August 2004
Volume 45, Issue 8
Free
Biochemistry and Molecular Biology  |   August 2004
Gene Expression Profiling of Purified Rat Retinal Ganglion Cells
Author Affiliations
  • Ronald H. Farkas
    From the Department of Ophthalmology, Wilmer Eye Institute, the
    Guerrieri Center for Genetic Engineering and Molecular Ophthalmology, and the
  • Jiang Qian
    From the Department of Ophthalmology, Wilmer Eye Institute, the
    Guerrieri Center for Genetic Engineering and Molecular Ophthalmology, and the
  • Jeffrey L. Goldberg
    Department of Neurobiology, Stanford University, Stanford, California.
    Present affiliation: Bascom Palmer Eye Institute, McKnight Vision Research Center, Miami, Florida.
  • Harry A. Quigley
    From the Department of Ophthalmology, Wilmer Eye Institute, the
    Dana Center for Preventive Ophthalmology at the Wilmer Eye Institute, Baltimore, Maryland; the Departments of
  • Donald J. Zack
    From the Department of Ophthalmology, Wilmer Eye Institute, the
    Guerrieri Center for Genetic Engineering and Molecular Ophthalmology, and the
    Molecular Biology and Genetics,
    Neuroscience, and the
    McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; and the
Investigative Ophthalmology & Visual Science August 2004, Vol.45, 2503-2513. doi:10.1167/iovs.03-1391
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      Ronald H. Farkas, Jiang Qian, Jeffrey L. Goldberg, Harry A. Quigley, Donald J. Zack; Gene Expression Profiling of Purified Rat Retinal Ganglion Cells. Invest. Ophthalmol. Vis. Sci. 2004;45(8):2503-2513. doi: 10.1167/iovs.03-1391.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

purpose. The phenotype of specialized cells arises, in part, from their characteristic gene expression patterns. Retinal ganglion cells (RGCs) are of wide interest in neuroscience and die in glaucoma and other optic neuropathies. In this study the genes expressed by RGCs were profiled by expressed sequence tag (EST) analysis.

methods. ESTs were generated from a cDNA library constructed from RGCs isolated by immunopanning. The RGC genes were compared with published microarray expression profiles from 13 different neural regions. Immunohistochemistry was performed by standard methods.

results. Clustering of 4791 RGC ESTs identified 2360 unique gene clusters. Of these, 60% represented known genes, 27% uncharacterized genes/ESTs, and 13% novel sequence. Unexpectedly, one of the largest RGC clusters, RESP18, corresponded to a neuroendocrine-specific gene preferentially expressed in the hypothalamus. RESP18 immunoreactivity within the retina was found mainly in the RGC layer. DDAH1, a gene involved in nitric oxide metabolism, was localized to RGC and amacrine layers. Comparison of gene expression patterns across neuronal regions revealed a prominent subset of RGC genes that were overexpressed in dorsal root and trigeminal ganglia. To narrow the search for candidate disease-related genes, RGC genes were mapped to known disease loci for optic neuropathies.

conclusions. This work is one of the first efforts to profile gene expression in a purified population of retinal neurons, the RGCs. The profiling, in addition to revealing both known and novel genes underlying the RGC phenotype, also uncovered common patterns of gene expression between RGCs and other sensory ganglia.

