IOVS
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

(Investigative Ophthalmology and Visual Science. 2004;45:3081-3090.)
© 2004 by The Association for Research in Vision and Ophthalmology, Inc.
DOI:  10.1167/iovs.04-0302
This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when eLetters are posted
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via ISI Web of Science (11)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Ahmed, F.
Right arrow Articles by Tomarev, S. I.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ahmed, F.
Right arrow Articles by Tomarev, S. I.

Gene Expression Profile of the Rat Eye Iridocorneal Angle: NEIBank Expressed Sequence Tag Analysis

Farid Ahmed,1,2 Mario Torrado,1,3 Rina D. Zinovieva,1,4 Vladimir V. Senatorov,1 Graeme Wistow,5 and Stanislav I. Tomarev1

1From the Section of Molecular Mechanisms of Glaucoma, Laboratory of Molecular and Developmental Biology, and the 5Section on Molecular Structure and Function, National Eye Institute, Bethesda, Maryland.


   Abstract
Top
 Abstract
Materials and Methods
 Results
 Discussion
 References
 
PURPOSE. To characterize gene expression pattern in the combined tissues of the rat iridocorneal angle by expressed sequence tag (EST) analysis, as part of the NEIBank project.

METHODS. RNA was extracted from dissected tissues of the rat iridocorneal angle (iris, ciliary body, trabecular meshwork, and Schlemm’s canal) and used to construct unamplified, non-normalized cDNA libraries in the pSPORT1 vector. Approximately 5000 clones were sequenced from the 5'-end. Clones were clustered and identified using the GRIST software, a procedure based on BLAST comparisons. Complete sequences of several novel cDNAs showing eye-preferred expression patterns were obtained. The expression patterns of several genes have been investigated by Northern blot and in situ hybridization, as well as by RT-PCR.

RESULTS. After analysis and removal of non-mRNA sequences, 2195 independent clusters, potentially representing individual eye angle-expressed clones were obtained. The expression profile of the combined rat eye angle tissues was more similar to that of the human iris than to human trabecular meshwork. Several cDNAs encoding transcription factors essential for normal eye development and function including Pax-6, Six3, c-Maf, Maf1, Sox-4, Foxc1, Rx, and Ldb2 were present among sequenced clones. A number of tested cDNAs showed eye-preferred expression patterns. Myocilin, which is abundant in human eye angle tissues, was not observed in the rat collection; however, transcripts for three other olfactomedin-domain proteins were seen. Latrotoxin receptor (CL1AA) and optimedin were shown to be expressed in the iris and ciliary body, as well as in the ganglion and inner nuclear cell layers of the retina, whereas the rat orthologue of the human HNOEL-iso gene was expressed in the iris and sclera and less actively in the trabecular meshwork, retina, and optic nerve.

CONCLUSIONS. The iridocorneal libraries are a good source of novel uncharacterized genes and molecular markers for the tissues of the eye angle. Although myocilin is not abundantly expressed in rat eye angle, other olfactomedin-containing genes are expressed there and may play important roles in normal eye function and disease.

Glaucoma is a group of neurodegenerative disorders characterized by the death of retinal ganglion cells and by a specific deformation of the optic nerve head, known as glaucomatous cupping. Primary open-angle glaucoma, the most common form, is often associated with elevated intraocular pressure (IOP). Elevated IOP develops as a result of imbalance between aqueous humor production and outflow. In many glaucoma cases elevated intraocular pressure develops as a result of abnormally high resistance to the outflow of aqueous humor. The gene expression profiles of several human tissues affected in glaucoma, trabecular meshwork (TM), iris, ciliary body, and retina, have been examined by expressed sequence tag (EST) analysis of cDNA libraries.1 2 3 4 5 6 Several SAGE libraries were also created from different areas of the human eye.7 Because studies of the molecular mechanisms of glaucoma are difficult to conduct in humans, appropriate animal models are needed to give insight into the molecular events in the retina and the optic nerve.

Several rat models of elevated pressure-induced optic nerve damage have been developed to study changes in the retina and the optic nerve. In these models, IOP elevation is achieved by injection of concentrated saline solution in the episcleral vein,8 cauterization of episcleral vein,9 trabecular laser photocoagulation after injection of india ink into the anterior chamber,10 or a laser injury to the TM.11 Chronic IOP elevation is accompanied by death of the retinal ganglion cells, optic nerve degeneration, and optic nerve head remodeling similar to that observed in glaucoma in humans.8 12 13 14

To study mechanisms of aqueous humor production and outflow, it is important to know the molecular composition of the tissues involved. Herein, we present characterization of more than 3400 cDNA clones from unamplified cDNA libraries derived from freshly isolated tissues of the rat iridocorneal angle (ICA) (iris, ciliary body, TM, and Schlemm’s canal). The expression patterns of genes in the rat ICA were compared to those in human eye tissues. Several novel genes were found in the library, and they were characterized in more detail. Some of these genes showed eye-preferred expression patterns.


   Materials and Methods
Top
 Abstract
 Materials and Methods
Results
 Discussion
 References
 
RNA Preparation and cDNA Libraries Construction
All experiments complied with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research. Wistar rats (Charles River Laboratory, Wilmington, MA) weighing 250 to 300 g were used for cDNA library construction and in all other experiments. Tissues of the ICA were dissected from 46 rat eyes under a dissection microscope. Total RNA was isolated from the indicated tissues (RNazol; TelTest, Friendswood, TX). 0.5 µg of total RNA was separated by electrophoresis on a 1.2% agarose-2.2 M formaldehyde gel to evaluate the quality of RNA samples. Total RNA (120 µg) were used for construction of the libraries. Poly(A)+RNA was prepared using an oligo(dT) cellulose affinity column. The cDNA was synthesized and directionally cloned in the pSPORT1 vector (Invitrogen, Carlsbad, CA) at Bioserve Biotechnology (Laurel MD). General details of the library construction for NEIBank cDNA libraries are described elsewhere.2 3 15 In this case, as an additional measure to remove small contaminant fragments, the cDNA was run over a resin column (Sephacryl S-500 HR; Invitrogen-Gibco, Grand Island, NY) designed to fractionate cDNA more than 500 bp. The columns were run in TEN buffer (10 mM Tris-HCl [pH 7.5], 0.1 mM EDTA, 25 mM NaCl). Sublibraries (designated gw and gx) were made from the first two 35-µL fractions, containing cDNA.

