T., Haverkamp,, S., Schubert,, T., & Baden,, T. (2014). Retinal bipolar cells: Elementary building blocks of vision. Nature Reviews. Neuroscience, 15, 507–519.
Fadl,, B. R., Brodie,, S. A., Malasky,, M., Boland,, J. F., Kelly,, M. C., Kelley,, M. W., Boger,, E., Fariss,, R., Swaroop,, A., & Campello,, L. (2020). An optimized protocol for retina single‐cell RNA sequencing. Molecular Vision, 26, 705–717.
Felszeghy,, S., Viiri,, J., Paterno,, J. J., Hyttinen,, J. M. T., Koskela,, A., Chen,, M., Leinonen,, H., Tanila,, H., Kivinen,, N., Koistinen,, A., Toropainen,, E., Amadio,, M., Smedowski,, A., Reinisalo,, M., Winiarczyk,, M., Mackiewicz,, J., Mutikainen,, M., Ruotsalainen,, A. K., Kettunen,, M., … Kaarniranta,, K. (2019). Loss of NRF‐2 and PGC‐1alpha genes leads to retinal pigment epithelium damage resembling dry age‐related macular degeneration. Redox Biology, 20, 1–12.
Fischer,, D., & Leibinger,, M. (2012). Promoting optic nerve regeneration. Progress in Retinal and Eye Research, 31, 688–701.
Gao,, Z., Mao,, C. A., Pan,, P., Mu,, X., & Klein,, W. H. (2014). Transcriptome of Atoh7 retinal progenitor cells identifies new Atoh7‐dependent regulatory genes for retinal ganglion cell formation. Developmental Neurobiology, 74, 1123–1140.
Garrett,, A. M., Tadenev,, A. L., Hammond,, Y. T., Fuerst,, P. G., & Burgess,, R. W. (2016). Replacing the PDZ‐interacting C‐termini of DSCAM and DSCAML1 with epitope tags causes different phenotypic severity in different cell populations. eLife, 5, e16144.
Grange,, L., Dalal,, M., Nussenblatt,, R. B., & Sen,, H. N. (2014). Autoimmune retinopathy. American Journal of Ophthalmology, 157, 266–272.
Greenblatt,, M. B., Ono,, N., Ayturk,, U. M., Debnath,, S., & Lalani,, S. (2019). The Unmixing problem: A guide to applying single‐cell RNA sequencing to bone. Journal of Bone and Mineral Research, 34, 1207–1219.
Gregg,, R. G., Mccall,, M. A., & Massey,, S. C. J. R. (2013). Function and anatomy of the mammalian. Retina, 1, 360–400.
Gregory‐Evans,, C. Y., Wallace,, V. A., & Gregory‐Evans,, K. (2013). Gene networks: Dissecting pathways in retinal development and disease. Progress in Retinal and Eye Research, 33, 40–66.
Grossniklaus,, H. E., Geisert,, E. E., & Nickerson,, J. M. (2015). Introduction to the retina. Progress in Molecular Biology and Translational Science, 134, 383–396.
Guimaraes,, R. P. M., Landeira,, B. S., Coelho,, D. M., Golbert,, D. C. F., Silveira,, M. S., Linden,, R., de Melo Reis,, R. A., & Costa,, M. R. (2018). Evidence of Muller glia conversion into retina ganglion cells using neurogenin2. Frontiers in Cellular Neuroscience, 12, 410.
Gupta,, R. K., & Kuznicki,, J. (2020). Biological and medical importance of cellular heterogeneity deciphered by single‐cell RNA sequencing. Cell, 9, 1751.
Haque,, A., Engel,, J., Teichmann,, S. A., & Lonnberg,, T. (2017). A practical guide to single‐cell RNA‐sequencing for biomedical research and clinical applications. Genome Medicine, 9, 75.
Heng,, J. S., Rattner,, A., Stein‐O`Brien,, G. L., Winer,, B. L., Jones,, B. W., Vernon,, H. J., Goff,, L. A., & Nathans,, J. (2019). Hypoxia tolerance in the Norrin‐deficient retina and the chronically hypoxic brain studied at single‐cell resolution. Proceedings of the National Academy of Sciences of the United States of America, 116, 9103–9114.
Hoon,, M., Okawa,, H., Della Santina,, L., & Wong,, R. O. (2014). Functional architecture of the retina: Development and disease. Progress in Retinal and Eye Research, 42, 44–84.