Retinal ganglion cells (RGCs) perform the final steps of retinal vision processing before carrying the visual signal to higher centers in the brain. The death of RGCs is a common cause of visual disability, most often occurring from glaucoma, a leading cause of irreversible blindness in developed countries and worldwide. 1 2 RGC death also occurs in many other optic neuropathies, which can be of environmental and/or genetic origin, with inheritance patterns ranging from mitochondrial to autosomal dominant. RGCs are widely used as a model system for neurobiological studies of development, trauma, and neuronal degeneration and regeneration. Thus, knowledge of RGC functions is important to the understanding of many neuronal processes. 
The behavior of RGCs, and of all cells on a fundamental level, arises in large part from the specific distribution of genes that the cells express. Relatively little is known about the genes expressed by RGCs. Gene expression studies have been performed on the retina as a whole, 3 using a variety of methods, including expressed sequence tag (EST) sequencing, 4 5 6 serial analysis of gene expression (SAGE), 7 8 and microarrays. 9 10 11 12 13 However, the retina is a complex tissue composed of neuronal, glial, and vascular cell types. The dominant cell type of the retina is the photoreceptor, with RGCs comprising 5% or less of all retinal cells. 14 15 Thus, gene expression profiles from whole retina are unrepresentative of RGC gene expression. Previous efforts to identify the complete picture of retinal gene expression may have missed important RGC genes, due to the low relative frequency of RGCs and, hence, their mRNA transcripts. 
Efforts to document gene expression of specific cell types in the eye have used EST sequencing from libraries derived separately from lens, iris, and retinal pigment epithelium-choroid. 4 Similarly, optic nerve astrocytes isolated from human retina have been studied with microarrays. 16 Efforts are currently underway to identify the expression pattern of single retinal cells. 17 Gene expression profiling has been undertaken for different subregions of the brain 18 19 20 21 22 23 24 25 and auditory system, 26 with the use of message amplification for cells microdissected individually 20 22 27 28 or purified by fluorescence-activated cell sorting. 29  
We describe herein an initial gene expression profile of rat RGCs that were separated from other cell types by immunopanning. RGCs purified by this method have provided information on the interactions that govern RGC physiology and development. 30 Through EST sequencing of a cDNA library prepared from purified RGCs, we found expression of both known and novel genes and have begun further investigation of how these genes relate to RGC function. 
Materials and Methods
RGC cDNA Library
All experiments were conducted with adherence to the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research. RGCs from postnatal day (P)21 Sprague-Dawley rats (Simonsen Laboratories, Gilroy, CA) were purified by sequential immunopanning using a monoclonal antibody to Thy1.1, by a method that has been reported to yield approximately 99% purity. 30 31 33 Briefly, whole retina tissue was removed from rats from four litters, incubated in a papain solution, dissociated into single-cell suspension, and subjected to negative selection with anti-macrophage antiserum (1:100; Axell Accurate Chemical and Scientific Corp, Westbury, NY) to remove macrophage and endothelial cells. Remaining cells were then placed on panning plates containing Thy1.1 antibody, and unbound cells were removed with washing. RGCs were released after incubation with a trypsin solution. RGCs were cultured overnight on poly-d-lysine (Sigma-Aldrich) and laminin (Invitrogen-Gibco, Grand Island, NY), in serum-free defined medium, as described. 31 32 The yield of RGC cells was between 50% and 70%, with a survival of more than 90%. 31 Total RNA was extracted and confirmed to be intact by denaturing gel electrophoresis. The total RNA was reverse transcribed, and a nonnormalized, nonsubtracted cDNA library was constructed from 1 μg total RNA using SMART technology and 16 rounds of PCR amplification (BD Biosciences-Clontech, Palo Alto, CA). This method is based on template-switching at the 5′ end of the mRNA transcript, with binding of an anchor sequence that can serve as a priming site for PCR. The cDNA was then size fractionated and ligated into pDNR-LIB plasmid (BD Biosciences-Clontech). Escherichia coli (Electromax DH10B; Invitrogen, San Diego, CA) was transformed by electroporation and grown for 1 hour in SOC medium without further amplification. Clones were plated and randomly chosen for 5′ sequencing (Michigan State University Genomics Facility, East Lansing, MI, or Integrated Genomics GmbH, Jena, Germany). RGC EST sequences were submitted to the National Center for Biotechnology Information (NCBI; accession numbers CF974889 to CF9749532). 
EST Sequence Clustering
Our clustering procedure consisted of two steps. First, the CAP3 sequence assembly program 34 was used with stringent criteria: overlap length of 200 bp and sequence identity percentage of 95% (command line options: -o 200 -p 95). Then, the sequence clusters resulting from the CAP3 program were aligned against the rat, mouse, and human Reference Sequence Project (RefSeq) databases 35 36 with BLASTn. 37 The e-value cutoff for the alignment was defined as 1e-50. The clusters aligning to the same RefSeq sequence were further merged into one cluster. The remaining clusters were then aligned against the rat, mouse, and human UniGene 38 and genomic databases with BLASTn at an e-value defined as 1e-20 and then further aligned with BLASTx alignment at an e-value cutoff of 1e-5. 
Cluster Annotation
All clusters were annotated to RefSeq preferentially 35 36 and otherwise to UniGene. Rat, mouse, and human RefSeq were used as complementary annotation resources. If a cluster aligned to a RefSeq from a different species than rat, the RefSeq with lowest e-value alignment was selected as the annotation for the cluster. In cases in which the alignments between a cluster and a RefSeq from different species yielded the same e-value (e.g., e-value = 0.0), the priority order of annotation was rat>mouse>human. 
dbEST Search
The sequences without a RefSeq or UniGene match were further aligned against rat, mouse, and human database for ESTs (dbEST) 39 with the same e-value cutoff (1e-20) applied. 
Comparative Gene Expression Clustering
The RGC genes used for hierarchical clustering composed the subset of RGC clusters represented in the microarray data compiled by Su et al. 19 (http://expression.gnf.org/cgi-bin/index.cgi, Gene Expression Atlas, Genomics Institute of the Novartis Research Foundation, San Diego, CA) from 13 different neural regions. Replicate array data available for each region were first averaged. The Cluster and TreeView programs developed by Michael Eisen (http://rana.lbl.gov/EisenSoftware.htm; provided in the public domain by Eisen Lab, Lawrence Berkeley, national Lab, University of California at Berkeley) were then used for clustering and visualization, respectively. Both genes and neural regions were normalized by median centering and filtered for genes with expression in at least one neural region. Negative expression levels were set to zero. The parameters used for clustering were “absolute correlation” and “average linkage clustering.” 
Disease Loci
All sequence clusters were mapped to the human genome with an mRNA alignment program, SPIDEY. 40 The program was run with the interspecies alignment option on. The clusters falling into the disease loci were identified as disease candidate genes. 
Immunohistochemistry
Eight-micrometer paraffin sections of rat retina were collected onto slides (Superfrost Plus; Fisher Scientific, Pittsburgh, PA) before immunolabeling by the streptavidin-biotin peroxidase method (Vector-SG detection kit; Vector Laboratories Inc., Burlingame, CA). Primary antibody was to RESP18 (a gift from Betty Eipper, University of Connecticut Health Center, Farmington, CT) or DDAH1 (a gift of Milan Vašák, Department of Biochemistry, Universität Zürich, Zürich, Switzerland). Negative controls included nonimmune serum of the same species as the primary antibody, or preimmune serum at the same protein concentration, or incubation buffer alone. Labeled sections were mounted in glycerol jelly and viewed by Nomarski optics (Axioskop; Carl Zeiss Meditec, Thornwood, NY). 
Results
RGC Library Clones: Known and Novel
A nonnormalized, nonsubtracted cDNA library was constructed from purified postnatal day (P)21 rat RGCs. Generation of the library incorporated 16 rounds of PCR amplification to compensate for the limiting quantities of RNA available. The library contained 1.2 × 105 primary transcripts, with an average insert size of 1.8 kb. No further amplification of the library was performed. Five thousand clones were randomly selected for 5′ sequencing, generating 4791 usable EST sequences, with an average usable read length of approximately 500 bp. 
Clustering of these ESTs to group together sequences representing the same transcript revealed 2360 unique gene clusters (complete listing available in Supplemental Table 1). Approximately 40% of the RGC library clones could be characterized as poorly characterized sequence, commonly termed ESTs. In a more detailed analysis, approximately 60% of the clusters (1408) represented known genes in the sense that they matched genes categorized in the NCBI Reference Sequence Project (RefSeq) sets for rat, mouse, and human genes. For the remaining 952 clusters a less stringent homology search was performed using UniGene for rat, mouse, and human. Approximately 60% of these clusters (n = 565) matched to UniGene clusters. Of the other 301 clusters, 92 matched to previously submitted EST sequences in dbEST. For each of the RGC clusters that matched only to otherwise unclassified dbEST ESTs, the tissue of origin of the matching dbEST ESTs was identified (Supplemental Table 1), to serve as a rough indication of the tissue types that express the gene. 
