[en] The retina is exquisitely patterned, with neuronal somata positioned at regular intervals to completely sample the visual field. Here, we show that phosphatase and tensin homolog (Pten) controls starburst amacrine cell spacing by modulating vesicular trafficking of cell adhesion molecules and Wnt proteins. Single-cell transcriptomics and double-mutant analyses revealed that Pten and Down syndrome cell adhesion moleculeDscam) are co-expressed and function additively to pattern starburst amacrine cell mosaics. Mechanistically, Pten loss accelerates the endocytic trafficking of DSCAM, FAT3, and MEGF10 off the cell membrane and into endocytic vesicles in amacrine cells. Accordingly, the vesicular proteome, a molecular signature of the cell of origin, is enriched in exocytosis, vesicle-mediated transport, and receptor internalization proteins in Pten conditional knockout (PtencKO) retinas. Wnt signaling molecules are also enriched in PtencKO retinal vesicles, and the genetic or pharmacological disruption of Wnt signaling phenocopies amacrine cell patterning defects. Pten thus controls vesicular trafficking of cell adhesion and signaling molecules to establish retinal amacrine cell mosaics.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Touahri, Yacine ✱; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada
Hanna, Joseph; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
Tachibana, Nobuhiko; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
Liu, Hedy; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
David, Luke Ajay; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
Olender, Thomas; Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada
Vasan, Lakshmy; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
Pak, Alissa; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
Mehta, Dhruv Nimesh; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada
Chinchalongporn, Vorapin; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
Balakrishnan, Anjali; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada, Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
Cantrup, Robert; Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
Dixit, Rajiv; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
Mattar, Pierre; Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
Saleh, Fermisk; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
Ilnytskyy, Yaroslav; Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
Murshed, Monzur; Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3G 1A6, Canada
Mains, Paul E; Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
Kovalchuk, Igor; Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
Lefebvre, Julie L; Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada, Program for Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
Leong, Hon S; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
Cayouette, Michel; Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada
Wang, Chao; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Immunology, University of Toronto, Toronto, ON M5G 1L7, Canada
DEL SOL MESA, Antonio ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Computational Biology
Brand, Marjorie; Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada
Reese, Benjamin E; Department of Psychological and Brain Sciences, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106-5060, USA
Schuurmans, Carol ✱; Biological Sciences Platform, Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada, Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada. Electronic address: cschuurm@sri.utoronto.ca
Wässle, H., Parallel processing in the mammalian retina. Nat. Rev. Neurosci. 5 (2004), 747–757.
Galli-Resta, L., Leone, P., Bottari, D., Ensini, M., Rigosi, E., Novelli, E., The genesis of retinal architecture: an emerging role for mechanical interactions?. Prog. Retin. Eye Res. 27 (2008), 260–283.
Galli-Resta, L., Putting neurons in the right places: local interactions in the genesis of retinal architecture. Trends Neurosci. 25 (2002), 638–643.
Whitney, I.E., Keeley, P.W., St John, A.J., Kautzman, A.G., Kay, J.N., Reese, B.E., Sox2 regulates cholinergic amacrine cell positioning and dendritic stratification in the retina. J. Neurosci. 34 (2014), 10109–10121.
Deans, M.R., Krol, A., Abraira, V.E., Copley, C.O., Tucker, A.F., Goodrich, L.V., Control of neuronal morphology by the atypical cadherin Fat3. Neuron 71 (2011), 820–832.
Galli-Resta, L., Resta, G., Tan, S.S., Reese, B.E., Mosaics of islet-1-expressing amacrine cells assembled by short-range cellular interactions. J. Neurosci. 17 (1997), 7831–7838.
Galli-Resta, L., Local, possibly contact-mediated signalling restricted to homotypic neurons controls the regular spacing of cells within the cholinergic arrays in the developing rodent retina. Development 127 (2000), 1509–1516.
Reese, B.E., Galli-Resta, L., The role of tangential dispersion in retinal mosaic formation. Prog. Retin. Eye Res. 21 (2002), 153–168.
Reese, B.E., Mosaic architecture of the mouse retina. L.M.C., (eds.) Eye, Retina and Visual Systems of the Mouse, 2008, MIT Press, 147–155.
Kozlowski, C., Hadyniak, S.E., Kay, J.N., Retinal neurons establish mosaic patterning by excluding homotypic somata from their dendritic territory. Preprint at bioRxiv, 2023, 10.1101/2023.11.17.567616.
