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1 From the Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton Alberta, Canada; 2 Laboratoire dendocrinologie moléculaire, Centre de recherche du Centre Hospitalier de lUniversité Laval, Quebec City, Quebec, Canada.
| Abstract |
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METHODS. A human adult iris cDNA library was constructed and subjected to a differential selection screen to identify genes preferentially expressed in iris or trabecular tissue versus those expressed in lymphoblasts. Selected cDNAs were partially sequenced. Novel cDNAs were chosen for further analysis. The cDNAs were localized within chromosomes using a radiation hybrid (RH) mapping panel. The tissue expression profile of each cDNA was found through computer-based searches. One novel cDNA was subjected to 5' rapid amplification of cDNA ends and Northern blot analysis.
RESULTS. Of 24 differentially selected clones, 14 cDNAs had homology to known genes, whereas the other 10 were previously uncharacterized cDNA clones. IR185 was one novel iris cDNA identified. Northern blot analysis with IR185 indicated that it is expressed in human fetal liver as a 2.7-kb transcript and in adult iris as a 1.6-kb transcript. Computer-based searches of public databases and reverse transcriptionpolymerase chain reaction experiments have determined that IR185 is also expressed in retina. RH mapping experiments have localized IR185 to the chromosomal interval 1q31-q32, near the loci for age-related degeneration (1q25-q31) and retinitis pigmentosa 12 (1q31-q32), and IR185 is in the region for posterior column ataxia with retinitis pigmentosa (1q31-q32). It has a 996-bp open reading frame encoding a putative protein with homology to the small leucine-rich proteoglycan (SLRP) family. The IR185 gene has been tentatively named oculoglycan.
CONCLUSIONS. Differential selection is a technique that has been useful in identifying genes specific to a variety of tissues. This is the first time this technique has been applied to the iris. Characterizing genes highly or uniquely expressed in the iris can assist in clarifying our understanding of iris function and lead to a better understanding of the molecular pathogenesis of ocular disease. IR185 is a tentative candidate for one eye disorder genetically localized to chromosome 1q31-q32.
| Introduction |
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One factor examined when considering the eligibility of any candidate gene is whether the gene is expressed in the tissue affected by the disorder. Alternatively, researchers can identify highly or specifically expressed genes in a given tissue. Genes expressed in this manner can be assumed to be important for the function of that tissue. Once isolated, genes that are highly expressed or tissue specific can become candidate genes for disorders that affect the tissue used for gene isolation. For example, genes expressed in the retina can be candidate genes for retinal disorders. There are a variety of techniques available to identify genes expressed in some tissues and not in others, including subtractive hybridization2 and computer-based (in Silico) searches of public databases.3 We have used another technique, differential selection,4 to search for genes expressed in the iris and trabecular meshwork. In a differential selection screen, cDNA pools from different tissues are used as probes against a cDNA library. cDNAs found to be expressed in the tissue of interest and not in the control tissue are selected for further analysis. cDNAs found to be more highly expressed in the tissue of interest than in the control tissue may also be chosen for further characterization, as we did in the current work. Differential selection has been successfully used to isolate new genes involved in retinal function (i.e., Rom1, Chx10),5 6 but this technique has not been applied previously to the iris. Genes identified using our differential selection screen can be tested as candidates for ocular disorders, including glaucoma.
This article describes the screening of an iris cDNA library to identify cDNAs preferentially expressed in the iris or trabecular meshwork. cDNAs were identified through a differential selection screen. One novel cDNA, IR185, isolated using this method, was analyzed in detail. The expression of IR185 in fetal liver, iris, and retina together with its genetic colocalization with posterior column ataxia with retinitis pigmentosa make IR185 a candidate for ocular disease.
| Materials and Methods |
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Differential Screen
The iris cDNA library was grown at low density on 245-mm square
bioassay dishes (Fisher Scientific, Nepean Ontario, Canada). Each dish
was plated with either 6,000 or 12,500 plaque forming units (pfu). A
total of 72,000 pfu, representing approximately 24,000 recombinant
cDNAs, was plated. Triplicate filter lifts were made of each plate
using Hybond-N (Amersham Pharmacia Biotech, Baie dUrfé,
Québec, Canada). Each filter lift was treated as follows: 5
minutes denaturing in 0.5 M NaOH and 1.5 M NaCl, followed by 5
minutes neutralizing in 1.5 M NaCl and 0.5 M Tris-HCl, and 5
minutes rinsing in 2x SSC. The filters were then air dried and baked
overnight at 80°C in a vacuum oven. Before hybridization, each nylon
blot was prewashed with 2x SSC before it was prehybridized for 1 hour
in Church and Gilbert hybridization solution7
at 65°C.
