Differential gene expression in mouse retina related to regional differences in vulnerability to hyperoxia.
OBJECTIVE
In the C57BL/6J mouse retina, hyperoxia-induced degeneration of photoreceptors shows strong regional variation, beginning at a locus ~0.5 mm inferior to the optic disc. To identify gene expression differences that might underlie this variability in vulnerability, we have used microarray techniques to describe regional (superior-inferior) variations in gene expression in the retina.


METHODS
Young adult C57BL/6J mice raised in dim cyclic illumination (12 h at 5 lx and 12 h in darkness) were exposed to hyperoxia (75% oxygen for two weeks). Retinas were collected from hyperoxia-exposed and control animals without fixation and divided into superior and inferior halves. RNA was extracted from each sample, purified, and hybridized to Mouse Gene 1.0 ST arrays (Affymetrix). The consistency of the microarray results was assessed using quantitative PCR for selected genes. Expression data were analyzed to identify genes and ncRNAs whose differential expression between the superior and inferior retina could be associated with relative vulnerability to hyperoxia.


RESULTS
In control retinas, only two genes showed a fold difference in expression >2 between the superior and inferior retina; another 25 showed a fold difference of 1.5-2.0. Of these 27, the functions of six genes, including ventral anterior homeobox containing gene 2 (Vax2) and T-box 5 (Tbox5), are related to parameters of anatomic development and the functions of five are related to sensory perception. Among the latter, short-wave-sensitive cone opsin (Opn1sw) was more strongly expressed in the inferior retina and medium-wave-sensitive cone opsin (Opn1mw) in the superior retina. This is consistent with known differences in S- and M-cone distribution, confirming our separation of retinal regions. The highest fold difference was reported for membrane metalloendopeptidase (Mme), a member from the metallothionein group of cytoprotective proteins. To identify genes whose regulation by hyperoxia was significantly different between the inferior and superior retina, we calculated the "fold margin" (FM, the difference between hyperoxia-induced regulation in the inferior and superior retina) for each gene, and identified genes for which abs(FM) > 0.5. Genes thus identified numbered 112, and included many immune-, cell defense-, and inflammation- related genes.