The next step in the partitioning of RGC genes involved the 209 RGC clusters that had no match in the EST database by BLASTn. To characterize these remaining clusters further, and to select those most likely to represent rarely transcribed sequences, we aligned the clusters against the rat genome using BLAST. This alignment demonstrated that 82 of the clusters possessed two or more discontinuous areas of alignment on the genome, as would occur for exons of transcribed genes. In agreement with this, most of these sequences, 73%, could be readily amplified by PCR. Of these 82 clusters with intron–exon structure, 74 showed no homology in the protein database or matched to predicted–theoretical protein records. 
Library Representation of RGC Gene Expression
The distribution of RGC gene cluster size is shown in Figure 1 . Most (77%) of the ESTs had no significant sequence overlap with other RGC ESTs,and so were in a cluster of size 1, as reflects the fact that most cellular mRNAs are expressed at low levels. As cluster size increased, the number of clusters at each increasing size was fewer, in an exponential-like decline, reflecting the fact that a smaller percentage of cellular genes are expressed at moderate levels, with fewer still expressed very highly. Though genes that are very highly expressed are few in number, they still account for a relatively large percentage of total mRNA produced by a cell, with the 10 largest RGC gene clusters containing approximately 500 of the 4791 total ESTs sequenced, or nearly 10% of the total (Table 1) . We observed a strong inverse correlation between cluster size and the percentage of clusters that represented an unknown EST. For singleton clusters, as mentioned earlier, approximately 40% were ESTs. As cluster size increased, the percentage of ESTs decreased, from 32% for cluster size 2, to 16%, 8%, 6%, and 0% for cluster sizes between 3 and 6 or more, respectively. 
Highly Expressed RGC Genes
Gene function assignments were made for the 100 most frequently sequenced RGC genes (Fig. 2) . For this purpose, each gene was assigned to a single main category. Despite being highly represented, some genes have poorly understood functions. Nevertheless, functional assignments were possible for most genes in this group. 
The protein modification enzyme ubiquitin was the single most frequently sequenced RGC gene, second only to the combination of mitochondria-encoded proteins. Of the 13 proteins encoded by the mitochondrial genome, 12 were sequenced from the RGC library (Table 2) . The number of ESTs encountered for each of these genes varied greatly, from 18 for the largest cluster (ATP synthase F0 subunit 6) to NADH dehydrogenase subunit 3, which was not encountered at all. Mitochondrial mutations lead to selective RGC death in Leber’s optic neuropathy, suggesting that mitochondrial gene expression levels may be particularly important in ganglion cell function. We therefore compared the cluster size found in the RGC library for each mitochondria-encoded gene to the cluster size in a non-normalized, nonsubtracted cDNA library (dbEST library ID.8847) from rat dorsal root ganglia, a cell type with similarities to RGCs that does not significantly degenerate in Leber’s optic neuropathy. Although our sample size was small, there was a good overall correlation between cluster sizes for the mitochondria-encoded genes in the two cell types (R 2 = 0.4; Fig. 3 ), and thus no evidence of large differences in expression levels of mitochondria-encoded genes between RGC and DRG cells. 
Also highly expressed in RGC cells were glycolytic and citric acid cycle enzymes, including malate dehydrogenase, lactate dehydrogenase, aldolase C, and aldolase A. These proteins are also highly represented in SAGE results from brain and retina, 7 8 and represent large clusters in UniGene, reflecting broad expression in many different tissues. Calcium-binding proteins were frequently encountered in the library, including calmodulin-1, -2, and -3; calretinin; calpactin 1; and calcyclin. Antioxidant genes were also prominent, including peroxiredoxin, glutathione S-transferase, and the poorly characterized selenoprotein W. After the five most represented functional categories (energy, protein synthesis/modification, lysosomal/vesicular, synaptic function, cytostructure), the next largest group was ESTs without known function. 
Photoreceptor-specific genes are among the most frequently encountered ESTs in cDNA libraries made from whole retina, whereas in contrast in the RGC ESTs they were almost entirely excluded. For example, no ESTs were encountered for rhodopsin, transducin, or rod photoreceptor cGMP phosphodiesterase subunits. Similarly, no clones were encountered in the RGC library for Müller cell genes, such as cellular retinaldehyde-binding protein (CRALBP), vimentin, or glutamine synthase. 
Neural- and Disease-Associated Gene Expression in RGCs
Surprisingly, a neuroendocrine-specific gene with poorly understood function, RESP18, was one of the most frequently encountered genes in the RGC library. We used immunohistochemistry to correlate RESP18 message found in the library with protein expression in the retina, and to localize its cellular expression pattern. RESP18 immunoreactivity was observed mainly in the RGC layer, with faint labeling of the inner plexiform layer and inner nuclear layer (Fig. 4) . Staining was present mainly in cell bodies, in a perinuclear distribution consistent with its previously identified localization to the lumen of the endoplasmic reticulum. 42  
The functions of the remaining RGC clusters were then examined for genes that might be involved in pathways particularly important to RGC disease. One of the singleton genes, DDAH1, has been investigated for its involvement in nitric oxide metabolism 43 44 45 46 and neuronal injury. We found immunoreactivity for DDAH1 to be present in RGC and amacrine cell layers (Fig. 5) . The sublaminae of the inner plexiform layer were particularly intensely immunoreactive, as was the retinal pigment epithelium. 
Comparative Gene Expression Profiling of RGC Genes
Just as knowing which genes are expressed by RGCs should be informative of cell function, knowing the different neuronal types that express a gene should be informative of gene function. We therefore sought to determine where else in the nervous system genes expressed in RGCs were also expressed. Using hierarchical clustering to visualize expression patterns (Fig. 6) , we compared our RGC data set to gene expression profiles generated using oligonucleotide microarrays from 13 separate neuronal regions 19 (http://expression.gnf.org/cgi-bin/index.cgi). Of the 2360 RGC gene clusters, 959 were represented on these arrays, with 89% (851/959) showing positive signal in at least one neural area. A major resultant feature of the clustering was a subgroup of 24 genes relatively overexpressed in both dorsal root and trigeminal ganglia (Fig. 6 , large oval). These sensory ganglia overexpressed genes, along with numerical expression level data are shown in Table 3 . Hierarchical clustering was also performed across neural regions, as indicated by the tree structure. For the subset of genes expressed in retinal ganglion cells, the dorsal root and trigeminal ganglia were more closely related to each other than to the other neural regions. 
To further explore the prominent RGC expression of RESP18, we focused on the smaller subset of RGC genes shown through clustering to be overexpressed in hypothalamus (Fig. 6 small oval, Table 4 ). One of these genes, necdin, has been reported to be overexpressed in hypothalamus, 47 48 whereas another, secretogranin 2, has known neuroendocrine functions. Necdin is thought to play a role in cell cycle arrest in terminally differentiated neurons, and secretogranin 2 is one of the chromogranin family of proteins, involved in secretory granulogenesis and the sorting and processing of secretory proteins. 
Candidate Optic Neuropathy Genes Expressed by RGCs
To aid in candidate gene approaches to finding optic neuropathy-associated genes, we mapped the RGC genes to syntenic regions of the human genome associated with the optic neuropathy–associated loci GLC1B, 49 GLC1C, 50 GLC1D, 51 GLC1F, 52 OPA2, 53 OPA4, 54 WFS2, 55 SCABD, 56 and ARTS 57 (Table 5)
Discussion
We have established an initial gene expression profile of purified rat RGCs through the approach of EST sequencing. This has allowed us to ascribe to RGCs the expression of a large number of known and novel genes. Several hundred novel sequences were identified from our sampling of only a minority of total genes expressed by RGCs, suggesting that we still have much to discover about RGC gene expression, especially about those genes expressed at low levels. 