Iris, trabecular meshwork, or lymphoblast cDNA (50 ng) were radiolabeled with 32P dCTP (Random Primed Labeling Kit; Roche Diagnostics, Laval, Québec). The radiolabeled probe was denatured at 95°C, cooled rapidly on ice, added to the prehybridized filter lifts, and hybridized at 65°C overnight. The filters were washed under low-stringency conditions with 2x SSC and 1% sodium dodecyl sulfate (SDS) for 30 minutes at room temperature, were washed again under high-stringency conditions with 0.2x SSC and 0.1% SDS for 45 minutes at 65°C, and were exposed to film (Biomax; Eastman Kodak, Rochester, NY) for 1 week at -70°C. Primary cDNA plaques detected with iris cDNA but not as highly with lymphoblast cDNA or those detected with trabecular meshwork cDNA but not as highly with iris or lymphoblast cDNA were selected for further analysis.
Plaques of interest were selected and the recombinant cDNAs isolated using the in vivo excision protocol supplied by the manufacturer (Stratagene). Individual cDNAs were manually sequenced using a 33P-radiolabeled terminator sequencing kit (ThermoSequenase Cycle Sequencing Kit; Pharmacia Biotech).
PCR Primers
cDNA-specific polymerase chain reaction (PCR) primers were
designed using the Primer 3 program at the Whitehead Institute for
Biomedical Research (Cambridge, MA; web page available at
http://www.genome.wi.mit.edu).
Northern Blot Hybridization
IR185 cDNA (50 ng) was randomly primed and radiolabeled
as described. Radiolabeled IR185 cDNA was hybridized to a
commercially available multiple tissue Northern blots (Human Multiple
Tissue Northern Blot I, Human Multiple Tissue Northern Blot II,
and Human Fetal Multiple Tissue Northern Blot II; Clontech, Palo Alto,
CA). Each Northern blot contained approximately 2 µg polyA+ RNA per
lane. Hybridization was performed at 68°C for 1 hour using
Express Hyb solution (Clontech). The Northern blots were washed under
low-stringency conditions (2x SSC and 0.05% SDS for 30 minutes at
room temperature), washed again under high-stringency conditions (0.1x
SSC and 0.1% SDS for 40 minutes at 50°C), and exposed to film
(Biomax; Kodak). Northern blots were probed with actin cDNA to control
for RNA loading. The actin control hybridization experiment was
performed in an identical manner.
A Northern blot containing 3 µg human iris, human retina, and human lymphocyte total RNA was made using standard methods. The Northern blot was probed using actin cDNA, as described, and was probed with IR185 cDNA at 42°C using UltraHyb solution (Ambion, Austin, TX). As before, the Northern blot was washed under low-stringency conditions (2x SSC and 0.1% SDS for 5 minutes at room temperature) and then under high-stringency conditions (0.1x SSC and 0.1% SDS for 30 minutes at 42°C) and exposed to film.
Radiation Hybrid Mapping
IR185 primers were used to screen the Genebridge 4 radiation
hybrid (RH) panel (Research Genetics, Huntsville, AL). Primers
IR1851F (cccaggtcatcatctcttggacc) and IR1851R
(atggagacctttgtccatgc) amplified a 142-bp fragment. PCRs were performed
under the following conditions: 94°C for 5 minutes; 30 cycles of
94°C for 30 seconds, 62°C for 30 seconds, and 72°C for 30
seconds; followed by a final extension step at 72°C for 7 minutes.
The PCR products from all 93 RH cell lines, HFL121 (human positive
control), and A23 (hamster negative control) were separated on agarose
gels and scored as positive, negative, or ambiguous. The results were
electronically submitted to the Whitehead Institute for Biomedical
Research Web site (http://www.genome.wi.mit.edu) and to the Sanger
Center (Hinxton, UK) Web site for analysis
(http://www.sanger.ac.uk/RHserver).
cDNA-specific primers were also used for RH mapping to chromosomal regions of any unlocalized novel or known cDNAs.
Computer-Based Searches
The in Silico expression profile of each cDNA was determined by an
electronic search of the cDNA sequence on the TIGR database
(http://www.tigr.org/tdb/hgi/hgi.html). The IR185 putative amino acid
sequence alignment was performed at the Baylor College of
Medicine search launcher Web site
(http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html).
The putative protein motifs of IR185 were found through analysis of the
predicted amino acid sequence of IR185 with software at the
ExPASy-Prosite Web site (http://www.expasy.ch/sprot/prosite.html).
RACE Experiments
Human choroidal rings (including iris and trabecular meshwork
tissue) were obtained from several donors less than 24 hours after
death. Choroidal rings were collected by the Comprehensive Tissue
Center of the Capital Health Authority with approval from the Research
Ethics Board of the Faculty of Medicine of the University of Alberta.
The tissues obtained were within the tenets of the Helsinki
Declaration. Total RNA was isolated using TRIzol reagent (Canadian Life
Technologies). PolyA+ RNA was isolated from choroidal rings using
oligo-dTcoated Dynabeads (Dynal), 1 µg of which was used as the
substrate for 5' rapid amplification of DNA ends (RACE) experiments.