Hu,, Y., Wang,, X., Hu,, B., Mao,, Y., Chen,, Y., Yan,, L., Yong,, J., Dong,, J., Wei,, Y., Wang,, W., Wen,, L., Qiao,, J., & Tang,, F. (2019). Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single‐cell RNA‐seq analysis. PLoS Biology, 17, e3000365.
Ivanescu,, A. A., Fernandez‐Robredo,, P., Heras‐Mulero,, H., Sadaba‐Echarri,, L. M., Garcia‐Garcia,, L., Fernandez‐Garcia,, V., Moreno‐Orduna,, M., Redondo‐Exposito,, A., Recalde,, S., & Garcia‐Layana,, A. (2015). Modifying choroidal neovascularization development with a nutritional supplement in mice. Nutrients, 7, 5423–5442.
Johnson,, L. V., Leitner,, W. P., Rivest,, A. J., Staples,, M. K., Radeke,, M. J., & Anderson,, D. H. (2002). The Alzheimer`s A beta‐peptide is deposited at sites of complement activation in pathologic deposits associated with aging and age‐related macular degeneration. Proceedings of the National Academy of Sciences of the United States of America, 99, 11830–11835.
Jusuf,, P. R., Albadri,, S., Paolini,, A., Currie,, P. D., Argenton,, F., Higashijima,, S., Harris,, W. A., & Poggi,, L. (2012). Biasing amacrine subtypes in the Atoh7 lineage through expression of Barhl2. The Journal of Neuroscience, 32, 13929–13944.
Kay,, J. N., Finger‐Baier,, K. C., Roeser,, T., Staub,, W., & Baier,, H. (2001). Retinal ganglion cell genesis requires lakritz, a zebrafish atonal homolog. Neuron, 30, 725–736.
Kolb,, H. (1995). Simple anatomy of the retina. In H. Kolb,, E. Fernandez,, & R. Nelson, (Eds.), Webvision: The organization of the retina and visual system. University of Utah Health Sciences Center.
Kolb,, H. (2003). How the retina works. American Scientist, 91, 28–35.
Kulkarni,, A., Anderson,, A. G., Merullo,, D. P., & Konopka,, G. (2019). Beyond bulk: A review of single cell transcriptomics methodologies and applications. Current Opinion in Biotechnology, 58, 129–136.
Lee,, E. J., Han,, J. C., Park,, D. Y., & Kee,, C. (2020). A neuroglia‐based interpretation of glaucomatous neuroretinal rim thinning in the optic nerve head. Progress in Retinal and Eye Research, 77, 100840.
Li,, H. B., You,, Q. S., Xu,, L. X., Sun,, L. X., Abdul Majid,, A. S., Xia,, X. B., & Ji,, D. (2017). Long non‐coding RNA‐MALAT1 mediates retinal ganglion cell apoptosis through the PI3K/Akt signaling pathway in rats with glaucoma. Cellular Physiology and Biochemistry, 43, 2117–2132.
Li,, S., Mo,, Z., Yang,, X., Price,, S. M., Shen,, M. M., & Xiang,, M. (2004). Foxn4 controls the genesis of amacrine and horizontal cells by retinal progenitors. Neuron, 43, 795–807.
Liu,, J., Tang,, M., Harkin,, K., Du,, X., Luo,, C., Chen,, M., & Xu,, H. (2020). Single‐cell RNA sequencing study of retinal immune regulators identified CD47 and CD59a expression in photoreceptors‐implications in subretinal immune regulation. Journal of Neuroscience Research, 98, 1498–1513.
Liu,, S., Liu,, X., Li,, S., Huang,, X., Qian,, H., Jin,, K., & Xiang,, M. (2020). Foxn4 is a temporal identity factor conferring mid/late‐early retinal competence and involved in retinal synaptogenesis. Proceedings of the National Academy of Sciences of the United States of America, 117, 5016–5027.
Lo Giudice,, Q., Leleu,, M., La Manno,, G., & Fabre,, P. J. (2019). Single‐cell transcriptional logic of cell‐fate specification and axon guidance in early‐born retinal neurons. Development, 146, 178103.