cDNA Sequencing and Bioinformatics
Methods for sequencing and bioinformatics analysis are described in detail elsewhere.16 Briefly, randomly picked clones were sequenced at the NIH Intramural Sequencing Center (NISC). Clones were sequenced from the 5' end. A specially developed software tool, GRIST (GRouping and Identification of Sequence Tags) was used to analyze the data and assemble the results in Web page format.17 Clusters of sequences were also examined (SeqMan II; DNAstar, Madison, WI) to examine alternative transcripts. Sequences were searched through genome resources at http://www.ncbi.nlm.nih.gov/; National Center for Biotechnology [NCBI], Bethesda, MD; and http://genome.ucsc.edu/; University of Santa Cruz, CA). cDNA inserts of selected clones were sequenced with fluorescent dideoxynucleotides on an automated sequencer (Model 310; Applied Biosystems, Foster City, CA). The analysis of domain architecture in the deduced protein sequences was performed using the Simple Modular Architecture Research Tool (SMART)18 19 (http://smart.embl.de/; provided in the public domain by the European Molecular Biology Laboratory, Heidelberg, Germany) and the Conserved Domain Architecture Retrieval Tool (CDART)20 (http://www.ncbi.nlm.nih.gov/; NCBI).

Northern Blot and In Situ Hybridization
For Northern blot experiments, 2 µg of total RNA were separated on agarose gel as above, transferred to a membrane (Nitran; Schleicher & Schuell, Keene, NH) and hybridized with [32P]-labeled cDNA probes for specific clones in hybridization solution (ExpressHyb; BD Biosciences-Clontech, Palo Alto, CA) at 68°C overnight. Membranes were washed in 2x SSC-0.1% SDS, and then in 1x SSC-0.1% SDS, and finally in 0.1x SSC-0.1% SDS solution at 65°. Filters were exposed for different amounts of time. Filters were stained with 0.02% methylene blue after autoradiography for normalization of the amount of loaded RNA.21 In some cases, 1 µg ethidium bromide was added to RNA samples before separation, and RNA was visualized after electrophoresis under UV light.

For in situ hybridization, rat eyes were fixed in 4% paraformaldehyde in 0.1 M phosphate buffered saline (PBS; pH 7.4) overnight and processed for paraffin embedding. Serial sections (6 µm) were hybridized with specific [33P]-labeled riboprobes. To prepare riboprobes, PCR fragments of the rat CL1AA (accession number AF081144, position 4253-5250), Cirl2 (accession number NM-134408, position 4367-5366), and Cirl3 (accession number NM-130822, position 4568-5279) cDNAs were cloned into a vector (pBluescriptII; Stratagene, La Jolla, CA). Plasmids were linearized by digestion with NotI, and antisense probes were transcribed from the T7 promoter. In situ hybridization, washes, and autoradiography were performed as previously described.22

Semiquantitative RT-PCR
Total RNA (1 µg) was used for cDNA synthesis using reverse transcriptase (SuperScript II; Invitrogen, Carlsbad, CA) and oligo(dT)-primer. The amount of synthesized cDNA was evaluated by PCR using primers specific for cyclophilin and ribosomal protein Rpl19 depending on the source of RNA. PCR reactions were performed (PTC-200 Thermal Cycler; MJ Research, Watertown, MA) using polymerase (AmpliTaq; Applied Biosystems). Each PCR reaction was repeated at least twice. The thermal cycling parameters were as follows: 1 minute 30 seconds at 94° followed by 30 cycles of 30 seconds at 94°, 1 minute 30 seconds at 59°, 1 minute at 72° and final incubation for 5 minutes at 72°. PCR reaction products were analyzed by agarose gel-electrophoresis. After adjustment of cDNA concentration, relative abundances of mRNA for different genes were estimated. Primers for each gene were designed to cross introns when possible. Dilutions of cDNA samples were adjusted for each gene to give a linear range in PCR reactions.


   Results
Top
 Abstract
 Materials and Methods
 Results
Discussion
 References
 
Library Statistics
Rat ICA cDNAs were collected and cloned as two sublibraries designated gx and gw. For the gx and gw libraries, there were 1.3 x 106 and 1.8 x 106 primary cDNA recombinant clones with an average insert size of 1.73 and 1.38 kb, respectively. For each sublibrary, approximately 2500 clones were picked, and sequenced and data were combined for subsequent analysis. Both sublibraries contained 3% to 4% mitochondrial genome clones and approximately 9% rRNA inserts. After removal of non-mRNA clones and repetitive sequences and vector trimming there were 3420 high-quality sequence reads of average length 530 bp. Analysis of these clones through GRIST17 resulted in 2195 clusters of sequences potentially representing individual genes expressed in the rat eye angle. Four hundred forty-eight clusters contained at least two clones, and 178 clusters contained at least 3 clones, representing mRNAs that may be highly or moderately abundant in the rat eye angle. Approximately 38% of the clones in the rat angle collection have no corresponding entry in GenBank (http://www.ncbi.nlm.nih.gov/Genbank; provided in the public domain by NCBI) at present and about half of these have no rat UniGene (http://www.ncbi.nlm.nih.gov/UniGene; provided in the public domain by NCBI) entry. Most of these clones have some sort of identified homologues in mouse or human, but even in these species, most cataloged genes have unknown biological functions. Information about all sequenced clones is available at http://neibank.nei.nih.gov/ (provided in the public domain by the National Eye Institute, Bethesda, MD). All clones were numbered according to their library designation and their position in 96-well plates (e.g., gx01d10).