Taylor, W.R., Smith, R.G., The role of starburst amacrine cells in visual signal processing. Vis. Neurosci. 29 (2012), 73–81.
Masland, R.H., The tasks of amacrine cells. Vis. Neurosci. 29 (2012), 3–9.
Rockhill, R.L., Euler, T., Masland, R.H., Spatial order within but not between types of retinal neurons. Proc. Natl. Acad. Sci. USA 97 (2000), 2303–2307.
Whitney, I.E., Keeley, P.W., Raven, M.A., Reese, B.E., Spatial patterning of cholinergic amacrine cells in the mouse retina. J. Comp. Neurol. 508 (2008), 1–12.
Reese, B.E., Necessary, B.D., Tam, P.P., Faulkner-Jones, B., Tan, S.S., Clonal expansion and cell dispersion in the developing mouse retina. Eur. J. Neurosci. 11 (1999), 2965–2978.
Reese, B.E., Tan, S.S., Clonal boundary analysis in the developing retina using X-inactivation transgenic mosaic mice. Semin. Cell Dev. Biol. 9 (1998), 285–292.
Cameron, D.A., Carney, L.H., Cellular patterns in the inner retina of adult zebrafish: quantitative analyses and a computational model of their formation. J. Comp. Neurol. 471 (2004), 11–25.
Tyler, M.J., Carney, L.H., Cameron, D.A., Control of cellular pattern formation in the vertebrate inner retina by homotypic regulation of cell-fate decisions. J. Neurosci. 25 (2005), 4565–4576.
Raven, M.A., Eglen, S.J., Ohab, J.J., Reese, B.E., Determinants of the exclusion zone in dopaminergic amacrine cell mosaics. J. Comp. Neurol. 461 (2003), 123–136.
Poché, R.A., Raven, M.A., Kwan, K.M., Furuta, Y., Behringer, R.R., Reese, B.E., Somal positioning and dendritic growth of horizontal cells are regulated by interactions with homotypic neighbors. Eur. J. Neurosci. 27 (2008), 1607–1614.
Stenkamp, D.L., Cameron, D.A., Cellular pattern formation in the retina: retinal regeneration as a model system. Mol. Vis. 8 (2002), 280–293.
Pollerberg, G.E., Thelen, K., Theiss, M.O., Hochlehnert, B.C., The role of cell adhesion molecules for navigating axons: density matters. Mech. Dev. 130 (2013), 359–372.
O'Sullivan, M.J., Lindsay, A.J., The Endosomal Recycling Pathway-At the Crossroads of the Cell. Int. J. Mol. Sci., 21, 2020.
Meltzer, H., Schuldiner, O., Spatiotemporal Control of Neuronal Remodeling by Cell Adhesion Molecules: Insights From Drosophila. Front. Neurosci., 16, 2022, 897706.
Fuerst, P.G., Bruce, F., Rounds, R.P., Erskine, L., Burgess, R.W., Cell autonomy of DSCAM function in retinal development. Dev. Biol. 361 (2012), 326–337.
Keeley, P.W., Sliff, B.J., Lee, S.C.S., Fuerst, P.G., Burgess, R.W., Eglen, S.J., Reese, B.E., Neuronal clustering and fasciculation phenotype in Dscam- and Bax-deficient mouse retinas. J. Comp. Neurol. 520 (2012), 1349–1364.
Garrett, A.M., Khalil, A., Walton, D.O., Burgess, R.W., DSCAM promotes self-avoidance in the developing mouse retina by masking the functions of cadherin superfamily members. Proc. Natl. Acad. Sci. USA 115 (2018), E10216–E10224.
Kay, J.N., Chu, M.W., Sanes, J.R., MEGF10 and MEGF11 mediate homotypic interactions required for mosaic spacing of retinal neurons. Nature 483 (2012), 465–469.
Lefebvre, J.L., Kostadinov, D., Chen, W.V., Maniatis, T., Sanes, J.R., Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature 488 (2012), 517–521.
Cantrup, R., Dixit, R., Palmesino, E., Bonfield, S., Shaker, T., Tachibana, N., Zinyk, D., Dalesman, S., Yamakawa, K., Stell, W.K., et al. Cell-type specific roles for PTEN in establishing a functional retinal architecture. PLoS One, 7, 2012, e32795.