Lu,, Y., Shiau,, F., Yi,, W., Lu,, S., Wu,, Q., Pearson,, J. D., Kallman,, A., Zhong,, S., Hoang,, T., Zuo,, Z., Zhao,, F., Zhang,, M., Tsai,, N., Zhuo,, Y., He,, S., Zhang,, J., Stein‐O`Brien,, G. L., Sherman,, T. D., Duan,, X., … Clark,, B. S. (2020). Single‐cell analysis of human retina identifies evolutionarily conserved and species‐specific mechanisms controlling development. Developmental Cell, 53, 473–491.
Lukowski,, S. W., Lo,, C. Y., Sharov,, A. A., Nguyen,, Q., Fang,, L., Hung,, S. S., Zhu,, L., Zhang,, T., Grunert,, U., Nguyen,, T., Senabouth,, A., Jabbari,, J. S., Welby,, E., Sowden,, J. C., Waugh,, H. S., Mackey,, A., Pollock,, G., Lamb,, T. D., Wang,, P. Y., … Wong,, R. C. (2019). A single‐cell transcriptome atlas of the adult human retina. The EMBO Journal, 38, e100811.
Lv,, B., Li,, F., Fang,, J., Xu,, L., Sun,, C., Han,, J., Hua,, T., Zhang,, Z., Feng,, Z., Wang,, Q., & Jiang,, X. (2016). Activated microglia induce bone marrow mesenchymal stem cells to produce glial cell‐derived neurotrophic factor and protect neurons against oxygen‐glucose deprivation injury. Frontiers in Cellular Neuroscience, 10, 283.
Macosko,, E. Z., Basu,, A., Satija,, R., Nemesh,, J., Shekhar,, K., Goldman,, M., Tirosh,, I., Bialas,, A. R., Kamitaki,, N., Martersteck,, E. M., Trombetta,, J. J., Weitz,, D. A., Sanes,, J. R., Shalek,, A. K., Regev,, A., & McCarroll,, S. A. (2015). Highly parallel genome‐wide expression profiling of individual cells using nanoliter droplets. Cell, 161, 1202–1214.
Mao,, X., An,, Q., Xi,, H., Yang,, X. J., Zhang,, X., Yuan,, S., Wang,, J., Hu,, Y., Liu,, Q., & Fan,, G. (2019). Single‐cell RNA sequencing of hESC‐derived 3D retinal organoids reveals novel genes regulating RPC commitment in early human retinogenesis. Stem Cell Reports, 13, 747–760.
Marioni,, J. C., Mason,, C. E., Mane,, S. M., Stephens,, M., & Gilad,, Y. (2008). RNA‐seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research, 18, 1509–1517.
Masland,, R. H. (2001). The fundamental plan of the retina. Nature Neuroscience, 4, 877–886.
Menon,, M., Mohammadi,, S., Davila‐Velderrain,, J., Goods,, B. A., Cadwell,, T. D., Xing,, Y., Stemmer‐Rachamimov,, A., Shalek,, A. K., Love,, J. C., Kellis,, M., & Hafler,, B. P. (2019). Single‐cell transcriptomic atlas of the human retina identifies cell types associated with age‐related macular degeneration. Nature Communications, 10, 4902.
Mortazavi,, A., Williams,, B. A., McCue,, K., Schaeffer,, L., & Wold,, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA‐Seq. Nature Methods, 5, 621–628.
Muraleva,, N. A., Kozhevnikova,, O. S., Zhdankina,, A. A., Stefanova,, N. A., Karamysheva,, T. V., Fursova,, A. Z., & Kolosova,, N. G. (2014). The mitochondria‐targeted antioxidant SkQ1 restores alphaB‐crystallin expression and protects against AMD‐like retinopathy in OXYS rats. Cell Cycle, 13, 3499–3505.
Muranishi,, Y., Terada,, K., Inoue,, T., Katoh,, K., Tsujii,, T., Sanuki,, R., Kurokawa,, D., Aizawa,, S., Tamaki,, Y., & Furukawa,, T. (2011). An essential role for RAX homeoprotein and NOTCH‐HES signaling in Otx2 expression in embryonic retinal photoreceptor cell fate determination. The Journal of Neuroscience, 31, 16792–16807.