Gene Expression Profile of Rat Eye Angle Tissues
Table 1 provides a list of the 63 the most abundant clones in the rat eye ICA library, those represented by 5 or more clones. The removal of tissues from the rat eye angle is a delicate procedure. Rigorous measures were followed to minimize contamination of the dissected tissues by surrounding tissues. To evaluate possible contamination of the eye ICA dissected tissues by corneal cells, the expression profile of the rat eye ICA library was compared to that of corneal epithelial cells produced by SAGE analysis.23 Transketolase and ALDH3 mRNAs were the most abundant message in the mouse corneal SAGE library. Although there were five ALDH3-encoding clones in the rat ICA library, there was only one transketolase-encoding clone among the sequenced clones in this library. This indicated that the tissues of the rat ICA were not heavily contaminated by corneal tissue in the course of dissection.


View this table:
[in this window]
[in a new window]
  		TABLE 1. The Most Abundant cDNA Clones in the Rat ICA cDNA Library

 
ß-Actin cDNAs were the most abundant in the rat eye ICA library (95 clones) with {gamma}-actin (4 clones) and {alpha}-actin (2 clones) being much less abundant. Although actins are ones of the most abundant proteins in many cell types, actin cDNA clones were not so abundant in the human TM4 or iris cDNA libraries.2 Moreover, the relative distribution of actin isoforms was also different in these libraries. There were 11 {alpha}-actin and 2 ß-actin cDNAs among 3459 sequenced clones in the human TM library, whereas there were 9 ß-actin, 5 {gamma}-actin and 2 {alpha}-actin cDNAs among approximately 2000 sequenced clones in the iris library.2 4

Overall, the expression profile of the combined rat ICA tissues was strikingly different from human TM and more similar to that of the human iris. For example, 8 of the 10 most abundant clones in the human iris library were also represented in the rat eye ICA collection (opticin or oculoglycan and plasma protease [C1] inhibitor were two genes that were abundant in human iris but not observed in rat), whereas only 5 of the 10 most abundant clones in the human TM library were seen in rat. In particular, cDNAs for myocilin and matrix Gla proteins, which were very highly expressed in the human TM library, were missing from the rat ICA collection. Mutations in myocilin are associated with glaucoma in humans24 although the functional role of myocilin in TM is not well understood. Myocilin is an olfactomedin domain-containing protein, and most of the glaucoma-causing mutations in this gene affect this domain.25 Three other olfactomedin domain-containing proteins were represented by sequenced clones in the rat ICA collection. One of these cDNA clones encoded a novel protein named optimedin, which has been characterized in detail.26 The second transcript observed (one cDNA clone) encoded a divergent olfactomedin-containing protein similar to human HNOEL-iso protein (accession number NM-020190). The third member of this family detected (two cDNA clones) was latrotoxin receptor 1 (CL1AA; accession number AF081144) which contains the olfactomedin domain in the extracellular N-terminal portion of the protein.27

Table 2 lists the transcription factors and proteins interacting with the transcriptional machinery identified among the sequenced clones. Several transcription factors essential for normal eye development and function, including Pax-6, Six3, c-maf, Maf1, Sox-4, Foxc1, Rx, and Ldb2,28 were present among sequenced clones. The list of the most abundant transcription factors identified in the rat eye ICA library was different from the list of such factors in the human TM and iris libraries. For example, v-fos, Pitx-2, cold shock domain A protein, and TSC-22 were abundant in the human TM library.4 Of these, only TSC-22 was abundant in the rat eye ICA library but this transcription factor is abundant in many cDNA libraries.


View this table:
[in this window]
[in a new window]
  		TABLE 2. Transcription Factors and Cofactors in the Rat Eye Angle Library

 
Expression Pattern of Selected Clones from the Eye Angle Library
Eight cDNA clones encoding novel or poorly characterized proteins were selected from the eye angle library and their expression patterns were analyzed by Northern blot hybridization. Figure 1 illustrates the results of these experiments for six cDNAs. Four cDNAs showed preferential expression in different eye structures. In particular, cDNAs gx01a07 and gx01a06 were highly expressed in the tissues of the ICA (Figs. 1A 1B) , whereas cDNA gw01d02 was highly expressed in the lens (Fig. 1C) . cDNA gx01d10 was highly expressed in the cornea and ICA (data not shown; Torrado M, Senatorov VV, Trivedi R, Fariss RN, and Tomarev SI, manuscript in preparation). cDNAs gw06g04 and gx01b08 were preferentially expressed in the retina and brain (Figs. 1E 1F) . cDNA gw01f11 was preferentially expressed in sclera and brain (data not shown), whereas cDNA gw01d04 was preferentially expressed in the tissues of the ICA, sclera, retina, brain, kidney, and lung (Fig. 1D) .



View larger version (68K):
[in this window]
[in a new window]
  		FIGURE 1. Northern blot analysis of selected genes expressed in rat tissues. The cDNA probes, used for these blots, are as follows: (A) gx01a07 (encoding a novel transmembrane protein); (B) gx01a06 (a novel protein); (C) gw01d02 (related to mammary tumor receptor 2 isoform); (D) gw01d04 (nonspecific dipeptidase); (E) gw06g04 (calsynthenin-1); (F) gx01b08 (stromal membrane-associated protein). Total RNA (2 µg) were loaded per lane. Loaded RNA was visualized by staining with ethidium bromide (not shown).