Although novel sequences from cDNA libraries are often described as ESTs, the term has certain limitations. For example, it does not distinguish rare novel sequences from more common sequences that are as yet unnamed. We therefore undertook a more detailed analysis of RGC gene clusters based on the full information available in NCBI databases. The RefSeq collections represent stable, curated databases of genes that have been documented at a higher level of certainty than those found in other experimental gene collections such as UniGene. The RGC genes that matched RefSeq entries were therefore considered known genes for this analysis. It is important to note, however, that most genes in RefSeq remain largely uncharacterized and that some characterized genes have not, at present, been included in RefSeq. The UniGene sets are based on automated partitioning of EST data into an experimental set of unique genes, based on sequence alignment combined with evidence of polyadenylation. Thus, in general, the RGC genes that matched to UniGene, but not to RefSeq, represented genes that are poorly characterized, possibly because of low expression levels. Those RGC sequences so rare as not to be found even in UniGene may represent transcripts of particular interest for future study. 
The RGC clones were randomly selected and sequenced from a non-normalized, nonsubtracted cDNA library. This methodology can provide approximate information about the relative expression level of genes, but must be considered with caution in this instance because PCR was used in library construction to compensate for the limited quantity of RGC RNA. Several observations suggest that the rank ordering of genes we obtained may still be a useful representation of RGC gene expression levels: (1) In general, within any population of total mRNA, a small number of genes are highly abundant, with each of their individual mRNAs accounting for up to 1% of total cellular mRNA transcripts. For example, rhodopsin transcripts account for 1% or more of total retinal mRNA, and it is often the case that the 10 most highly expressed genes in a tissue account for approximately 10% of total mRNA. Such a distribution of highly expressed genes was encountered in this library, and included polyubiquitin and tubulin, among other genes expected to be highly expressed. (2) Along these same lines, nearly all genes in a tissue are of medium (0.1%–1%) or low abundance (0.1% or less of total mRNA). 58 59 Single EST sequences represented 77% of clusters in the RGC library, and the overall cluster size distribution was similar to that of a non-PCR amplified retinal cDNA library 11 as would be expected if the RGC library also contained a sampling of low-, medium-, and high-abundance mRNA species. (3) Mitochondria-encoded genes were expressed in the RGC library at ratios similar to levels in a non-PCR amplified library from dorsal root ganglion cells (Fig. 4) . Lastly, (4) a strong correlation was present between RGC cluster size and the likelihood of the cluster’s representing a known gene, as would be expected if highly expressed genes are more likely to be known, whereas low expression level genes are more likely to be unstudied ESTs. 
Within the 35 genes most frequently sequenced from the RGC library (Table 1) , a surprising number have poorly understood functions, and/or have not been studied in the retina. One of these for which there is some interesting information available is RESP18, which is expressed in endocrine and neural cells that secrete peptide hormones 60 61 and is suggested to be involved in intracellular signaling pathways. 62 In the brain, expression of RESP18 is limited to very specific regions, including the paraventricular and supraoptic nuclei of the hypothalamus, and the neurointermediate and anterior lobes of the pituitary. RESP18 is homologous to a region of the luminal domain of neuroendocrine-specific receptor-type protein tyrosine phosphatases and appears to be involved in intracellular signaling from the Golgi to the nucleus. 62 We speculate that further study of RESP18 may uncover a group of functionally interrelated genes that act within similar pathways in RGCs and the small subset of specialized neurons that preferentially express this gene. 
Most mammalian genes remain poorly characterized, and similarly most of the genes we identified as singletons in the RGC library remain poorly characterized, both in general and in the retina. We selected DDAH1 for further study based on its involvement in nitric oxide metabolism, which has been particularly implicated in glaucomatous RGC death. 63 64 65 66 Also of interest, DDAH1 is increased in neurons with neurofibrillary tangles in Alzheimer disease 67 and in neuronal trauma. 68 DDAH1 hydrolyzes arginine residues that are asymmetrically methylated and endogenously generated. Such residues are competitive inhibitors of all three isoforms of nitric oxide synthase (NOS). Thus, inhibiting DDAH1 leads to decreased NO synthesis. This action may provide a therapeutic avenue for modulating NO levels in disease. The observation that DDAH1 is present both in the RGC and amacrine cell layers, as well as in multiple sublaminae of the inner plexiform layer, suggests a role for DDAH1 in ganglion and amacrine cell signaling. 
Several of the genes most frequently sequenced from the RGC library have been found to change expression in RGC injury. Synuclein gamma is increased in retinal glial cells in human glaucoma. 69 In an optic nerve crush model of ganglion cell death, stathmin showed reduced expression, whereas malate dehydrogenase and heat shock protein cognate 70 were both increased. 70  
Human genetic studies have identified several loci for inherited optic neuropathies. Candidate gene approaches to finding the specific gene causing these RGC diseases will be aided by knowledge of which genes in mapped loci are in fact expressed by RGCs (recognizing that a gene causing RGC death need not be expressed by RGCs). Of the RGC-expressed genes in these regions (Table 5) , those known to be involved in neuronal degenerations or that are specifically expressed in neurons may be stronger candidates for RGC disease. Thus, the OPA4 region contained an “EST similar to ELAV (Embryonic lethal abnormal vision)-type RNA-binding protein 3” as annotated by NCBI. The ELAV family of genes is essential for Drosophila visual system development, and autoimmunity to these proteins can cause encephalomyelitis with sensory neuropathy. 71 Also within the OPA4 region was Ras-like without CAAX/Rin/Rit2, a small guanosine triphosphate (GTP)–binding protein that is expressed exclusively in neurons and in the retina is found only in ganglion cells and in the inner nuclear layer. 72 73 The GLC1D region similarly contained a neuron-restricted gene, potassium channel alpha subunit (Kv8.1). This gene has been analyzed in a positional candidate approach for adult familial myoclonic epilepsy, but without findings of pathogenic changes. 74  
One way to understand how the genome influences cell function is to compare the gene expression profiles among different cell types. This approach is amenable to high-throughput methods, such as EST sequencing, microarrays, and SAGE, and is particularly useful for gaining an initial insight into the roles of the large number of mammalian genes for which no detailed studies have been undertaken. In general, genes that are expressed at high levels in one neuronal type, but not in others, are likely contributors to phenotypic differences. In contrast, genes expressed at similar levels across neuronal subtypes might be expected to perform general cellular or neuronal functions and not to have a large role in establishing phenotypic differences. We examined the expression profile of the RGC genes in 13 different neural regions, as determined by the oligonucleotide microarray analysis of Su et al. 19 It is known that RGCs and other sensory ganglia such as the dorsal root and trigeminal ganglia share transcription factors such as the Brn-3 family. 75 As a consequence, it has been proposed that these neurons share similar genetic regulatory hierarchies. 75 Consequently, it might be expected that the cells would show downstream gene expression patterns with some significant similarities. This, in fact, appeared to be the case, with hierarchical clustering of gene expression revealing a pattern of RGC genes that were preferentially expressed in both the dorsal root and trigeminal ganglia. Several of these genes were among the largest RGC clusters, including tubulin, synuclein gamma, stathmin-like 2, and HSC70. Ion channels were also prominent in this group, including chloride intracellular channel 1, annexin 5, calpactin 1, and aquaporin 1. 
There are many RGC subtypes, some of which have properties such as photoreception that set them apart from others. 76 77 78 This suggests that diversity will be found in gene expression patterns, even among RGCs, and highlights the need for increasingly stringent cell-type separations for future gene expression studies. The method of RGC purification used in the present study did not specifically bias against particular RGC subtypes, and the yield and survival of RGCs suggests that a fairly representative sample of RGCs was obtained. As a consequence, those subtypes present in small numbers, such as photoreceptive RGCs, would have made little contribution to the overall gene expression profile obtained. It is important to consider that gene expression patterns can vary greatly between seemingly similar samples, even controlling for such factors as genetic background, age, sex, and environment. 79 The RGC population examined in the current study was collected at a single time point in the midmorning, and the expression of some genes may be altered at different circadian time points, for example. Similarly, the specific conditions during RGC purification and overnight culture probably affected the expression levels of some genes. Thus, instead of a single, static gene expression profile defining a cell type, it appears that a range of profiles, when combined, better illustrates the more dynamic nature of transcriptional control of cellular phenotype. 
 