Norrie,, J. L., Lupo,, M. S., Xu,, B., Al Diri,, I., Valentine,, M., Putnam,, D., Griffiths,, L., Zhang,, J., Johnson,, D., Easton,, J., Shao,, Y., Honnell,, V., Frase,, S., Miller,, S., Stewart,, V., Zhou,, X., Chen,, X., & Dyer,, M. A. (2019). Nucleome dynamics during retinal development. Neuron, 104, 512–528.
Pauly,, D., Agarwal,, D., Dana,, N., Schafer,, N., Biber,, J., Wunderlich,, K. A., Jabri,, Y., Straub,, T., Zhang,, N. R., Gautam,, A. K., Weber,, B. H. F., Hauck,, S. M., Kim,, M., Curcio,, C. A., Stambolian,, D., Li,, M., & Grosche,, A. (2019). Cell‐type‐specific complement expression in the healthy and diseased retina. Cell Reports, 29, 2835–2848.
Peng,, Y. R., Shekhar,, K., Yan,, W., Herrmann,, D., Sappington,, A., Bryman,, G. S., van Zyl,, T., Do,, M. T. H., Regev,, A., & Sanes,, J. R. (2019). Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina. Cell, 176, 1222–1237.
Pernet,, V., & Schwab,, M. E. (2014). Lost in the jungle: New hurdles for optic nerve axon regeneration. Trends in Neurosciences, 37, 381–387.
Picelli,, S. (2017). Single‐cell RNA‐sequencing: The future of genome biology is now. RNA Biology, 14, 637–650.
Potter,, S. S. (2018). Single‐cell RNA sequencing for the study of development, physiology and disease. Nature Reviews. Nephrology, 14, 479–492.
Qiu,, X., Mao,, Q., Tang,, Y., Wang,, L., Chawla,, R., Pliner,, H. A., & Trapnell,, C. (2017). Reversed graph embedding resolves complex single‐cell trajectories. Nature Methods, 14, 979–982.
Ramón,, Y., & Cajal,, S. (1972). The structure of the retina (Thorpe SA, Glickstein M, trad.). Charles C Thomas Publisher.
Ramskold,, D., Luo,, S., Wang,, Y. C., Li,, R., Deng,, Q., Faridani,, O. R., Daniels,, G. A., Khrebtukova,, I., Loring,, J. F., Laurent,, L. C., Schroth,, G. P., & Sandberg,, R. (2012). Full‐length mRNA‐Seq from single‐cell levels of RNA and individual circulating tumor cells. Nature Biotechnology, 30, 777–782.
Regev,, A., Teichmann,, S. A., Lander,, E. S., Amit,, I., Benoist,, C., Birney,, E., Bodenmiller,, B., Campbell,, P., Carninci,, P., Clatworthy,, M., Clevers,, H., Deplancke,, B., Dunham,, I., Eberwine,, J., Eils,, R., Enard,, W., Farmer,, A., Fugger,, L., Gottgens,, B., … Human Cell Atlas Meeting Participants. (2017). The human cell atlas. eLife, 6, e27041.
Rheaume,, B. A., Jereen,, A., Bolisetty,, M., Sajid,, M. S., Yang,, Y., Renna,, K., Sun,, L., Robson,, P., & Trakhtenberg,, E. F. (2018). Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes. Nature Communications, 9, 2759.
Seritrakul,, P., & Gross,, J. M. (2019). Genetic and epigenetic control of retinal development in zebrafish. Current Opinion in Neurobiology, 59, 120–127.
Shekhar,, K., Lapan,, S. W., Whitney,, I. E., Tran,, N. M., Macosko,, E. Z., Kowalczyk,, M., Adiconis,, X., Levin,, J. Z., Nemesh,, J., Goldman,, M., McCarroll,, S. A., Cepko,, C. L., Regev,, A., & Sanes,, J. R. (2016). Comprehensive classification of retinal bipolar neurons by single‐cell transcriptomics. Cell, 166, 1308–1323.
Sherpa,, T., Lankford,, T., McGinn,, T. E., Hunter,, S. S., Frey,, R. A., Sun,, C., Ryan,, M., Robison,, B. D., & Stenkamp,, D. L. (2014). Retinal regeneration is facilitated by the presence of surviving neurons. Developmental Neurobiology, 74, 851–876.
Sinha,, R., Hoon,, M., Baudin,, J., Okawa,, H., Wong,, R. O. L., & Rieke,, F. (2017). Cellular and circuit mechanisms shaping the perceptual properties of the primate fovea. Cell, 168, 413–426.