 
Clone gw11g07 encoded optimedin and was expressed in the ICA tissues, retina, and brain, as described previously.26 Because olfactomedin domain-containing proteins may play important roles in normal eye development and disease,24 26 29 30 expression of the CL1AA gene,27 31 another member of the family that was present twice among the sequenced clones, was investigated by in situ hybridization. Two other genes, Cirl2 and Cirl3, which belong to the same family of latrotoxin receptors as the CL1AA gene,32 33 were also included in this study, although Cirl2 and Cirl3 were not present among the sequenced clones. The results demonstrated (Fig. 2) that CL1AA and Cirl3 have very similar patterns of expression in the adult rat eye. They were expressed in the iris and ciliary body as well as in the ganglion and inner nuclear cell layers of the retina. The Cilr2 gene was expressed only in the inner nuclear layer of the retina, but not in the tissues of the eye angle.



View larger version (102K):
[in this window]
[in a new window]
  		FIGURE 2. Radioactive in situ hybridization of CL1AA (A, G), Cirl2 (C, I), and Cirl3 (E, K) antisense probes with rat eye sections. (A–F) correspond to the ICA area, whereas (G–L) show retina. The first and third rows show dark-field images. The second and fourth rows show the same regions in bright field after hematoxylin staining. c, cornea; cb, ciliary body; i, iris; inl, inner nuclear layer; onl, outer nucler layer; gcl, retinal ganglion cell layer; tm, trabecular meshwork.

 
Clone gx21f10 is a rat orthologue of the human HNOEL-iso gene (accession number NM-020190). This gene encoded a divergent olfactomedin-containing protein. Its expression was studied by semiquantitative RT-PCR (Fig. 3) . The results demonstrated that this gene was more actively expressed in the iris and sclera than in the TM, retina, and optic nerve. Its expression was not detected in the lens, cornea, and brain in the conditions used in these experiments.



View larger version (58K):
[in this window]
[in a new window]
  		FIGURE 3. Semiquantitative RT-PCR analysis of the rat orthologue of the human HNOEL-iso gene expression in different rat eye tissues and brain. Primers 5'-CCGGAGAAATGAGAAATACGAT-3' and 5'-CAGCCATGGTGAGGGTGAAG-3' are located in different exons of the rat Noel-iso gene. Primers 5'-TCCTCCTTTCACAGAATTATTCC-3' and 5'-AATTAGAGTTGTCCACAGTCGG-3' were used to amplify cyclophilin cDNA for normalization of the amount of synthesized cDNA. Normalization with Rpl19 cDNA gave very similar results (data not shown).

 
On the basis of all these results, we concluded that the rat ICA library is a rich source of clones with interesting eye-preferred expression patterns.

Sequencing of the Selected Clones
Some of these potentially eye-preferred clones were selected for full-length sequencing. Clone gx01a07 (accession number AY569010) contained an insert of 2882 bp, not counting the poly(A) tail, and encoded a novel conserved protein with a length of 541 amino acids (Fig. 4) . Analysis of the encoded sequence using the SMART package18 19 suggested that it may represent a transmembrane protein with seven transmembrane helices (Fig. 4) . Recently a related cDNA clone has been identified in a rat prostate cDNA library (accession number BC062391). This clone and clone gx01a07 were different in the 3'-untranslated region (UTR) as a result of alternative splicing. However, these two clones encoded the same protein. The rat gene contains at least 12 exons. The rat protein has 98%, 96%, and 78% identity to mouse (AK044810), human (AK074984), and zebrafish (BC053246) proteins, respectively. It shows 45% identity to a Drosophila protein with unknown functions (NM_168450). The human orthologue maps to 1p31.2. In the human eye, this gene is expressed in the RPE-choroid, iris, and lens, as demonstrated by comparison of the rat sequence with the NEIBank.2 15 34 Recently, the human gene has been shown to be involved in the activation of the NF-{kappa}B signaling pathway.35



View larger version (18K):
[in this window]
[in a new window]
  		FIGURE 4. Encoded protein sequence (A) and exon–intron structure of the gene (B) corresponding to gx01a07 cDNA (accession number AY569010). (A) Yellow: potential signal peptide sequence; blue: transmembrane domains; black triangles: boundaries between different exons. (B) Diagram of gx01a07 gene structure drawn approximately to scale. The length of the last intron is not known.

 
Clone gx01a06 (accession number AY569011) contained an insert with a length of 1790 bp and encoded a novel conserved protein with a length of 553 amino acids. Analysis of the protein sequence using the CDART package20 revealed that it contains an IMP-GMP–specific 5-nucleosidase domain (positions 50-551 in the rat protein sequence). The existence of this gene has been predicted recently on the basis of the computational analysis of the rat genome (accession number XM_214258). The encoded rat protein has 98%, 96%, and 74% identity to mouse (BC011230), human (AK022504), and Xenopus (BC046742) proteins, respectively. The rat gene consists of at least 14 exons, and its mRNA is alternatively spliced. The human orthologue maps to 3p21.31. In the human eye, this gene is expressed in the RPE/choroid and lens as judged by NEIBank EST analyses.15 34

cDNA gw01d02 (accession number AY569012) had a length of 1347 bp without the poly(A) tail and encoded a protein with a length of 176 amino acids. This gene consists of only two exons. The encoded protein is related to mammary tumor receptor 2 isoform.36

cDNA gw06g04 (accession number AY569014) had a length of 4391 bp and encoded a conserved protein with a length of 952 amino acids. This protein is a rat homologue of a recently identified postsynaptic membrane protein, calsynthenin-1.37 Calsyntenin-1 contains a cadherin repeat domain (positions 41-248 in the protein sequence) and a SCOP domain (positions 351-532 in the protein sequence), which is present in galectins, laminin G-like module, and calnexin. The cadherin repeat domain may mediate cell–cell contacts when bound to calcium. The rat calsyntenin-1 gene contains at least 17 exons, and its mRNA was alternatively spliced. In the human eye, calsyntenin-1 is expressed in the human lens, retina, and RPE-choroid.3 15 34 In the mouse brain, the calsyntenin-1 gene is expressed in most neurons of central nervous system (CNS) with relatively little variation in its expression level.38

cDNA gw01d04 (accession number AY569013) had a length of 2088 bp without the poly(A) tail and encoded a protein with a length of 475 amino acids. This protein was 99% identical with a recently described nonspecific mouse dipeptidase.39 Examination of sequences in GenBank showed that this gene has at least 12 exons and is alternatively spliced at the 5'-end as well as at internal positions. The human homologue maps to 18q22.3.