RACE experiments were performed with kits (Marathon cDNA Amplification
Kit and the Advantage cDNA Polymerase Mix; Clontech). Amplified DNA was
purified (QIAquick PCR Purification Kit; Qiagen, Chatsworth, CA) and
cloned into a vector (pGEM-T EasyVector System II; Promega, Madison,
WI). Cloned cDNAs were sequenced manually, as described.
Reverse TranscriptionPolymerase Chain Reaction
Total choroidal ring RNA, total lymphoblast RNA, total trabecular
meshwork RNA, and total retina RNA were used as a substrate for reverse
transcriptionpolymerase chain reaction (RT-PCR). First-strand cDNA
synthesis was performed with a commercially available reverse
transcriptase (Superscript Reverse Transcriptase; Canadian Life
Technologies), and oligo-dT using 1 µg total RNA. cDNA-specific PCR
primers were used to test whether the cDNAs could be amplified from
choroidal ring, lymphoblast, trabecular meshwork, or retina cDNA. PCR
products were separated using agarose gel electrophoresis and
visualized with ethidium bromide.
| Results |
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| Discussion |
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We have isolated and partially characterized a novel gene,
IR185, from a differential selection screen. IR185 is
homologous to osteoglycin11
and epiphycan,12
two members of the SLRP family of proteins, which are secreted and
associated with the extracellular matrix.13
14
SLRP
proteins are characterized by several leucine-rich
motifs14
bounded by conserved cysteine residues that are
hypothesized to form internal disulfide bonds.15
The
24amino acid leucine-rich repeat consensus sequence is:
x-x-I/V/l-x-x-x-x-F/P/l-x-x-L/P-x-x-L-x-x-L/I-x-L-x-x-N-x-I/l, where x
represents any amino acid.14
Within the consensus
sequence, the multiple amino acids listed in positions 3, 8, 11, 17,
and 24 are in order of decreasing frequency.14
Leucine-rich repeat consensus amino acids 3 to 11 and 14 to 24 are
predicted to form a ß-sheet and an
-helix,
respectively.14
The SLRP family is divided into three main
classes based on the cysteine spacings on the amino flank of the
leucine repeats.14
Osteoglycin and epiphycan are the sole
members of the class 3 SLRPs. IR185s predicted homology to these
proteins at the amino acid level and conservation of cysteine residues
among the three proteins strongly suggest that IR185 is also a class 3
SLRP.
Expression of SLRP genes appears to vary depending on their class. Class 1 SLRP genes, decorin and biglycan, are expressed in virtually every tissue tested,14 whereas class 2 genes, fibromodulin, keratocan, lumican, and proline-argininerich and leucine-rich repeat protein (PRELP) are expressed in seven or fewer tissues.16 17 18 Class 3 genes appear to be expressed in the fewest tissues. Mouse osteoglycin is expressed in skeletal muscle, lung, kidney, and testis.19 Osteoglycin was originally cloned from bovine bone.11 Epiphycan was only seen in placenta in Northern blot experiments.20 IR185 also has a limited tissue expression profile, suggesting that the class 3 SLRP proteins may have a more tissue-specific function than the other SLRP proteins. Because other SLRPs are known to bind to collagen,21 22 23 IR185 may be a novel collagen-associated glycoprotein with a role in eye function.
The size differences between the iris and fetal liver IR185 transcripts may be the result of alternative splicing of IR185. Alternatively, the increased transcript size may be additional untranslated 3' or 5' sequence or could encode for a larger IR185 protein product in fetal liver. Further studies are needed to determine the nature of the longer IR185 transcript in fetal liver.
IR185 is located near the same chromosomal region as two eye-related disorders, age-related macular degeneration (1q25-q31) and retinitis pigmentosa 12 (1q311q32).8 9 Of interest, IR185 is located within the same chromosomal region as posterior column ataxia with retinitis pigmentosa (1q31-q32).10 Further studies are needed to determine whether IR185 is a candidate for posterior column ataxia with retinitis pigmentosa. Because IR185 is not very highly expressed in retina, the candidacy of IR185 for posterior column ataxia with retinitis pigmentosa should be considered tentative.
Based on IR185s putative glycosylation site and expression in iris and retinal tissues we have named IR185 oculoglycan. Oculoglycan and the other genes identified in our screen will be subjected to further analysis to examine their roles in eye function and disease.
| Acknowledgements |
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| Footnotes |
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Submitted for publication May 27, 1999; revised December 10, 1999 and January 18, 2000; accepted January 31, 2000.
Commercial relationships policy: N.
Corresponding author: James S. Friedman, Department of Ophthalmology, University of Alberta, Room 832, Medical Sciences Building, Edmonton Alberta, T6G-2H7, Canada. jafriedm{at}ualberta.ca
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