Lee, M.F., Trotman, L.C., PTEN: Bridging Endocytosis and Signaling. Cold Spring Harb. Perspect. Med., 10, 2020, a036103.
Fang, C., Manes, T.D., Liu, L., Liu, K., Qin, L., Li, G., Tobiasova, Z., Kirkiles-Smith, N.C., Patel, M., Merola, J., et al. ZFYVE21 is a complement-induced Rab5 effector that activates non-canonical NF-κB via phosphoinosotide remodeling of endosomes. Nat. Commun., 10, 2019, 2247.
Fuerst, P.G., Koizumi, A., Masland, R.H., Burgess, R.W., Neurite arborization and mosaic spacing in the mouse retina require DSCAM. Nature 451 (2008), 470–474.
Keeley, P.W., Reese, B.E., Morphology of dopaminergic amacrine cells in the mouse retina: independence from homotypic interactions. J. Comp. Neurol. 518 (2010), 1220–1231.
Elshatory, Y., Everhart, D., Deng, M., Xie, X., Barlow, R.B., Gan, L., Islet-1 controls the differentiation of retinal bipolar and cholinergic amacrine cells. J. Neurosci. 27 (2007), 12707–12720.
Backman, S.A., Stambolic, V., Suzuki, A., Haight, J., Elia, A., Pretorius, J., Tsao, M.S., Shannon, P., Bolon, B., Ivy, G.O., Mak, T.W., Deletion of Pten in mouse brain causes seizures, ataxia and defects in soma size resembling Lhermitte-Duclos disease. Nat. Genet. 29 (2001), 396–403.
Marquardt, T., Ashery-Padan, R., Andrejewski, N., Scardigli, R., Guillemot, F., Gruss, P., Pax6 is required for the multipotent state of retinal progenitor cells. Cell 105 (2001), 43–55.
Amano, K., Fujii, M., Arata, S., Tojima, T., Ogawa, M., Morita, N., Shimohata, A., Furuichi, T., Itohara, S., Kamiguchi, H., et al. DSCAM deficiency causes loss of pre-inspiratory neuron synchroneity and perinatal death. J. Neurosci. 29 (2009), 2984–2996.
Jo, H.S., Kang, K.H., Joe, C.O., Kim, J.W., Pten coordinates retinal neurogenesis by regulating Notch signalling. EMBO J., 2012.
Tachibana, N., Touahri, Y., Dixit, R., David, L.A., Adnani, L., Cantrup, R., Aavani, T., Wong, R.O., Logan, C., Kurek, K.C., Schuurmans, C., Hamartoma-like lesions in the mouse retina: an animal model of Pten hamartoma tumour syndrome. Dis. Model. Mech., 11, 2018, dmm031005.
Tachibana, N., Cantrup, R., Dixit, R., Touahri, Y., Kaushik, G., Zinyk, D., Daftarian, N., Biernaskie, J., McFarlane, S., Schuurmans, C., Pten Regulates Retinal Amacrine Cell Number by Modulating Akt, Tgfbeta, and Erk Signaling. J. Neurosci. 36 (2016), 9454–9471.
Haverkamp, S., Wässle, H., Immunocytochemical analysis of the mouse retina. J. Comp. Neurol. 424 (2000), 1–23.
Yan, W., Laboulaye, M.A., Tran, N.M., Whitney, I.E., Benhar, I., Sanes, J.R., Mouse Retinal Cell Atlas: Molecular Identification of over Sixty Amacrine Cell Types. J. Neurosci. 40 (2020), 5177–5195.
Famiglietti, E.V. Jr., Kolb, H., Structural basis for ON-and OFF-center responses in retinal ganglion cells. Science 194 (1976), 193–195.
Raven, M.A., Reese, B.E., Horizontal cell density and mosaic regularity in pigmented and albino mouse retina. J. Comp. Neurol. 454 (2002), 168–176.
Fuerst, P.G., Bruce, F., Tian, M., Wei, W., Elstrott, J., Feller, M.B., Erskine, L., Singer, J.H., Burgess, R.W., DSCAM and DSCAML1 function in self-avoidance in multiple cell types in the developing mouse retina. Neuron 64 (2009), 484–497.