cDNA gx01b08 was 96% and 98% identical with recently described human and mouse cDNAs, encoding stromal membrane-associated proteins.40 Although the gx01b08 cDNA insert was longer at the 5'-end than the corresponding human and mouse sequences, it was not complete at the 3'-end. The encoded protein contains a putative ArfGap domain, which is found in activators of small guanosine triphosphatases (GTPases) and may therefore be involved in the signal transduction.41 42 43


   Discussion
Top
 Abstract
 Materials and Methods
 Results
 Discussion
References
 
In the present study, we constructed cDNA libraries from the tissues of the rat ICA. We had two main goals in mind. The first was to characterize gene expression patterns in the tissues involved in aqueous humor production and outflow. We were also looking for novel genes that might be essential for normal function of eye tissues and might be involved in eye diseases such as glaucoma.

The tissues of the ICA have various embryological origins and contain multiple cell types. The iris consists of the stroma and two layers of pigmented epithelium. Pigmented epithelium cells share a developmental origin with retinal pigmented epithelium cells, which are derived from the external walls of the optic vesicle and therefore have a neuroepithelial origin. Iris sphincter and dilator muscle also have neuroepithelial origin. The iris stroma is derived from cranial paraxial mesoderm and neural crest and contains small blood vessels, two types of pigmented cells, and myelinated and unmyelinated nerves, dendriform macrophages, and major histocompatibility complex (MHC) class II dendritic cells. The ciliary body consists of the epithelium, vascular stroma, and muscle. The layer of the ciliary body facing the vitreous is nonpigmented and is continuous with retina, whereas the external epithelium layer is pigmented and continuous with retinal pigmented epithelium and the iris pigmented epithelium. TM is derived from neural crest and consists of trabecular beams covered with endothelial cells.44

ß-Actin cDNAs were the most abundant in the rat ICA library. Although actins are among the most abundant proteins in many cell types, the level of expression seems to be higher in rat angle than in human TM or iris cDNA libraries.2 4 Moreover, the relative distribution of actin isoforms was also different in these libraries. Although there is no necessary correlation between transcript and protein levels, these data may indicate high activity in synthesis or maintenance of the actin cytoskeleton in the tissues of the rat ICA. This idea is supported by the presence of cDNA clones for several actin-binding proteins involved in the regulation of actin microfilament (cofilin, actinins, coronin, Arp2/3, and profilin).45 Among actin isoforms, ß-actin is expressed in all cell types, {gamma}-actin is preferentially expressed in the neural tissues, whereas {alpha}-actin is considered to be cardiac or vessel specific.46 {gamma}-Actin cDNAs were more abundant in the rat ICA and human iris libraries than {alpha}-actin cDNAs,2 whereas {alpha}-actin cDNAs were the most abundant in the human TM library and no {gamma}-actin cDNAs were detected among sequenced clones in this library.4

The third most abundant group of clones in the rat ICA libraries corresponded to insulin-like growth factor protein 7 (IGFBP7), also known as mac25 and angiomodulin. IGFBP7 clones were also abundant in the human TM, iris, and RPE-choroid libraries.2 4 15 IGFBP7 is also expressed in a many normal human tissues including heart, spleen, ovary, small intestine, and colon.47 It is a multifunctional secreted protein that exhibits growth-stimulatory activity in synergy with insulin or insulin-like growth factors and may interact with glycosaminoglycans and extracellular matrix proteins as well as immobilize chemokines.48 The high levels of IGFBP7 gene expression in the rat ICA and several human eye tissues indicate that the encoded protein may be essential for their function.

Myocilin cDNAs formed the third most abundant group of clones in the human TM cDNA library.4 Furthermore, 3 myocilin clones were also present among approximately 2000 sequenced clones in the human iris cDNA library.2 Although myocilin mRNA is expressed in the rat TM,26 we did not identify rat myocilin clones among sequenced clones in the rat ICA libraries. There are two possible explanations for the absence of myocilin clones. One is that TM tissue represents a relatively small fraction of the tissues used for library construction. The second explanation is that there are species-specific differences in gene expression patterns in the tissues of ICA and myocilin expression may be lower in rat than in human eye. Indeed, it is not only myocilin that is "missing" from rat ICA. Opticin/oculoglycan and plasma protease (C1) inhibitor clones, which are among the most abundant in the human iris cDNA library, are also absent from the rat collection.

Although myocilin is missing, several other olfactomedin-domain proteins clones were represented among the sequenced clones in the eye angle library. One of them was optimedin which is expressed in the iris and ciliary body epithelial cells as judged by in situ hybridization.26 Another olfactomedin-related gene (accession number XM-227535) was preferentially expressed in the iris and sclera among eye tissues tested (Fig. 3) . This gene has been identified recently in a large-scale project designed to identify novel human secreted and transmembrane proteins.49 The calcium-independent latrophilin receptor genes (CL1AA, Cirl2, and Cirl3) encode membrane proteins containing the olfactomedin-related domain in the extracellular N-terminal part.27 31 32 33 50 cDNAs encoding CL1AA were present twice among sequenced clones. In situ hybridization experiments demonstrated that the CL1AA and Cirl3 are expressed in the same rat eye tissues as the previously described optimedin. These genes were expressed in the epithelial cells of the iris and ciliary body as well as in the retinal ganglion and inner nuclear cell layers. Cirl2 was expressed only in the inner nuclear layer. CL1AA is a G-protein–coupled receptor that is able to bind {alpha}-latrotoxin. Natural ligands for this family of latrotoxin receptors have not been identified yet. It has been reported that CL1AA and Cirl3 are brain specific, whereas Cirl2 is ubiquitously expressed.32 50 Our data demonstrate that these genes are expressed in the adult rat eyes where they may play an important role in G-protein–mediated signaling and in the formation of contacts between cells.