Figure 1.
 
Cluster analysis for 4791 RGC ESTs. The histogram groups the EST clusters by size, from clusters made of only 1 EST sequence, to clusters containing 34 or more overlapping ESTs that collectively represent a single expressed sequence. Most (77%) of the ESTs had no significant sequence overlap with other RGC ESTs and so were in a cluster of size 1. As cluster size increased, the number of clusters at a given size decreased exponentially, reflecting the fact that fewer cellular genes are expressed at moderate and high levels.
Figure 1.
 
Cluster analysis for 4791 RGC ESTs. The histogram groups the EST clusters by size, from clusters made of only 1 EST sequence, to clusters containing 34 or more overlapping ESTs that collectively represent a single expressed sequence. Most (77%) of the ESTs had no significant sequence overlap with other RGC ESTs and so were in a cluster of size 1. As cluster size increased, the number of clusters at a given size decreased exponentially, reflecting the fact that fewer cellular genes are expressed at moderate and high levels.
Table 1.
 
Large RGC Gene Clusters by Cluster Size
Table 1.
 
Large RGC Gene Clusters by Cluster Size
Mitochondrial proteins (226) Tubulin beta 15 (21)
Polyubiquitin (151) Heat shock cognate protein 70 (19)
Calretinin (74) Selenoprotein W (18)
Peptidylprolyl isomerase A (62) Malate dehydrogenase (18)
Alpha-tubulin (61) Calmodulin 1 (17)
Aldolase C (56) Transgelin 3 (17)
Calmodulin 2 (36) Aldolase A (17)
H+ transporting ATPase, lysosomal 16 kDA (34) Peroxiredoxin 2 (15)
Synaptic vesicle glycoprotein 2b (33) Enolase 1 alpha (15)
Transcription elongation factor B 15 kDa (30) Lactate dehydrogenase B (14)
Stathmin 1 (29) Heat shock factor binding protein 1 (13)
SNAP25 interacting protein 30 (26) Synuclein alpha (13)
Synuclein gamma (24) Interferon alpha–inducible 27-like (13)
Microtubule-associated proteins 1A/1B light chain 3 (21) Lactate dehydrogenase A (13)
Regulated endocrine-specific protein 18 (12)
Thymus cell surface antigen, Thy1 (21) Guanine nucleotide–binding protein gamma 3 (12)
Synaptic glycoprotein SC2 (21) Myosin light polypeptide 6 (11)
Synaptosomal-associated protein Snap25 (21) Triosephosphate isomerase 1 (11)
Heat shock protein 84 kDa 1 (21)
Figure 2.
 
Gene ontogeny of the 100 most frequently sequenced RGC clones. Each gene was assigned to a single category corresponding to the main functional role of the gene, as determined by literature review.
Figure 2.
 
Gene ontogeny of the 100 most frequently sequenced RGC clones. Each gene was assigned to a single category corresponding to the main functional role of the gene, as determined by literature review.
Table 2.
 
Mitochondria-Encoded Genes
Table 2.
 
Mitochondria-Encoded Genes
RGC Cluster Size Protein Accession Mitochondrial Proteins
18 NP_007230 ATP synthase F0 subunit 6
16 NP_007237 Cytochrome b
15 NP_007226 NADH dehydrogenase subunit 2
14 NP_007231 Cytochrome c oxidase subunit III
12 NP_007228 Cytochrome c oxidase subunit II
6 NP_007227 Cytochrome c oxidase subunit I
3 NP_007225 NADH dehydrogenase subunit 1
2 NP_007234 NADH dehydrogenase subunit 4
2 NP_007236 NADH dehydrogenase subunit 6
2 NP_007233 NADH dehydrogenase subunit 4L
1 NP_007229 ATP synthase F0 subunit 8
1 NP_007235 NADH dehydrogenase subunit 5
Figure 3.
 
Scatterplot showing similar expression levels (as represented by cluster size) of mitochondria-encoded genes in the RGC library compared with a library derived from dorsal root ganglion (DRG) cells (dbEST Library ID.8847, 41 ). The 13 mitochondria-encoded genes were assigned rank-order values (1–13) based on the number of ESTs/cluster in each library (R 2 = 0.4).
Figure 3.
 
Scatterplot showing similar expression levels (as represented by cluster size) of mitochondria-encoded genes in the RGC library compared with a library derived from dorsal root ganglion (DRG) cells (dbEST Library ID.8847, 41 ). The 13 mitochondria-encoded genes were assigned rank-order values (1–13) based on the number of ESTs/cluster in each library (R 2 = 0.4).
Figure 4.
 
Expression of RESP18 in rat retina. RESP18 immunoreactivity was present mainly in large cell bodies in the ganglion cell layer, with faint immunoreactivity in the inner plexiform and inner nuclear layers and negligible labeling elsewhere. Immunoperoxidase staining with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 4.
 
Expression of RESP18 in rat retina. RESP18 immunoreactivity was present mainly in large cell bodies in the ganglion cell layer, with faint immunoreactivity in the inner plexiform and inner nuclear layers and negligible labeling elsewhere. Immunoperoxidase staining with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 5.
 
Expression of DDAH1 in rat retina. DDAH1 immunoreactivity was present in the ganglion cell layer, multiple sublaminae of the inner plexiform layer, and amacrine cell regions of the inner nuclear layer. Strong immunoreactivity was also present in the retinal pigment epithelium. Immunoperoxidase labeling with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 5.
 
Expression of DDAH1 in rat retina. DDAH1 immunoreactivity was present in the ganglion cell layer, multiple sublaminae of the inner plexiform layer, and amacrine cell regions of the inner nuclear layer. Strong immunoreactivity was also present in the retinal pigment epithelium. Immunoperoxidase labeling with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 6.
 
Comparative gene expression profiles of RGC genes. Comparison was made between the gene expression profile derived from RGCs through EST sequencing versus the gene expression profiles of 13 separate neuronal regions derived by Su et al. 18 using oligonucleotide microarrays. Hierarchical clustering is shown of the microarray output from the resultant 851 genes present in both ganglion cell and microarray data sets. Mean-centered normalization was applied across rows, so that red represents expression higher than average across the neural regions and green represents below average expression level. Overall brightness represents microarray signal intensity. Genes with similar expression patterns across neuronal areas are placed in proximity to each other. Genes relatively overexpressed in both dorsal root and trigeminal ganglia are indicated by the large oval and genes relatively overexpressed in hypothalamus are indicated by the small oval.
Figure 6.
 
Comparative gene expression profiles of RGC genes. Comparison was made between the gene expression profile derived from RGCs through EST sequencing versus the gene expression profiles of 13 separate neuronal regions derived by Su et al. 18 using oligonucleotide microarrays. Hierarchical clustering is shown of the microarray output from the resultant 851 genes present in both ganglion cell and microarray data sets. Mean-centered normalization was applied across rows, so that red represents expression higher than average across the neural regions and green represents below average expression level. Overall brightness represents microarray signal intensity. Genes with similar expression patterns across neuronal areas are placed in proximity to each other. Genes relatively overexpressed in both dorsal root and trigeminal ganglia are indicated by the large oval and genes relatively overexpressed in hypothalamus are indicated by the small oval.
Table 3.
 