Sridhar,, A., Hoshino,, A., Finkbeiner,, C. R., Chitsazan,, A., Dai,, L., Haugan,, A. K., Eschenbacher,, K. M., Jackson,, D. L., Trapnell,, C., Bermingham‐McDonogh,, O., Glass,, I., & Reh,, T. A. (2020). Single‐cell transcriptomic comparison of human fetal retina, hPSC‐derived retinal organoids, and long‐term retinal cultures. Cell Reports, 30, 1644–1659.
Stevens,, C. F. (1998). Neuronal diversity: Too many cell types for comfort? Current Biology, 8, R708–R710.
Sumbul,, U., Song,, S., McCulloch,, K., Becker,, M., Lin,, B., Sanes,, J. R., Masland,, R. H., & Seung,, H. S. (2014). A genetic and computational approach to structurally classify neuronal types. Nature Communications, 5, 3512.
Syc‐Mazurek,, S. B., Fernandes,, K. A., Wilson,, M. P., Shrager,, P., & Libby,, R. T. (2017). Together JUN and DDIT3 (CHOP) control retinal ganglion cell death after axonal injury. Molecular Neurodegeneration, 12, 71.
Tang,, F., Barbacioru,, C., Wang,, Y., Nordman,, E., Lee,, C., Xu,, N., Wang,, X., Bodeau,, J., Tuch,, B. B., Siddiqui,, A., Lao,, K., & Surani,, M. A. (2009). mRNA‐Seq whole‐transcriptome analysis of a single cell. Nature Methods, 6, 377–382.
Tasic,, B., Menon,, V., Nguyen,, T. N., Kim,, T. K., Jarsky,, T., Yao,, Z., Levi,, B., Gray,, L. T., Sorensen,, S. A., Dolbeare,, T., Bertagnolli,, D., Goldy,, J., Shapovalova,, N., Parry,, S., Lee,, C., Smith,, K., Bernard,, A., Madisen,, L., Sunkin,, S. M., … Zeng,, H. (2016). Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nature Neuroscience, 19, 335–346.
Tran,, N. M., Shekhar,, K., Whitney,, I. E., Jacobi,, A., Benhar,, I., Hong,, G., Yan,, W., Adiconis,, X., Arnold,, M. E., Lee,, J. M., Levin,, J. Z., Lin,, D., Wang,, C., Lieber,, C. M., Regev,, A., He,, Z., & Sanes,, J. R. (2019). Single‐cell profiles of retinal ganglion cells differing in resilience to injury reveal neuroprotective genes. Neuron, 104, 1039–1055.
Trapnell,, C., Cacchiarelli,, D., Grimsby,, J., Pokharel,, P., Li,, S., Morse,, M., Lennon,, N. J., Livak,, K. J., Mikkelsen,, T. S., & Rinn,, J. L. (2014). The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology, 32, 381–386.
Ueda,, K., Kim,, H. J., Zhao,, J., Song,, Y., Dunaief,, J. L., & Sparrow,, J. R. (2018). Iron promotes oxidative cell death caused by bisretinoids of retina. Proceedings of the National Academy of Sciences of the United States of America, 115, 4963–4968.
Vandenbon,, A., & Diez,, D. (2020). A clustering‐independent method for finding differentially expressed genes in single‐cell transcriptome data. Nature Communications, 11, 4318.
Voigt,, A. P., Binkley,, E., Flamme‐Wiese,, M. J., Zeng,, S., DeLuca,, A. P., Scheetz,, T. E., Tucker,, B. A., Mullins,, R. F., & Stone,, E. M. (2020). Single‐cell RNA sequencing in human retinal degeneration reveals distinct glial cell populations. Cell, 9, 438.
Voigt,, A. P., Whitmore,, S. S., Flamme‐Wiese,, M. J., Riker,, M. J., Wiley,, L. A., Tucker,, B. A., Stone,, E. M., Mullins,, R. F., & Scheetz,, T. E. (2019). Molecular characterization of foveal versus peripheral human retina by single‐cell RNA sequencing. Experimental Eye Research, 184, 234–242.
Wagner,, A., Regev,, A., & Yosef,, N. (2016). Revealing the vectors of cellular identity with single‐cell genomics. Nature Biotechnology, 34, 1145–1160.