Another important signaling mechanism in the eye is the Wnt-frizzled pathway that plays an important role in establishing cell polarity, cell proliferation, and specification of cell fate.51 Wnt members can be divided into two functionally different classes: wnt1 and wnt5a. Wnt proteins belonging to the wnt1 class preferentially signal through ß-catenin, which is considered to be the canonical pathway. Proteins of the Wnt5a class can stimulate intracellular Ca2+ release through interactions with the frizzled-2 receptor. Two cDNA clones corresponding to Wnt5a and two cDNA clones corresponding to frizzled-2 receptor are present in the rat ICA collection, whereas cDNAs encoding wnt4 and wnt10a are present once each. It is interesting to note that wnt4 is critical for kidney development52 and may stimulate expression of C-type natriuretic peptide through the canonical signaling pathway.53 cDNA for atrial natriuretic peptide has been previously identified in the human ciliary body cDNA library54 and it has been suggested that natriuretic peptides may play a role in IOP regulation in human eyes.55 Three cDNA clones encoding secreted frizzled-related protein 1 were also present among sequenced clones. Secreted frizzled-related proteins are modulators of the Wnt-frizzled pathways.56

Overall the EST analysis suggests several new avenues for further investigation. Sequencing of several cDNA inserts from the rat ICA library demonstrated that this library is a good source of novel or not well-characterized genes. Most of these cDNAs represented full coding sequences. Analysis of the promoter sequences of genes preferentially expressed in the tissues of the eye ICA may lead to the development of angle-specific or angle-preferred promoters.


   Acknowledgements
 
The authors thank Jeff Touchman and Gerry Bouffard of NIH Intramural Sequencing Center and Don Smith, Patee Buchoff, and James Gao of the National Eye Institute for support in sequencing and organizing data; Irina Karavanova (National Institute of Child Health and Human Development) for help with in situ hybridization; and Patrick Chang for performing some of the RT-PCR experiments.


   Footnotes
 
2 Present affiliations: the Department of Neuroscience, Georgetown University Medical Center, Washington, DC; the Back

3 Institute of Health Sciences, University of La Coruna, Campus de Oza, Edificio El Fortin, La Coruna, Spain; and Back

4 N. K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia. Back

Supported by the National Eye Institute Intramural Program and by Russian Federation Basic Research Grant 02-04-48435 (RDZ).

Submitted for publication March 16, 2004; revised April 13, 2004; accepted April 14, 2004.

Disclosure: F. Ahmed, None; M. Torrado, None; R.D. Zinovieva, None; V.V. Senatorov, None; G. Wistow, None; S.I. Tomarev, None

The publication costs of this article were defrayed in part by page charge payment. This article must therefore be marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

Corresponding author: Stanislav I. Tomarev, Section of Molecular Mechanisms of Glaucoma, Laboratory of Molecular and Developmental Biology, National Eye Institute, NIH, DHHS, Building 7, Room 103, Bethesda, MD 20814-9692; tomarevs{at}nei.nih.gov.