Kawauchi, T., Cell adhesion and its endocytic regulation in cell migration during neural development and cancer metastasis. Int. J. Mol. Sci. 13 (2012), 4564–4590.
Fuerst, P.G., Harris, B.S., Johnson, K.R., Burgess, R.W., A novel null allele of mouse DSCAM survives to adulthood on an inbred C3H background with reduced phenotypic variability. Genesis 48 (2010), 578–584.
de Andrade, G.B., Kunzelman, L., Merrill, M.M., Fuerst, P.G., Developmentally dynamic colocalization patterns of DSCAM with adhesion and synaptic proteins in the mouse retina. Mol. Vis. 20 (2014), 1422–1433.
Colombo, M., Raposo, G., Théry, C., Biogenesis, secretion, and intercellular interactions of exosomes and other extracellular vesicles. Annu. Rev. Cell Dev. Biol. 30 (2014), 255–289.
Zhou, J., Benito-Martin, A., Mighty, J., Chang, L., Ghoroghi, S., Wu, H., Wong, M., Guariglia, S., Baranov, P., Young, M., et al. Retinal progenitor cells release extracellular vesicles containing developmental transcription factors, microRNA and membrane proteins. Sci. Rep., 8, 2018, 2823.
Kalargyrou, A.A., Guilfoyle, S.E., Smith, A.J., Ali, R.R., Pearson, R.A., Extracellular vesicles in the retina - putative roles in physiology and disease. Front. Mol. Neurosci., 15, 2022, 1042469.
Hurwitz, S.N., Olcese, J.M., Meckes, D.G. Jr., Extraction of Extracellular Vesicles from Whole Tissue. J. Vis. Exp., 144, 2019.
Kosaka, N., Iguchi, H., Yoshioka, Y., Takeshita, F., Matsuki, Y., Ochiya, T., Secretory mechanisms and intercellular transfer of microRNAs in living cells. J. Biol. Chem. 285 (2010), 17442–17452.
Alebrahim, S., Khavandgar, Z., Marulanda, J., Murshed, M., Inducible transient expression of Smpd3 prevents early lethality in fro/fro mice. Genesis 52 (2014), 408–416.
Dixson, A.C., Dawson, T.R., Di Vizio, D., Weaver, A.M., Context-specific regulation of extracellular vesicle biogenesis and cargo selection. Nat. Rev. Mol. Cell Biol. 24 (2023), 454–476.
Hallal, S., Tűzesi, Á., Grau, G.E., Buckland, M.E., Alexander, K.L., Understanding the extracellular vesicle surface for clinical molecular biology. J. Extracell. Vesicles, 11, 2022, e12260.
Liu, H., Mohamed, O., Dufort, D., Wallace, V.A., Characterization of Wnt signaling components and activation of the Wnt canonical pathway in the murine retina. Dev. Dynam. 227 (2003), 323–334.
Huang, S.M.A., Mishina, Y.M., Liu, S., Cheung, A., Stegmeier, F., Michaud, G.A., Charlat, O., Wiellette, E., Zhang, Y., Wiessner, S., et al. Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling. Nature 461 (2009), 614–620.
Fabris, F., Conrad Hal Waddington (1905–1975). Nuño de la Rosa, L., Müller, G.B., (eds.) Evolutionary Developmental Biology: A Reference Guide, 2021, Springer International Publishing, 299–313.
Bizzarri, M., Giuliani, A., Minini, M., Monti, N., Cucina, A., Constraints Shape Cell Function and Morphology by Canalizing the Developmental Path along the Waddington's Landscape. Bioessays, 42, 2020, e1900108.
Cullen, P.J., Steinberg, F., To degrade or not to degrade: mechanisms and significance of endocytic recycling. Nat. Rev. Mol. Cell Biol. 19 (2018), 679–696.
Naguib, A., Bencze, G., Cho, H., Zheng, W., Tocilj, A., Elkayam, E., Faehnle, C.R., Jaber, N., Pratt, C.P., Chen, M., et al. PTEN functions by recruitment to cytoplasmic vesicles. Mol. Cell 58 (2015), 255–268.
Ellenbroek, S.I.J., Iden, S., Collard, J.G., Cell polarity proteins and cancer. Semin. Cancer Biol. 22 (2012), 208–215.