Wang,, S., Wang,, X., Cheng,, Y., Ouyang,, W., Sang,, X., Liu,, J., Su,, Y., Liu,, Y., Li,, C., Yang,, L., Jin,, L., & Wang,, Z. (2019). Autophagy dysfunction, cellular senescence, and abnormal immune‐inflammatory responses in AMD: From mechanisms to therapeutic potential. Oxidative Medicine and Cellular Longevity, 2019, 1–13.
Wang,, Z., Gerstein,, M., & Snyder,, M. (2009). RNA‐Seq: A revolutionary tool for transcriptomics. Nature Reviews. Genetics, 10, 57–63.
Wassle,, H., Grunert,, U., Rohrenbeck,, J., & Boycott,, B. B. (1989). Cortical magnification factor and the ganglion cell density of the primate retina. Nature, 341, 643–646.
Wu,, F., Kaczynski,, T. J., Sethuramanujam,, S., Li,, R., Jain,, V., Slaughter,, M., & Mu,, X. (2015). Two transcription factors, Pou4f2 and Isl1, are sufficient to specify the retinal ganglion cell fate. Proceedings of the National Academy of Sciences of the United States of America, 112, E1559–E1568.
Yan,, W., Laboulaye,, M. A., Tran,, N. M., Whitney,, I. E., Benhar,, I., & Sanes,, J. R. (2020). Mouse retinal cell atlas: Molecular identification of over sixty amacrine cell types. The Journal of Neuroscience, 40, 5177–5195.
Yao,, J., Jia,, L., Feathers,, K., Lin,, C., Khan,, N. W., Klionsky,, D. J., Ferguson,, T. A., & Zacks,, D. N. (2016). Autophagy‐mediated catabolism of visual transduction proteins prevents retinal degeneration. Autophagy, 12, 2439–2450.
Yao,, J., Wang,, X. Q., Li,, Y. J., Shan,, K., Yang,, H., Wang,, Y. N., Yao,, M. D., Liu,, C., Li,, X. M., Shen,, Y., Liu,, J. Y., Cheng,, H., Yuan,, J., Zhang,, Y. Y., Jiang,, Q., & Yan,, B. (2016). Long non‐coding RNA MALAT1 regulates retinal neurodegeneration through CREB signaling. EMBO Molecular Medicine, 8, 1113.
Yu,, D. Y., Cringle,, S. J., Balaratnasingam,, C., Morgan,, W. H., Yu,, P. K., & Su,, E. N. (2013). Retinal ganglion cells: Energetics, compartmentation, axonal transport, cytoskeletons and vulnerability. Progress in Retinal and Eye Research, 36, 217–246.
Zappia,, L., Phipson,, B., & Oshlack,, A. (2018). Exploring the single‐cell RNA‐seq analysis landscape with the scRNA‐tools database. PLoS Computational Biology, 14, e1006245.
Zeng,, Z., Miao,, N., & Sun,, T. (2018). Revealing cellular and molecular complexity of the central nervous system using single cell sequencing. Stem Cell Research %26 Therapy, 9, 234.
Zerti,, D., Collin,, J., Queen,, R., Cockell,, S. J., & Lako,, M. (2020). Understanding the complexity of retina and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: Current progress, remaining challenges and future prospective. Current Eye Research, 45, 385–396.
Zhang,, X., Hamblin,, M. H., & Yin,, K. J. (2017). The long noncoding RNA Malat1: Its physiological and pathophysiological functions. RNA Biology, 14, 1705–1714.
Zhou,, H., Su,, J., Hu,, X., Zhou,, C., Li,, H., Chen,, Z., Xiao,, Q., Wang,, B., Wu,, W., Sun,, Y., Zhou,, Y., Tang,, C., Liu,, F., Wang,, L., Feng,, C., Liu,, M., Li,, S., Zhang,, Y., Xu,, H., … Yang,, H. (2020). Glia‐to‐neuron conversion by CRISPR‐CasRx alleviates symptoms of neurological disease in mice. Cell, 181, 590–603.
Ziegenhain,, C., Vieth,, B., Parekh,, S., Reinius,, B., Guillaumet‐Adkins,, A., Smets,, M., Leonhardt,, H., Heyn,, H., Hellmann,, I., & Enard,, W. (2017). Comparative analysis of single‐cell RNA sequencing methods. Molecular Cell, 65, 631–643.

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