   References
Top
 Abstract
 Materials and Methods
 Results
 Discussion
 References
 

  1. Gonzalez P, Epstein DL, Borras T. Characterization of gene expression in human trabecular meshwork using single-pass sequencing of 1060 clones. Invest Ophthalmol Vis Sci. 2000;41:3678–3693.[Abstract/Free Full Text]
  2. Wistow G, Berstein SL, Ray S, et al. Expressed sequence tag analysis of adult human iris for the NEIBank Project: steroid-response factors and similarities with retinal pigment epithelium. Mol Vis. 2002;8:185–195.[ISI][Medline][Order article via Infotrieve]
  3. Wistow G, Berstein SL, Wyatt MK, et al. Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Mol Vis. 2002;8:196–204.[ISI][Medline][Order article via Infotrieve]
  4. Tomarev SI, Wistow G, Raymond V, Dubois S, Malyukova I. Gene expression profile of the human trabecular meshwork: NEIBank sequence tag analysis. Invest Ophthalmol Vis Sci. 2003;44:2588–2596.[Abstract/Free Full Text]
  5. Buraczynska M, Mears AJ, Zareparsi S, et al. Gene expression profile of native human retinal pigment epithelium. Invest Ophthalmol Vis Sci. 2002;43:603–607.[Abstract/Free Full Text]
  6. 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.[Abstract/Free Full Text]
  7. Sharon D, Blackshaw S, Cepko CL, et al. 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.[Abstract/Free Full Text]
  8. Morrison JC, Moore CG, Deppmeier LM, Gold BG, Meshul CK, Johnson EC. A rat model of chronic pressure-induced optic nerve damage. Exp Eye Res. 1997;64:85–96.[CrossRef][ISI][Medline][Order article via Infotrieve]
  9. Shareef SR, Garcia-Valenzuela E, Salierno A, Walsh J, Sharma SC. Chronic ocular hypertension following episcleral venous occlusion in rats. Exp Eye Res. 1995;61:379–382.[CrossRef][ISI][Medline][Order article via Infotrieve]
  10. Ueda J, Sawaguchi S, Hanyu T, et al. Experimental glaucoma model in the rat induced by laser trabecular photocoagulation after an intracameral injection of India ink. Jpn J Ophthalmol. 1998;42:337–344.[CrossRef][Medline][Order article via Infotrieve]
  11. Levkovitch-Verbin H, Quigley HA, Martin KR, Valenta D, Baumrind LA, Pease ME. Translimbal laser photocoagulation to the trabecular meshwork as a model of glaucoma in rats. Invest Ophthalmol Vis Sci. 2002;43:402–410.[Abstract/Free Full Text]
  12. Garcia-Valenzuela E, Shareef S, Walsh J, Sharma SC. Programmed cell death of retinal ganglion cells during experimental glaucoma. Exp Eye Res. 1995;61:33–44.[CrossRef][ISI][Medline][Order article via Infotrieve]
  13. Johnson EC, Morrison JC, Farrell S, Deppmeier L, Moore CG, McGinty MR. The effect of chronically elevated intraocular pressure on the rat optic nerve head extracellular matrix. Exp Eye Res. 1996;62:663–674.[CrossRef][ISI][Medline][Order article via Infotrieve]
  14. Johnson EC, Deppmeier LMH, Wentzien SKF, Hsu I, Morrison JC. Chronology of optic nerve head and retinal responses to elevated intraocular pressure. Invest Ophthalmol Vis Sci. 2000;41:431–442.[Abstract/Free Full Text]
  15. Wistow G, Bernstein SL, Wyatt MK, et al. Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants. Mol Vis. 2002;8:205–220.[ISI][Medline][Order article via Infotrieve]
  16. Wistow G. A project for ocular bioinformatics: NEIBank. Mol Vis. 2002;8:161–163.[ISI][Medline][Order article via Infotrieve]
  17. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998;8:186–194.[Abstract/Free Full Text]
  18. Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA. 1998;95:5857–5864.[Abstract/Free Full Text]
  19. Letunic I, Goodstadt L, Dickens NJ, et al. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 2002;30:242–244.[Abstract/Free Full Text]
  20. Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. Genome Res. 2002;12:1619–1623.[Abstract/Free Full Text]
  21. Herrin DL, Schmidt GW. Rapid, reversible staining of northern blots prior to hybridization. Biotechniques. 1988;6:196–197.199–200[ISI][Medline][Order article via Infotrieve]
  22. Ozaki M, Sasner M, Yano R, Lu HS, Buonanno A. Neuregulin-beta induces expression of an NMDA-receptor subunit. Nature. 1997;390:691–694.[Medline][Order article via Infotrieve]
  23. Norman B, Davis J, Piatigorsky J. Postnatal gene expression in the normal mouse cornea by SAGE. Invest Ophthalmol Vis Sci. 2004;45:429–440.[Abstract/Free Full Text]
  24. Stone EM, Fingert JH, Alward WM, et al. Identification of a gene that causes primary open angle glaucoma. Science. 1997;275:668–670.[Abstract/Free Full Text]
  25. Fingert JH, Heon E, Liebmann JM, et al. Analysis of myocilin mutations in 1703 glaucoma patients from five different populations. Hum Mol Genet. 1999;8:899–905.[Abstract/Free Full Text]
  26. Torrado M, Trivedi R, Zinovieva R, Karavanova I, Tomarev SI. Optimedin: a novel olfactomedin-related protein that interacts with myocilin. Hum Mol Genet. 2002;11:1291–1301.[Abstract/Free Full Text]
  27. Lelianova VG, Davletov BA, Sterling A, et al. Alpha-latrotoxin receptor, latrophilin, is a novel member of the secretin family of G protein-coupled receptors. J Biol Chem. 1997;272:21504–21508.[Abstract/Free Full Text]
  28. Graw J. The genetic and molecular basis of congenital eye defects. Nat Rev Genet. 2003;4:876–888.[CrossRef][ISI][Medline][Order article via Infotrieve]
  29. Barembaum M, Moreno TA, LaBonne C, Sechrist J, Bronner-Fraser M. Noelin-1 is a secreted glycoprotein involved in generation of the neural crest. Nature Cell Biology. 2000;2:219–225.[CrossRef][ISI][Medline][Order article via Infotrieve]
  30. Tsuda H, Sasai N, Matsuo-Takasaki M, Sakuragi M, Murakami Y, Sasai Y. Dorsalization of the neural tube by Xenopus tiarin, a novel patterning factor secreted by the flanking nonneural head ectoderm. Neuron. 2002;33:515–528.[CrossRef][ISI][Medline][Order article via Infotrieve]
  31. Davletov BA, Shamotienko OG, Lelianova VG, Grishin EV, Ushkaryov YA. Isolation and biochemical characterization of a Ca2+-independent alpha-latrotoxin-binding protein. J Biol Chem. 1996;271:23239–23245.[Abstract/Free Full Text]
  32. Matsushita H, Lelianova VG, Ushkaryov YA. The latrophilin family: multiply spliced G protein-coupled receptors with differential tissue distribution. FEBS Lett. 1999;443:348–352.[CrossRef][ISI][Medline][Order article via Infotrieve]
  33. Sudhof TC. alpha-Latrotoxin and its receptors: neurexins and CIRL/latrophilins. Annu Rev Neurosci. 2001;24:933–962.[CrossRef][ISI][Medline][Order article via Infotrieve]
  34. Wistow G, Berstein SL, Wyatt MK, et al. Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants. Mol Vis. 2002;8:171–184.[ISI][Medline][Order article via Infotrieve]
  35. Matsuda A, Suzuki Y, Honda G, et al. Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK signaling pathways. Oncogene. 2003;22:3307–3318.[CrossRef][ISI][Medline][Order article via Infotrieve]
  36. Golovkina TV, Dzuris J, van den HB , et al. A novel membrane protein is a mouse mammary tumor virus receptor. J Virol. 1998;72:3066–3071.[Abstract/Free Full Text]
  37. Vogt L, Schrimpf SP, Meskenaite V, et al. Calsyntenin-1, a proteolytically processed postsynaptic membrane protein with a cytoplasmic calcium-binding domain. Mol Cell Neurosci. 2001;17:151–166.[CrossRef][ISI][Medline][Order article via Infotrieve]
  38. Hintsch G, Zurlinden A, Meskenaite V, et al. The calsyntenins: a family of postsynaptic membrane proteins with distinct neuronal expression patterns. Mol Cell Neurosci. 2002;21:393–409.[CrossRef][ISI][Medline][Order article via Infotrieve]
  39. Teufel M, Saudek V, Ledig JP, et al. Sequence identification and characterization of human carnosinase and a closely related non-specific dipeptidase. J Biol Chem. 2003;278:6521–6531.[Abstract/Free Full Text]
  40. Strausberg RL, Feingold EA, Grouse LH, et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci USA. 2002;99:16899–16903.[Abstract/Free Full Text]
  41. Cukierman E, Huber I, Rotman M, Cassel D. The ARF1 GTPase-activating protein: zinc finger motif and Golgi complex localization. Science. 1995;270:1999–2002.[Abstract/Free Full Text]
  42. Poon PP, Wang X, Rotman M, et al. Saccharomyces cerevisiae Gcs1 is an ADP-ribosylation factor GTPase-activating protein. Proc Natl Acad Sci USA. 1996;93:10074–10077.[Abstract/Free Full Text]
  43. Brown MT, Andrade J, Radhakrishna H, Donaldson JG, Cooper JA, Randazzo PA. ASAP1, a phospholipid-dependent arf GTPase-activating protein that associates with and is phosphorylated by Src. Mol Cell Biol. 1998;18:7038–7051.[Abstract/Free Full Text]
  44. Tripathi BJ, Tripathi RC. Neural crest origin of human trabecular meshwork and its implications for the pathogenesis of glaucoma (see comments). Am J Ophthalmol. 1989;107:583–590.[ISI][Medline][Order article via Infotrieve]
  45. Dos Remedios CG, Chhabra D, Kekic M, et al. Actin binding proteins: regulation of cytoskeletal microfilaments. Physiol Rev. 2003;83:433–473.[Abstract/Free Full Text]
  46. Kaech S, Fischer M, Doll T, Matus A. Isoform specificity in the relationship of actin to dendritic spines. J Neurosci. 1997;17:9565–9572.[Abstract/Free Full Text]
  47. Oh Y, Nagalla SR, Yamanaka Y, Kim HS, Wilson E, Rosenfeld RG. Synthesis and characterization of insulin-like growth factor-binding protein (IGFBP)-7: recombinant human mac25 protein specifically binds IGF-I and -II. J Biol Chem. 1996;271:30322–30325.[Abstract/Free Full Text]
  48. Nagakubo D, Murai T, Tanaka T, et al. A high endothelial venule secretory protein, mac25/angiomodulin, interacts with multiple high endothelial venule-associated molecules including chemokines. J Immunol. 2003;171:553–561.[Abstract/Free Full Text]
  49. Clark HF, Gurney AL, Abaya E, et al. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Genome Res. 2003;13:2265–2270.[Abstract/Free Full Text]
  50. Ichtchenko K, Bittner MA, Krasnoperov V, et al. A novel ubiquitously expressed alpha-latrotoxin receptor is a member of the CIRL family of G-protein-coupled receptors. J Biol Chem. 1999;274:5491–5498.[Abstract/Free Full Text]
  51. Yanfeng W, Saint-Jeannet JP, Klein PS. Wnt-frizzled signaling in the induction and differentiation of the neural crest. Bioessays. 2003;25:317–325.[CrossRef][ISI][Medline][Order article via Infotrieve]
  52. Stark K, Vainio S, Vassileva G, McMahon AP. Epithelial transformation of metanephric mesenchyme in the developing kidney regulated by Wnt-4. Nature. 1994;372:679–683.[CrossRef][Medline][Order article via Infotrieve]
  53. Surendran K, Simon TC. CNP gene expression is activated by Wnt signaling and correlates with Wnt4 expression during renal injury. Am J Physiol. 2003;284:F653–F662.
  54. Coca-Prados M, Escribano J, Ortego J. Differential gene expression in the human ciliary epithelium. Prog Retin Eye Res. 1999;18:403–429.[CrossRef][ISI][Medline][Order article via Infotrieve]
  55. Salzmann J, Flitcroft D, Bunce C, Gordon D, Wormald R, Migdal C. Brain natriuretic peptide: identification of a second natriuretic peptide in human aqueous humour. Br J Ophthalmol. 1998;82:830–834.[Abstract/Free Full Text]
  56. Jones SE, Jomary C. Secreted Frizzled-related proteins: searching for relationships and patterns. Bioessays. 2002;24:811–820.[CrossRef][ISI][Medline][Order article via Infotrieve]