RGC Genes Overexpressed in Both Dorsal Root and Trigeminal Ganglia
Table 3.
 
RGC Genes Overexpressed in Both Dorsal Root and Trigeminal Ganglia
Cer Olf Amg DRG Trig Cort Stri Sp-u Sp-l FroC Hip Hyp
Alpha-tubulin 5233 5528 4591 10771 10154 6491 4141 5638 5215 4154 5010 5782
Deleted in polyposis 1 759 1037 1762 5658 4407 1346 1311 1247 1205 1297 1222 1611
Calpain, small subunit 1 925 879 704 3161 2162 698 913 1087 1278 850 748 964
Serpinb6 31 21 110 1986 1096 80 56 187 266 99 154 115
Cathepsin L 282 357 183 3294 2299 182 181 347 467 212 276 507
S100a10 0 35 33 3258 2100 0 0 88 152 0 0 0
Synuclein, gamma 56 88 45 6720 4595 73 30 342 579 97 26 212
CD151 antigen 512 409 345 1607 1436 388 262 436 592 412 291 432
Chloride intracellular channel 1 26 0 0 331 305 0 0 0 23 0 0 0
Annexin A2 0 0 0 7328 6987 0 0 111 645 0 0 0
Annexin 5 508 808 378 4929 4196 717 875 1365 1362 697 458 907
Serping1 155 229 190 919 816 183 66 164 195 137 213 160
Proteasome 26s subunit 808 683 731 1620 1435 618 739 913 772 571 685 829
Riken 1110020C13 314 130 273 825 612 143 134 234 235 207 230 268
Stathmin-like 2 2791 1059 1845 4942 5120 2003 1441 2309 1954 1855 1453 2174
Aquaporin 1 225 324 311 8859 9737 179 52 1168 3885 145 897 203
CD59 antigen 21 39 64 997 948 0 99 237 337 81 125 130
CD151 antigen 512 409 345 1607 1436 388 262 436 592 412 291 432
Janus Kinase 1 128 30 83 834 649 209 168 391 308 16 163 142
Hmgcs1 352 480 642 2537 1834 721 724 1512 1047 619 470 879
HSC70 2510 2151 2642 5251 4385 2222 2612 3346 2663 2283 2047 3224
COP9 subunit 5 364 377 363 762 734 411 343 467 444 411 323 451
Squalene epoxidase 224 445 391 1114 954 438 297 590 549 349 373 541
FK506 binding protein 4 1340 845 522 2053 1584 506 523 586 673 565 393 578
Table 4.
 
Hypothalamus Overexpressed Genes in RGCs
Table 4.
 
Hypothalamus Overexpressed Genes in RGCs
Cer Olf Am DR Trig Cort Stri Sp-u Sp-l Fro Hip Hyp
Nascent polypeptide–associated complex alpha 981 1040 953 884 1104 818 1179 1118 1043 930 854 1463
Ribosomal protein L6 1977 2170 2437 2206 2874 2323 2399 2456 2425 2363 2267 3230
Melanoma antigen D1 594 1448 1812 1259 1753 1262 1451 1196 1198 1366 1681 2721
Centrin 2 (Cetn2) 0 34 118 79 95 9 26 34 58 24 76 145
Necdin (Ndn) 1853 901 2188 1749 769 1624 1697 1317 1389 1304 1628 4602
Secretogranin 2 (Scg2) 333 1609 865 980 776 746 1098 872 725 611 418 2691
Riken cDNA 6330403K07 6 1535 1496 522 321 1422 1450 1014 1043 1271 985 4696
Paternally expressed 3 682 918 885 810 631 705 1100 943 1012 820 598 2074
Regulated endocrine-specific protein 18 187 256 665 569 816 469 426 1062 938 535 390 3109
Ras-like without CAAX 2 284 221 206 286 215 120 234 652 419 169 180 933
Chromobox homolog 5 313 384 435 356 246 404 524 423 366 414 359 617
Table 5.
 
Candidate Optic Neuropathy Genes Expressed by RGCs
Table 5.
 