Balakrishnan, A., Roy, S., Fleming, T., Leong, H.S., Schuurmans, C., The Emerging Role of Extracellular Vesicles in the Glioma Microenvironment: Biogenesis and Clinical Relevance. Cancers, 12, 2020, 1964.
Schramm, R.D., Li, S., Harris, B.S., Rounds, R.P., Burgess, R.W., Ytreberg, F.M., Fuerst, P.G., A novel mouse Dscam mutation inhibits localization and shedding of DSCAM. PLoS One, 7, 2012, e52652.
Vinyoles, M., Del Valle-Pérez, B., Curto, J., Viñas-Castells, R., Alba-Castellón, L., García de Herreros, A., Duñach, M., Multivesicular GSK3 sequestration upon Wnt signaling is controlled by p120-catenin/cadherin interaction with LRP5/6. Mol. Cell 53 (2014), 444–457.
Sarin, S., Zuniga-Sanchez, E., Kurmangaliyev, Y.Z., Cousins, H., Patel, M., Hernandez, J., Zhang, K.X., Samuel, M.A., Morey, M., Sanes, J.R., Zipursky, S.L., Role for Wnt Signaling in Retinal Neuropil Development: Analysis via RNA-Seq and In Vivo Somatic CRISPR Mutagenesis. Neuron 98 (2018), 109–126.e8.
Tanaka, S.S., Kojima, Y., Yamaguchi, Y.L., Nishinakamura, R., Tam, P.P.L., Impact of WNT signaling on tissue lineage differentiation in the early mouse embryo. Dev. Growth Differ. 53 (2011), 843–856.
Rizzoli, S.O., Synaptic vesicle recycling: steps and principles. EMBO J. 33 (2014), 788–822.
Barrows, C.M., McCabe, M.P., Chen, H., Swann, J.W., Weston, M.C., PTEN Loss Increases the Connectivity of Fast Synaptic Motifs and Functional Connectivity in a Developing Hippocampal Network. J. Neurosci. 37 (2017), 8595–8611.
Butler, M.G., Dasouki, M.J., Zhou, X.P., Talebizadeh, Z., Brown, M., Takahashi, T.N., Miles, J.H., Wang, C.H., Stratton, R., Pilarski, R., Eng, C., Subset of individuals with autism spectrum disorders and extreme macrocephaly associated with germline PTEN tumour suppressor gene mutations. J. Med. Genet. 42 (2005), 318–321.
Crino, P.B., A pathogenic signaling pathway in developmental brain malformations. Trends Mol. Med. 17 (2011), 734–742.
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9 (2012), 676–682.
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., Satija, R., Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36 (2018), 411–420.
Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.H., Pagès, F., Trajanoski, Z., Galon, J., ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25 (2009), 1091–1093.
Ulgen, E., Ozisik, O., Sezerman, O.U., pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet., 10, 2019, 858.
Alam, S., Zinyk, D., Ma, L., Schuurmans, C., Members of the Plag gene family are expressed in complementary and overlapping regions in the developing murine nervous system. Dev. Dynam. 234 (2005), 772–782.
Touahri, Y., Adnani, L., Mattar, P., Markham, K., Klenin, N., Schuurmans, C., Non-isotopic RNA In Situ Hybridization on Embryonic Sections. Curr. Protoc. Neurosci. 70 (2015), 1.22.1–25.
Thery, C., Amigorena, S., Raposo, G., Clayton, A., Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Curr. Protoc. Cell Biol., Chapter 3, 2006, Unit 3 22.
Chaturvedi, C.P., Somasundaram, B., Singh, K., Carpenedo, R.L., Stanford, W.L., Dilworth, F.J., Brand, M., Maintenance of gene silencing by the coordinate action of the H3K9 methyltransferase G9a/KMT1C and the H3K4 demethylase Jarid1a/KDM5A. Proc. Natl. Acad. Sci. USA 109 (2012), 18845–18850.
Clark, B.S., Stein-O'Brien, G.L., Shiau, F., et al. Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification. Neuron 102 (2019), 1111–1126.e1115.
Rodieck, R.W., The density recovery profile: a method for the analysis of points in the plane applicable to retinal studies. Vis. Neurosci. 6 (1991), 95–111.
Keeley, P.W., Eglen, S.J., Reese, B.E., From random to regular: Variation in the patterning of retinal mosaics. J. Comp. Neurol. 528 (2020), 2135–2160.