This article has been cited by other articles:


Home page
 J. Neurosci.Home page
V. Senatorov, I. Malyukova, R. Fariss, E. F. Wawrousek, S. Swaminathan, S. K. Sharan, and S. Tomarev
Expression of Mutated Mouse Myocilin Induces Open-Angle Glaucoma in Transgenic Mice.
J. Neurosci., November 15, 2006; 26(46): 11903 - 11914.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
O. Grinchuk, Z. Kozmik, X. Wu, and S. Tomarev
The Optimedin Gene Is a Downstream Target of Pax6
J. Biol. Chem., October 21, 2005; 280(42): 35228 - 35237.
[Abstract] [Full Text] [PDF]

Home page
 IOVSHome page
M. Torrado, V. V. Senatorov, R. Trivedi, R. N. Fariss, and S. I. Tomarev
Pdlim2, a Novel PDZ-LIM Domain Protein, Interacts with {alpha}-Actinins and Filamin A
Invest. Ophthalmol. Vis. Sci., November 1, 2004; 45(11): 3955 - 3963.
[Abstract] [Full Text] [PDF]

This Article
Right arrow Abstract Freely available
Right arrow Full Text (PDF)
Right arrow Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when eLetters are posted
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via ISI Web of Science (11)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Ahmed, F.
Right arrow Articles by Tomarev, S. I.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ahmed, F.
Right arrow Articles by Tomarev, S. I.

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS