Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq

Experimental Eye Research

Volumn 129, Issue , 2014, Pages 93-106

  Whitmore, S Scott ^a,b   Wagner, Alex H ^a,c   DeLuca, Adam P ^a,b   Drack, Arlene V ^a,b   Stone, Edwin M ^a,b   Tucker, Budd A ^a,b   Zeng, Shemin ^a,b   Braun, Terry A ^a,b,c   Mullins, Robert F ^a,b   Scheetz, Todd E ^a,b,c  

^a UNIVERSITY OF IOWA   (United States)

^b UNIVERSITY OF IOWA   (United States)

^c IA United States   (United States)

Author keywords

Choroid; Gene expression; Macular degeneration; Retina; Retinitis pigmentosa; RNA Seq; RPE; Transcriptome

Indexed keywords

MICRORNA; RNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME; MESSENGER RNA;

AGED; ARTICLE; CELL TYPE; CHOROID; CLINICAL ARTICLE; FEMALE; GENE EXPRESSION; HUMAN; MACULAR DEGENERATION; MALE; PHENOTYPE; PHOTORECEPTOR; PIGMENT EPITHELIUM; RETINA CELL; RETINA DISEASE; RETINA MACULA LUTEA; RETINA NEUROEPITHELIAL LAYER; RETINITIS PIGMENTOSA; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; VERY ELDERLY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; PATHOLOGY;

AGED; AGED, 80 AND OVER; CHOROID; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MACULA LUTEA; MALE; PIGMENT EPITHELIUM OF EYE; RETINAL DISEASES; RNA, MESSENGER;

EID: 84910626381     PISSN: 00144835     EISSN: 10960007     Source Type: Journal    
DOI: 10.1016/j.exer.2014.11.001     Document Type: Article

References (34)

