Gene expression profiling of purified rat retinal ganglion cells

Investigative Ophthalmology and Visual Science

Volumn 45, Issue 8, 2004, Pages 2503-2513

  Farkas, Ronald H ^a,b   Qian, Jiang ^a,b   Goldberg, Jeffrey L ^d,e   Quigley, Harry A ^a   Zack, Donald J ^a,b,c  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b Guerrieri Ctr Genet Eng/Mol O   (United States)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d STANFORD UNIVERSITY   (United States)

^e UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; NITRIC OXIDE;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DDAH1 GENE; EXPRESSED SEQUENCE TAG; GENE; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE LOCUS; HYPOTHALAMUS; IMMUNOHISTOCHEMISTRY; IMMUNOREACTIVITY; NEUROSECRETORY CELL; NONHUMAN; OPTIC NERVE DISEASE; PATHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; RAT; RETINA GANGLION CELL; SENSORY GANGLION; SEQUENCE ANALYSIS;

ANIMALS; EXPRESSED SEQUENCE TAGS; EYE PROTEINS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE LIBRARY; IMMUNOENZYME TECHNIQUES; NERVE TISSUE PROTEINS; OPTIC NERVE DISEASES; PHENOTYPE; RATS; RATS, SPRAGUE-DAWLEY; RETINAL GANGLION CELLS; SEQUENCE TAGGED SITES;

EID: 3242878876     PISSN: 01460404     EISSN: None     Source Type: Journal    
DOI: 10.1167/iovs.03-1391     Document Type: Article

References (79)

1. Sommer A, Tielsch JM, Katz J, et al. Racial differences in the cause-specific prevalence of blindness in east Baltimore. N Engl J Med. 1991;325:1412-1417.
2. Quigley HA. Number of people with glaucoma worldwide. Br J Ophthalmol. 1996;80:389-393.
3. Swaroop A, Zack DJ. Transcriptome analysis of the retina. Genome Biol. 2002;3:REVIEWS1022.
4. Wistow G. A project for ocular bioinformatics: NEIBank. Mol Vis. 2002;8:161-163.
5. Sinha S, Sharma A, Agarwal N, Swaroop A, Yang-Feng TL. Expression profile and chromosomal location of cDNA clones, identified from an enriched adult retina library. Invest Ophthalmol Vis Sci. 2000;41:24-28.
6. Katsanis N, Worley KC, Gonzalez G, Ansley SJ, Lupski JR. A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. Proc Natl Acad Sci USA. 2002;99:14326-14331.
7. Sharon D, Blackshaw S, Cepko CL, Dryja TP. Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE). Proc Natl Acad Sci USA. 2002;99:315-320.
8. Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell. 2001;107:579-589.
9. Chowers I, Liu D, Farkas RH, et al. Gene expression variation in the adult human retina. Hum Mol Genet. 2003;12:2881-2893.
10. Chowers I, Gunatilaka TL, Farkas RH, et al. Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray. Invest Opthalmol Vis Sci. 2003;44:3732-3741.
11. Mu X, Zhao S, Pershad R, et al. Gene expression in the developing mouse retina by EST sequencing and microarray analysis. Nucleic Acids Res. 2001;29:4983-4993.
12. Livesey FJ, Furukawa T, Steffen MA, Church GM, Cepko CL. Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx. Curr Biol. 2000;10:301-310.
13. Farjo R, Yu J, Othman MI, et al. Mouse eye gene microarrays for investigating ocular development and disease. Vision Res. 2002;42:463-470.
14. Jeon CJ, Strettoi E, Masland RH. The major cell populations of the mouse retina. J Neurosci. 1998;18:8936-8946.
15. Ahmad KM, Klug K, Herr S, Sterling P, Schein S. Cell density ratios in a foveal patch in macaque retina. Vis Neurosci. 2003;20:189-209.
16. Hernandez MR, Agapova OA, Yang P, Salvador-Silva M, Ricard CS, Aoi S. Differential gene expression in astrocytes from human normal and glaucomatous optic nerve head analyzed by cDNA microarray. Glia. 2002;38:45-64.
17. Wahlin KJ, Grice EA, Hackam AS, et al. A method for analysis of gene expression in isolated mouse photoreceptor and Müller cells. Mol Vis. 2004;10:366-375.
18. Miki R, Kadota K, Bono H, et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci USA. 2001;98:2199-2204.
19. Su AI, Cooke MP, Ching KA, et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA. 2002;99:4465-4470.
20. Bonaventure P, Guo H, Tian B, et al. Nuclei and subnuclei gene expression profiling in mammalian brain. Brain Res. 2002;943:38-47.
21. Zhao X, Lein ES, He A, Smith SC, Aston C, Gage FH. Transcriptional profiling reveals strict boundaries between hippocampal subregions. J Comp Neurol. 2001;441:187-196.
22. Che S, Ginsberg SD. Amplification of RNA transcripts using terminal continuation. Lab Invest. 2004;84:131-137.
23. Pavlidis P, Noble WS. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol. 2001;2:RESEARCH0042.
24. Zirlinger M, Kreiman G, Anderson DJ. Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei. Proc Natl Acad Sci USA. 2001;98:5270-5275.
25. Lee CK, Weindruch R, Prolla TA. Gene-expression profile of the ageing brain in mice. Nat Genet. 2000;25:294-297.
26. Cho Y, Gong TW, Stover T, Lomax MI, Altschuler RA. Gene expression profiles of the rat cochlea, cochlear nucleus, and inferior colliculus. J Assoc Res Otolaryngol. 2002;3:54-67.
27. Zirlinger M. Selection and validation of microarray candidate genes from subregions and subnuclei of the brain. Methods. 2003;31:290-300.
28. Dent GW, O'Dell DM, Eberwine JH. Gene expression profiling in the amygdala: an approach to examine the molecular substrates of mammalian behavior. Physiol Behav. 2001;73:841-847.
29. Barrett T, Xie T, Piao Y, et al. A murine dopamine neuron-specific cDNA library and microarray: increased COX1 expression during methamphetamine neurotoxicity. Neurobiol Dis. 2001;8:822-833.
30. Goldberg JL, Espinosa JS, Xu Y, Davidson N, Kovacs GT, Barres BA. Retinal ganglion cells do not extend axons by default: promotion by neurotrophic signaling and electrical activity. Neuron. 2002;33:689-702.
31. Meyer-Franke A, Kaplan MR, Pfrieger FW, Barres BA. Characterization of the signaling interactions that promote the survival and growth of developing retinal ganglion cells in culture. Neuron. 1995;15:805-819.
32. Barres BA, Silverstein BE, Corey DP, Chun LL. Immunological, morphological, and electrophysiological variation among retinal ganglion cells purified by panning. Neuron. 1988;1:791-803.
33. Goldberg JL, Klassen MP, Hua Y, Barres BA. Amacrine-signaled loss of intrinsic axon growth ability by retinal ganglion cells. Science. 2002;296:1860-1864.
34. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res. 1999;9:868-877.
35. Pruitt KD, Katz KS, Sicotte H, Maglott DR. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet. 2000;16:44-47.
36. Pruitt KD, Maglott DR. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 2001;29:137-140.
37. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-3402.
38. Schuler GD, Boguski MS, Stewart EA, et al. A gene map of the human genome. Science. 1996;274:540-546.
39. Boguski MS, Lowe TM, Tolstoshev CM. dbEST: database for "expressed sequence tags." Nat Genet. 1993;4:332-333.
40. Wheelan SJ, Church DM, Ostell JM. Spidey: a tool for mRNA-to-genomic alignments. Genome Res. 2001;11:1952-1957.
41. Xiao HS, Huang QH, Zhang FX, et al. Identification of gene expression profile of dorsal root ganglion in the rat peripheral axotomy model of neuropathic pain. Proc Natl Acad Sci USA. 2002;99:8360-8365.
42. Schiller MR, Mains RE, Eipper BA. A neuroendocrine-specific protein localized to the endoplasmic reticulum by distal degradation. J Biol Chem. 1995;270:26129-26138.
43. Bogumil R, Knipp M, Fundel SM, Vasak M. Characterization of dimethylargininase from bovine brain: evidence for a zinc binding site. Biochemistry. 1998;37:4791-4798.
44. Knipp M, Charnock JM, Garner CD, Vasak M. Structural and functional characterization of the Zn(II) site in dimethylargminase-1 (DDAH-1) from bovine brain: Zn(II) release activates DDAH-1. J Biol Chem. 2001;276:40449-40456.
45. Kimoto M, Tsuji H, Ogawa T, Sasaoka K. Detection of NG,NG- dimethylarginine dimethylaminohydrolase in the nitric oxide-generating systems of rats using monoclonal antibody. Arch Biochem Biophys. 1993;300:657-662.
46. MacAllister RJ, Parry H, Kimoto M, et al. Regulation of nitric oxide synthesis by dimethylarginine dimethylaminohydrolase. Br J Pharmacol. 1996;119:1533-1540.
47. Niinobe M, Koyama K, Yoshikawa K. Cellular and subcellular localization of necdin in fetal and adult mouse brain. Dev Neurosci. 2000;22:310-319.
48. Aizawa T, Maruyama K, Kondo H, Yoshikawa K. Expression of necdin, an embryonal carcinoma-derived nuclear protein, in developing mouse brain. Brain Res Dev Brain Res. 1992;68:265-274.
49. Stoilova D, Child A, Trifan OC, Crick RP, Coakes RL, Sarfarazi M. Localization of a locus (GLC1B) for adult-onset primary open angle glaucoma to the 2cen-q13 region. Genomics. 1996;36:142-150.
50. Wirtz MK, Samples JR, Kramer PL, et al. Mapping a gene for adult-onset primary open-angle glaucoma to chromosome 3q. Am J Hum Genet. 1997;60:296-304.
51. Trifan OC, Traboulsi EI, Stoilova D, et al. A third locus (GLC1D) for adult-onset primary open-angle glaucoma maps to the 8q23 region. Am J Ophthalmol. 1998;126:17-28.
52. Wirtz MK, Samples JR, Rust K, et al. GLC1F, a new primary open-angle glaucoma locus, maps to 7q35-q36. Arch Ophthalmol. 1999;117:237-241.
53. Assink JJ, Tijmes NT, ten Brink JB, et al. A gene for X-linked optic atrophy is closely linked to the Xp11.4-Xp11.2 region of the X chromosome. Am J Hum Genet. 1997;61:934-939.
54. Kerrison JB, Arnould VJ, Ferraz Sallum JM, et al. Genetic heterogeneity of dominant optic atrophy, Kjer type: Identification of a second locus on chromosome 18q12.2-12.3. Arch Ophthalmol. 1999;117:805-810.
55. El-Shanti H, Lidral AC, Jarrah N, Druhan L, Ajlouni K. Homozygosity mapping identifies an additional locus for Wolfram syndrome on chromosome 4q. Am J Hum Genet. 2000;66:1229-1236.
56. Bomont P, Watanabe M, Gershoni-Barush R, et al. Homozygosity mapping of spinocerebellar ataxia with cerebellar atrophy and peripheral neuropathy to 9q33-34, and with hearing impairment and optic atrophy to 6p21-23. Eur J Hum Genet. 2000;8:986-990.
57. Kremer H, Hamel BC, van den Helm B, et al. Localization of the gene (or genes) for a syndrome with X-linked mental retardation, ataxia, weakness, hearing impairment, loss of vision and a fatal course in early childhood. Hum Genet. 1996;98:513-517.
58. Bishop JO, Smith GP. The determination of RNA homogeneity by molecular hybridization. Cell. 1974;3:341-346.
59. Getz MJ, Birnie GD, Young BD, MacPhail E, Paul J. A kinetic estimation of base sequence complexity of nuclear poly(A)-containing RNA in mouse Friend cells. Cell. 1975;4:121-129.
60. Bloomquist BT, Darlington DN, Mains RE, Eipper BA. RESP18, a novel endocrine secretory protein transcript, and four other transcripts are regulated in parallel with pro-opiomelanocortin in melanotropes. J Biol Chem. 1994;269:9113-9122.
61. Darlington DN, Schiller MR, Mains RE, Eipper BA. Expression of RESP18 in peptidergic and catecholantinergic neurons. J Histochem Cytochem. 1997;45:1265-1277.
62. Schiller MR, Mains RE, Eipper BA. A novel neuroendocrine intracellular signaling pathway. Mol Endocrinol. 1997;11:1846-1857.
63. Franco-Bourland RE, Guizar-Sahagun G, Garcia GA, et al. Retinal vulnerability to glutamate excitotoxicity in canine glaucoma: induction of neuronal nitric oxide synthase in retinal ganglion cells. Proc West Pharmacol Soc. 1998;41:201-204.
64. Morgan J, Caprioli J, Koseki Y. Nitric oxide mediates excitotoxic and anoxic damage in rat retinal ganglion cells cocultured with astroglia. Arch Ophthalmol. 1999;117:1524-1529.
65. Neufeld AH, Hernandez MR, Gonzalez M. Nitric oxide synthase in the human glaucomatous optic nerve head. Arch Ophthalmol. 1997;115:497-503.
66. Neufeld AH, Sawada A, Becker B. Inhibition of nitric-oxide synthase 2 by aminoguanidine provides neuroprotection of retinal ganglion cells in a rat model of chronic glaucoma. Proc Natl Acad Sci USA. 1999;96:9944-9948.
67. Smith MA, Vasak M, Knipp M, Castellani RJ, Perry G. Dimethylargininase, a nitric oxide regulatory protein, in Alzheimer disease. Free Radic Biol Med. 1998;25:898-902.
68. Nakagomi S, Kiryu-Seo S, Kimoto M, Emson PC, Kiyama H. Dimethylarginine dimethylaminohydrolase (DDAH) as a nerve-injury-associated molecule: mRNA localization in the rat brain and its coincident up-regulation with neuronal NO synthase (nNOS) in axotomized motoneurons. Eur J Neurosci. 1999;11:2160-2166.
69. Surgucheva I, McMahan B, Ahmed F, Tomarev S, Wax MB, Surguchov A. Synucleins in glaucoma: implication of gamma-synuclein in glaucomatous alterations in the optic nerve. J Neurosci Res. 2002;68:97-106.
70. Wang AG, Chen CH, Yang CW, et al. Change of gene expression profiles in the retina following optic nerve injury. Brain Res Mol Brain Res. 2002;101:82-92.
71. Szabo A, Dalmau J, Manley G, et al. HuD, a paraneoplastic encephalomyelitis antigen, contains-RNA-binding domains and is homologous to Elav and Sex-lethal. Cell. 1991;67:325-333.
72. Lee CH, Della NG, Chew CE, Zack DJ. Rin, a neuron-specific and calmodulin-binding small G-protein, and Rit define a novel subfamily of ras proteins. J Neurosci. 1996;16:6784-6794.
73. Wes PD, Yu M, Montell C. RIC, a calmodulin-binding Ras-like GTPase. EMBO J. 1996;15:5839-5848.
74. Sano A, Mikami M, Nakamura M, Ueno S, Tanabe H, Kaneko S. Positional candidate approach for the gene responsible for benign adult familial myoclonic epilepsy. Epilepsia. 2002;43:26-31.
75. Xiang M, Zhou L, Macke JP, et al. The Brn-3 family of POU-domain factors: primary structure, binding specificity, and expression in subsets of retinal ganglion cells and somatosensory neurons. J Neurosci. 1995;15:4762-4785.
76. Gooley JJ, Lu J, Chou TC, Scammell TE, Saper CB. Melanopsin in cells of origin of the retinohypothalamic tract. Nat Neurosci. 2001;4:1165.
77. Hattar S, Liao HW, Takao M, Berson DM, Yau KW. Melanopsin-containing retinal ganglion cells: architecture, projections, and intrinsic photosensitivity. Science. 2002;295:1065-1070.
78. Provencio I, Rodriguez IR, Jiang G, Hayes WP, Moreira EF, Rollag MD. A novel human opsin in the inner retina. J Neurosci. 2000;20:600-605.
79. Blackshaw S, Kuo WP, Park PJ, et al. MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol. 2003;4:R17.