CONCLUSIONS
Gene expression analysis revealed relatively subtle differences between inferior and superior regions of control C57BL/6J retinas, with only 27 genes showing an expression difference >1.5 fold. Among these, genes related to cytoprotection and apoptosis were included, along with genes related to central projections and cone-type differences. After hyperoxia-induced photoreceptor degeneration had begun, the number of genes that showed significant expression differences between the inferior and superior retina more than quadrupled, with genes related to immune processes, defense processes, and inflammation being numerically dominant.
Zhu
Yuan
Y
ARC Centre of Excellence in Vision Science, Canberra, Australia. yuan.zhu@anu.edu.au
Natoli
Riccardo
R
Valter
Krisztina
K
Stone
Jonathan
J
D000818:Animals; D017209:Apoptosis / Q000235:genetics; D019610:Cytoprotection / Q000235:genetics; D004198:Disease Susceptibility; D015870:Gene Expression; D018496:Hyperoxia / Q000150:complications / Q000235:genetics / Q000378:metabolism* / Q000503:physiopathology; D007107:Immune System / Q000378:metabolism; D007249:Inflammation / Q000235:genetics / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D046228:Microarray Analysis; D005810:Multigene Family; D020419:Photoreceptor Cells, Vertebrate / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D012160:Retina / Q000378:metabolism* / Q000503:physiopathology; D017949:Retinal Cone Photoreceptor Cells / Q000378:metabolism; D012162:Retinal Degeneration / Q000209:etiology / Q000235:genetics / Q000378:metabolism; D009435:Synaptic Transmission; D014018:Tissue Distribution
BMC Genomics. 2008 Feb 08;9:73
18261226
Am J Ophthalmol. 1999 Aug;128(2):155-64
10458170
Invest Ophthalmol Vis Sci. 2007 Jan;48(1):405-11
17197561
Mol Vis. 2008;14:1983-94
18989387
Br J Ophthalmol. 1959 Jan;43(1):34-9
13618528
Exp Eye Res. 2008 Sep;87(3):292-5
18586030
Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11830-5
12189211
Br J Pharmacol. 1996 Jan;117(1):184-8
8825361
Invest Ophthalmol Vis Sci. 2006 Sep;47(9):3975-82
16936113
Proc Natl Acad Sci U S A. 1999 Sep 14;96(19):10729-34
10485894
J Cell Physiol. 1999 May;179(2):149-56
10199554
Invest Ophthalmol Vis Sci. 1997 Aug;38(9):1667-77
9286255
Ann Surg. 1938 Jun;107(6):1005-21
17857197
Invest Ophthalmol Vis Sci. 1995 Jun;36(7):1201-14
7775098
Exp Eye Res. 2006 Sep;83(3):620-8
16677633
Exp Eye Res. 1997 Jul;65(1):45-50
9237863
Invest Ophthalmol Vis Sci. 2008 Jul;49(7):3207-15
18579766
Nat Med. 2005 Apr;11(4):434-9
15778722
Invest Ophthalmol Vis Sci. 2008 Oct;49(10):4561-7
18539939
Invest Ophthalmol Vis Sci. 2005 Aug;46(8):2726-35
16043844
J Biol Chem. 1993 Oct 5;268(28):21394-8
8407980
Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8428-30
9671693
Surv Ophthalmol. 2008 Mar-Apr;53(2):112-20
18348877
Invest Ophthalmol Vis Sci. 2006 Mar;47(3):1024-9
16505037
Arch Ophthalmol. 2006 Jun;124(6):860-8
16769840
Exp Eye Res. 2004 Aug;79(2):239-47
15325571
J Renin Angiotensin Aldosterone Syst. 2002 Mar;3(1):1-15
11984741
J Neurosci. 2008 Dec 17;28(51):13765-74
19091967
N Engl J Med. 2007 Aug 9;357(6):553-61
17634448
Brain Res. 1997 Sep 26;769(2):385-90
9374211
Neuron. 2002 Aug 1;35(3):475-87
12165470
Matrix Biol. 2005 Feb;24(1):3-13
15748997
Science. 2000 Jan 7;287(5450):134-7
10615048
Vis Neurosci. 2008 Mar-Apr;25(2):167-77
18442439
J Cardiovasc Pharmacol. 1993;22 Suppl 8:S26-8
7509960
J Neurosci. 1995 Jul;15(7 Pt 1):4738-47
7623107
Bioessays. 2001 Mar;23(3):261-9
11223883
Am J Pathol. 2001 Sep;159(3):1113-20
11549604
Neuron. 2000 Sep;27(3):513-23
11055434
J Immunol. 2005 Jan 1;174(1):491-7
15611275
Vis Neurosci. 2005 Jul-Aug;22(4):501-7
16212707
J Neurosci. 2005 May 4;25(18):4540-9
15872101
Invest Ophthalmol Vis Sci. 1999 Sep;40(10):2448-53
10476818
Exp Eye Res. 2007 Jan;84(1):82-91
17069800
Am J Ophthalmol. 1999 Aug;128(2):165-72
10458171
Nat Genet. 2007 Oct;39(10):1200-1
17767156
J Comp Neurol. 2001 Feb 12;430(3):343-56
11169472
Annu Rev Pharmacol Toxicol. 1999;39:267-94
10331085
Prog Retin Eye Res. 2001 Nov;20(6):705-32
11587915
Nucleic Acids Res. 2001 May 1;29(9):e45
11328886
Invest Ophthalmol Vis Sci. 2010 Sep;51(9):4821-30
20393118
Nat Med. 2002 Jul;8(7):718-24
12068288
Annu Rev Neurosci. 2005;28:327-55
16022599
J Comp Neurol. 1992 Nov 15;325(3):327-42
1447405
Cell. 1994 Aug 12;78(3):473-85
8062389
Proc Natl Acad Sci U S A. 1989 Apr;86(8):2863-7
2649896
J Hypertens. 1992 Nov;10(11):1379-86
1336523
Graefes Arch Clin Exp Ophthalmol. 2008 Jan;246(1):93-8
17674017
Invest Ophthalmol Vis Sci. 2001 Mar;42(3):804-15
11222544
Arch Ophthalmol. 2003 Sep;121(9):1316-23
12963616
Curr Eye Res. 2004 Dec;29(6):441-7
15764088
Nature. 1998 Jul 30;394(6692):485-90
9697772
Exp Eye Res. 2002 Jan;74(1):83-92
11878821