1. Aranda J., Rivera J.C., Jeziorski M.C., Riesgo-Escovar J., Nava G., López-Barrera F., et al. Prolactins are natural inhibitors of angiogenesis in the retina. Investigative Ophthalmol. Vis. Sci. 2005 Aug, 46(8):2947-2953.
2. Arnold E., Rivera J.C., Thebault S., Moreno-Páramo D., Quiróz-Mercado H., Quintanar-Stéphano A., et al. High levels of serum prolactin protect against diabetic retinopathy by increasing ocular vasoinhibins. Diabetes 2010 Dec, 59(12):3192-3197. PMCID: PMC2992782.
3. Booij J.C., Baas D.C., Beisekeeva J., Gorgels T.G.M.F., Bergen A.A.B. The dynamic nature of Bruch's membrane. Prog. Retin. Eye Res. 2010 Jan, 29(1):1-18.
4. Bowes Rickman C., Ebright J.N., Zavodni Z.J., Yu L., Wang T., Daiger S.P., et al. Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE. Investigative Ophthalmol. Vis. Sci. 2006 Jun, 47(6):2305-2316. PMCID: PMC2813776.
5. Braun T.A., Mullins R.F., Wagner A.H., Andorf J.L., Johnston R.M., Bakall B.B., et al. Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease. Hum. Mol. Genet. 2013, 22(25):5136-5145.
6. Curcio C.A., Allen K.A. Topography of ganglion cells in human retina. J.Comp. Neurology 1990 Oct 1, 300(1):5-25.
7. Curcio C.A., Sloan K.R., Kalina R.E., Hendrickson A.E. Human photoreceptor topography. J.Comp. Neurology 1990 Feb 22, 292(4):497-523.
8. de Jong P.T.V.M. Age-related macular degeneration. N.Engl. J. Med. 2006 Oct 5, 355(14):1474-1485.
9. DeLuca D.S., Levin J.Z., Sivachenko A., Fennell T., Nazaire M.-D., Williams C., et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 2012 Jun 1, 28(11):1530-1532. PMCID: PMC3356847.
10. Diehn J.J., Diehn M., Marmor M.F., Brown P.O. Differential gene expression in anatomical compartments of the human eye. Genome Biol. 2005, 6(9):R74. PMCID: PMC1242209.
11. Gonzalez P., Caballero M., Liton P.B., Stamer W.D., Epstein D.L. Expression analysis of the matrix GLA protein and VE-cadherin gene promoters in the outflow pathway. Investigative Ophthalmol. Vis. Sci. 2004 May, 45(5):1389-1395.
12. Ishibashi K., Tian J., Handa J.T. Similarity of mRNA phenotypes of morphologically normal macular and peripheral retinal pigment epithelial cells in older human eyes. Investigative Ophthalmol. Vis. Sci. 2004 Sep, 45(9):3291-3301.
13. Jonas J.B., Schneider U., Naumann G.O. Count and density of human retinal photoreceptors. Graefes Arch. Clin. Exp. Ophthalmol. 1992, 230(6):505-510.
14. Kim C.Y., Kuehn M.H., Clark A.F., Kwon Y.H. Gene expression profile of the adult human retinal ganglion cell layer. Mol. Vis. 2006, 12:1640-1648.
15. Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R., Salzberg S.L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013 Apr 25, 14(4):R36.
16. Klein M.L., Jorizzo P.A., Watzke R.C. Growth features of choroidal neovascular membranes in age-related macular degeneration. Ophthalmology 1989 Sep, 96(9):1416-1419. discussion1420-1.
17. Kociok N., Joussen A.M. Varied expression of functionally important genes of RPE and choroid in the macula and in the periphery of normal human eyes. Graefes Arch. Clin. Exp. Ophthalmol. 2007 Jan, 245(1):101-113.
18. Li M., Jia C., Kazmierkiewicz K.L., Bowman A.S., Tian L., Liu Y., et al. Comprehensive analysis of gene expression in human retina and supporting tissues. Hum. Mol. Genet. 2014, 23(15):4001-4014.
19. Mullins R.F., Kuehn M.H., Faidley E.A., Syed N.A., Stone E.M. Differential macular and peripheral expression of bestrophin in human eyes and its implication for Best disease. Investigative Ophthalmol. Vis. Sci. 2007 Jul, 48(7):3372-3380.
20. Radeke M.J., Peterson K.E., Johnson L.V., Anderson D.H. Disease susceptibility of the human macula: differential gene transcription in the retinal pigmented epithelium/choroid. Exp. Eye Res. 2007 Sep, 85(3):366-380.
21. Rivera J.C., Aranda J., Riesgo J., Nava G., Thebault S., López-Barrera F., et al. Expression and cellular localization of prolactin and the prolactin receptor in mammalian retina. Exp. Eye Res. 2008 Feb, 86(2):314-321.
22. Rouhani F., Kumasaka N., de Brito M.C., Bradley A., Vallier L., Gaffney D. Genetic background drives transcriptional variation in human induced pluripotent stem cells. PLoS Genet. 2014 Jun, 10(6):e1004432. PMCID: PMC4046971.
23. Schulz H.L., Stoehr H., White K., van Driel M.A., Hoyng C.B., Cremers F., et al. Genomic structure and assessment of the retinally expressed RFamide-related peptide gene in dominant cystoid macular dystrophy. Mol. Vis. 2002 Mar 19, 8:67-71.
24. Siegert S., Cabuy E., Scherf B.G., Kohler H., Panda S., Le Y.-Z., et al. Transcriptional code and disease map for adult retinal cell types. Nat. Neurosci. 2012 Mar, 15(3):487-495. S1-2.
25. Skeie J.M., Mahajan V.B. Proteomic landscape of the human choroid-retinal pigment epithelial complex. JAMA Ophthalmol. 2014 Jul 24, (in press).
26. Stone E.M., Luo X., Héon E., Lam B.L., Weleber R.G., Halder J.A., et al. Autosomal recessive retinitis pigmentosa caused by mutations in the MAK gene. Investigative Ophthalmol. Vis. Sci. 2011 Dec, 52(13):9665-9673. PMCID: PMC3341124.
27. Trapnell C., Hendrickson D.G., Sauvageau M., Goff L., Rinn J.L., Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 2013, 31(1):46-53.
28. Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D.R., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 2012, 7(3):562-578. PMCID: PMC3334321.
29. Trapnell C., Williams B.A., Pertea G., Mortazavi A., Kwan G., van Baren M.J., et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010 May, 28(5):511-515. PMCID: PMC3146043.
30. Tucker B.A., Scheetz T.E., Mullins R.F., DeLuca A.P., Hoffmann J.M., Johnston R.M., et al. Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase (MAK) as a cause of retinitis pigmentosa. Proc. Natl. Acad. Sci. 2011 Aug 23, 108(34):E569-E576. PMCID: PMC3161526.
31. van Soest S.S., de Wit G.M.J., Essing A.H.W., Brink ten J.B., Kamphuis W., de Jong P.T.V.M., et al. Comparison of human retinal pigment epithelium gene expression in macula and periphery highlights potential topographic differences in Bruch's membrane. Mol. Vis. 2007, 13:1608-1617.
32. Wagner A.H., Anand V.N., Wang W.-H., Chatterton J.E., Sun D., Shepard A.R., et al. Exon-level expression profiling of ocular tissues. Exp. Eye Res. 2013 Jun, 111:105-111. PMCID: PMC3664108.
33. Whitmore S.S., Braun T.A., Skeie J.M., Haas C.M., Sohn E.H., Stone E.M., et al. Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells. Mol. Vis. 2013, 19:2274-2297. PMCID: PMC3834599.
34. Zhang L., Wahlin K., Li Y., Masuda T., Yang Z., Zack D.J., et al. RIT2, a neuron-specific small guanosine triphosphatase, is expressed in retinal neuronal cells and its promoter is modulated by the POU4 transcription factors. Mol. Vis. 2013, 19:1371-1386. PMCID: PMC3692409.