Candidate Optic Neuropathy Genes Expressed by RGCs
GLC1B
 NM_031100.1 Ribosomal protein L10 (Rpl10)
 NM_025379.1 Cytochrome c oxidase subunit VIIb (Cox7b)
 NM_175838.1 Eukaryotic translation elongation factor 1 alpha 1 (Eef1a1)
 NM_016774.1 ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit (Atp5b)
 NM_021261.1 Thymosin, beta 10 (Tmsb10)
 NM_017101.1 Peptidylprolyl isomerase A (cyclophilin A) (Ppia)
 NM_031099.1 Ribosomal protein L5 (Rpl5)
GLC1C
 NM_024351.1 Heat shock protein 8 (Hspa8)
 Rn.3357 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c, isoform 1
 NM_007951.1 Enhancer of rudimentary homologue (Drosophila) (Erh),
 Rn.1425 RAB7, member RAS oncogene family
 NM_053330.1 Ribosomal protein L21 (Rpl21)
 NM_012497.1 Aldolase C, fructose-biphosphate (Aldoc)
 NM_012963.1 High mobility group box 1 (Hmgb1)
 NM_030873.1 Profilin II (Pfn2)
 Rn.82741 Actin, beta
 NM_013067.1 Ribophorin I (Rpn1)
GLC1F
 CF978681 EST
 Rn.1463 Peptidylprolyl isomerase A (cyclophilin A)
 CF978691 EST
 NM_031113.1 Ribosomal protein S27a (Rps27a)
 NM_013216.1 Ras homologue enriched in brain (Rheb)
GLC1D
 NM_021697.1 Neuronal potassium channel alpha subunit (Kv8.1)
WFS2
 CF978606 EST
 NM_007410.1 Alcohol dehydrogenase 5 (class III), chi polypeptide (Adh5)
 NM_008015.1 Fibroblast growth factor inducible 14 (Fin14)
 NM_175838.1 Eukaryotic translation elongation factor 1 alpha 1 (Eef1a1)
 NM_145455.1 Similar to transcription factor BTF3 (RNA polymerase B transcription factor 3) (LOC218490)
SCABD
 NM_013226.1 Ribosomal protein L32 (Rpl32)
 Rn.999 Laminin receptor 1 (67kD, ribosomal protein SA)
 Rn.37758 Putative protein phosphatase 1 nuclear targeting subunit
 NM_008210.1 H3 histone, family 3A (H3f3a)
 NM_031100.1 Ribosomal protein L10 (Rpl10)
 Rn.2458 Class 1 beta-tubulin, complete cds
 Rn.82741 Actin, beta
 Mm.66 Ribosomal protein S4, X-linked
 NM_027148.1 RIKEN cDNA 2310032N20 gene (2310032N20Rik)
 NM_022891.1 Ribosomal protein L23 (Rpl23)
 NM_019678.1 Trk-fused gene (Tfg)
 NM_173119.1 Heat shock factor binding protein 1 (Hsbp1)
 NM_025592.2 Ribosomal protein L35 (Rpl35)
 Rn.880 Cytochrome c oxidase subunit Vla (liver)
 NM_029632.1 Protein phosphatase 1, regulatory (inhibitor) subunit 11 (Ppp1r11)
 NM_173102.1 Tubulin, beta 5 (Tubb5)
 NM_130823.1 ATPase, H+ transporting, lysosomal (vacuolar proton pump) 16 kDa (Atp6l)
 NM_017101.1 Peptidylprolyl isomerase A (cyclophilin A) (Ppia)
 NM_013663.2 Splicing factor, arginine/serine-rich 3 (SRp20) (Sfrs3)
 NM_031099.1 Ribosomal protein L5 (Rpl5)
 NM_013762.1 Ribosomal protein L3 (Rpl3)
 NM_000984.2 Homo sapiens ribosomal protein L23a (RPL23A)
 CF979103 EST
OPA4
 Mm.5163 Ras-like without CAAX/Rin
 NM_013721.1 Ribosomal protein L7a (Rpl7a)
 Rn.23878 ESTs, Weakly similar to elav-type RNA-binding protein 3
OPA2
 NM_031144.1 Actin, beta (Actb)
 NM_029814.1 RIKEN cDNA 2210412K09 gene (2210412K09Rik)
 NM_013226.1 Ribosomal protein L32 (Rpl32)
 Rn.999 Laminin receptor 1 (67kD, ribosomal protein SA)
 NM_012963.1 High mobility group box 1 (Hmgb1)
 NM_031683.1 SMC-like 1 (yeast) (Smc1l1)
 NM_008015.1 Fibroblast growth factor inducible 14 (Fin14)
 NM_013721.1 Ribosomal protein L7a (Rpl7a)
 NM_025449.1 Nicolin 1 (Nicn1)
 Rn.2890 Ribosomal protein S15a
 NM_027439.1 ATPase, H+ transporting, lysosomal interacting protein 1 (Atp6ip2)
 NM_172372.1 DNA segment, Chr X, Immunex 38, expressed (DXlmx38e)
 NM_000984.2 Homo sapiens ribosomal protein L23a (RPL23A)
ARTS
 NM_027870.1 ALEX3 protein (Alex3-pending)
 NM_139254.1 Tubulin, beta 3 (Tubb3)
 NM_008210.1 H3 histone, family 3A (H3f3a)
 NM_022934.1 DnaJ-like protein (Hsj2)
 NM_031119.1 Sjogren syndrome antigen B (Ssb)
 NM_022298.1 Alpha-tubulin (Tuba1)
 NM_012497.1 Aldolase C, fructose-biphosphate (Aldoc)
 NM_021766.1 Progesterone receptor membrane component 1 (Pgrmc1)
 NM_019979.1 Selenoprotein K (Selk-pending)
 NM_145629.1 Expressed sequence Al115446 (Al115446)
 Rn.1463 Peptidylprolyl isomerase A (cyclophilin A)
 NM_026007.2 RIKEN cDNA 2610301D06 gene (2610301D06Rik)
 NM_012570.1 Glutamate dehydrogenase 1 (Glud1)
 NM_024351.1 Heat shock protein 8 (Hspa8)
 Rn.2605 Thymosin beta-4
 NM_007951.1 Enhancer of rudimentary homologue (Drosophila) (Erh)
 NM_173119.1 Heat shock factor binding protein 1 (Hsbp1)
 Rn.1463 Peptidylprolyl isomerase A (cyclophilin A)
 NM_007451.2 Solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 (Slc25a5)
 CF978610 EST
 NM_053297.1 Pyruvate kinase, muscle (Pkm2)
 NM_023716.1 RIKEN cDNA 2410129E14 gene (2410129E14Rik)
 NM_017101.1 Peptidylprolyl isomerase A (cyclophilin A) (Ppia)
 NM_013762.1 Ribosomal protein L3 (Rpl3)
 NM_001696.2 Homo sapiens ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 1 (ATP6V1E1)
Supplementary Materials
The authors thank Danielle Valenta and Mary Ellen Pease for technical assistance. 
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Figure 1.
 
Cluster analysis for 4791 RGC ESTs. The histogram groups the EST clusters by size, from clusters made of only 1 EST sequence, to clusters containing 34 or more overlapping ESTs that collectively represent a single expressed sequence. Most (77%) of the ESTs had no significant sequence overlap with other RGC ESTs and so were in a cluster of size 1. As cluster size increased, the number of clusters at a given size decreased exponentially, reflecting the fact that fewer cellular genes are expressed at moderate and high levels.
Figure 1.
 
Cluster analysis for 4791 RGC ESTs. The histogram groups the EST clusters by size, from clusters made of only 1 EST sequence, to clusters containing 34 or more overlapping ESTs that collectively represent a single expressed sequence. Most (77%) of the ESTs had no significant sequence overlap with other RGC ESTs and so were in a cluster of size 1. As cluster size increased, the number of clusters at a given size decreased exponentially, reflecting the fact that fewer cellular genes are expressed at moderate and high levels.
Figure 2.
 
Gene ontogeny of the 100 most frequently sequenced RGC clones. Each gene was assigned to a single category corresponding to the main functional role of the gene, as determined by literature review.
Figure 2.
 
Gene ontogeny of the 100 most frequently sequenced RGC clones. Each gene was assigned to a single category corresponding to the main functional role of the gene, as determined by literature review.
Figure 3.
 
Scatterplot showing similar expression levels (as represented by cluster size) of mitochondria-encoded genes in the RGC library compared with a library derived from dorsal root ganglion (DRG) cells (dbEST Library ID.8847, 41 ). The 13 mitochondria-encoded genes were assigned rank-order values (1–13) based on the number of ESTs/cluster in each library (R 2 = 0.4).
Figure 3.
 
Scatterplot showing similar expression levels (as represented by cluster size) of mitochondria-encoded genes in the RGC library compared with a library derived from dorsal root ganglion (DRG) cells (dbEST Library ID.8847, 41 ). The 13 mitochondria-encoded genes were assigned rank-order values (1–13) based on the number of ESTs/cluster in each library (R 2 = 0.4).
Figure 4.
 
Expression of RESP18 in rat retina. RESP18 immunoreactivity was present mainly in large cell bodies in the ganglion cell layer, with faint immunoreactivity in the inner plexiform and inner nuclear layers and negligible labeling elsewhere. Immunoperoxidase staining with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 4.
 
Expression of RESP18 in rat retina. RESP18 immunoreactivity was present mainly in large cell bodies in the ganglion cell layer, with faint immunoreactivity in the inner plexiform and inner nuclear layers and negligible labeling elsewhere. Immunoperoxidase staining with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 5.
 
Expression of DDAH1 in rat retina. DDAH1 immunoreactivity was present in the ganglion cell layer, multiple sublaminae of the inner plexiform layer, and amacrine cell regions of the inner nuclear layer. Strong immunoreactivity was also present in the retinal pigment epithelium. Immunoperoxidase labeling with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 5.
 
Expression of DDAH1 in rat retina. DDAH1 immunoreactivity was present in the ganglion cell layer, multiple sublaminae of the inner plexiform layer, and amacrine cell regions of the inner nuclear layer. Strong immunoreactivity was also present in the retinal pigment epithelium. Immunoperoxidase labeling with brown 3-amino-9-ethylcarbazole (AEC) reaction product. INL, inner nuclear layer; IPL, inner plexiform layer; RGC, retinal ganglion cell layer. Bar, 15 μm.
Figure 6.
 
Comparative gene expression profiles of RGC genes. Comparison was made between the gene expression profile derived from RGCs through EST sequencing versus the gene expression profiles of 13 separate neuronal regions derived by Su et al. 18 using oligonucleotide microarrays. Hierarchical clustering is shown of the microarray output from the resultant 851 genes present in both ganglion cell and microarray data sets. Mean-centered normalization was applied across rows, so that red represents expression higher than average across the neural regions and green represents below average expression level. Overall brightness represents microarray signal intensity. Genes with similar expression patterns across neuronal areas are placed in proximity to each other. Genes relatively overexpressed in both dorsal root and trigeminal ganglia are indicated by the large oval and genes relatively overexpressed in hypothalamus are indicated by the small oval.
Figure 6.
 
Comparative gene expression profiles of RGC genes. Comparison was made between the gene expression profile derived from RGCs through EST sequencing versus the gene expression profiles of 13 separate neuronal regions derived by Su et al. 18 using oligonucleotide microarrays. Hierarchical clustering is shown of the microarray output from the resultant 851 genes present in both ganglion cell and microarray data sets. Mean-centered normalization was applied across rows, so that red represents expression higher than average across the neural regions and green represents below average expression level. Overall brightness represents microarray signal intensity. Genes with similar expression patterns across neuronal areas are placed in proximity to each other. Genes relatively overexpressed in both dorsal root and trigeminal ganglia are indicated by the large oval and genes relatively overexpressed in hypothalamus are indicated by the small oval.
Table 1.
 
Large RGC Gene Clusters by Cluster Size
Table 1.
 
Large RGC Gene Clusters by Cluster Size
Mitochondrial proteins (226) Tubulin beta 15 (21)
Polyubiquitin (151) Heat shock cognate protein 70 (19)
Calretinin (74) Selenoprotein W (18)
Peptidylprolyl isomerase A (62) Malate dehydrogenase (18)
Alpha-tubulin (61) Calmodulin 1 (17)
Aldolase C (56) Transgelin 3 (17)
Calmodulin 2 (36) Aldolase A (17)
H+ transporting ATPase, lysosomal 16 kDA (34) Peroxiredoxin 2 (15)
Synaptic vesicle glycoprotein 2b (33) Enolase 1 alpha (15)
Transcription elongation factor B 15 kDa (30) Lactate dehydrogenase B (14)
Stathmin 1 (29) Heat shock factor binding protein 1 (13)
SNAP25 interacting protein 30 (26) Synuclein alpha (13)
Synuclein gamma (24) Interferon alpha–inducible 27-like (13)
Microtubule-associated proteins 1A/1B light chain 3 (21) Lactate dehydrogenase A (13)
Regulated endocrine-specific protein 18 (12)
Thymus cell surface antigen, Thy1 (21) Guanine nucleotide–binding protein gamma 3 (12)
Synaptic glycoprotein SC2 (21) Myosin light polypeptide 6 (11)
Synaptosomal-associated protein Snap25 (21) Triosephosphate isomerase 1 (11)
Heat shock protein 84 kDa 1 (21)
Table 2.
 
Mitochondria-Encoded Genes
Table 2.
 
Mitochondria-Encoded Genes
RGC Cluster Size Protein Accession Mitochondrial Proteins
18 NP_007230 ATP synthase F0 subunit 6
16 NP_007237 Cytochrome b
15 NP_007226 NADH dehydrogenase subunit 2
14 NP_007231 Cytochrome c oxidase subunit III
12 NP_007228 Cytochrome c oxidase subunit II
6 NP_007227 Cytochrome c oxidase subunit I
3 NP_007225 NADH dehydrogenase subunit 1
2 NP_007234 NADH dehydrogenase subunit 4
2 NP_007236 NADH dehydrogenase subunit 6
2 NP_007233 NADH dehydrogenase subunit 4L
1 NP_007229 ATP synthase F0 subunit 8
1 NP_007235 NADH dehydrogenase subunit 5
Table 3.
 
RGC Genes Overexpressed in Both Dorsal Root and Trigeminal Ganglia
Table 3.
 
RGC Genes Overexpressed in Both Dorsal Root and Trigeminal Ganglia
Cer Olf Amg DRG Trig Cort Stri Sp-u Sp-l FroC Hip Hyp
Alpha-tubulin 5233 5528 4591 10771 10154 6491 4141 5638 5215 4154 5010 5782
Deleted in polyposis 1 759 1037 1762 5658 4407 1346 1311 1247 1205 1297 1222 1611
Calpain, small subunit 1 925 879 704 3161 2162 698 913 1087 1278 850 748 964
Serpinb6 31 21 110 1986 1096 80 56 187 266 99 154 115
Cathepsin L 282 357 183 3294 2299 182 181 347 467 212 276 507
S100a10 0 35 33 3258 2100 0 0 88 152 0 0 0
Synuclein, gamma 56 88 45 6720 4595 73 30 342 579 97 26 212
CD151 antigen 512 409 345 1607 1436 388 262 436 592 412 291 432
Chloride intracellular channel 1 26 0 0 331 305 0 0 0 23 0 0 0
Annexin A2 0 0 0 7328 6987 0 0 111 645 0 0 0
Annexin 5 508 808 378 4929 4196 717 875 1365 1362 697 458 907
Serping1 155 229 190 919 816 183 66 164 195 137 213 160
Proteasome 26s subunit 808 683 731 1620 1435 618 739 913 772 571 685 829
Riken 1110020C13 314 130 273 825 612 143 134 234 235 207 230 268
Stathmin-like 2 2791 1059 1845 4942 5120 2003 1441 2309 1954 1855 1453 2174
Aquaporin 1 225 324 311 8859 9737 179 52 1168 3885 145 897 203
CD59 antigen 21 39 64 997 948 0 99 237 337 81 125 130
CD151 antigen 512 409 345 1607 1436 388 262 436 592 412 291 432
Janus Kinase 1 128 30 83 834 649 209 168 391 308 16 163 142
Hmgcs1 352 480 642 2537 1834 721 724 1512 1047 619 470 879
HSC70 2510 2151 2642 5251 4385 2222 2612 3346 2663 2283 2047 3224
COP9 subunit 5 364 377 363 762 734 411 343 467 444 411 323 451
Squalene epoxidase 224 445 391 1114 954 438 297 590 549 349 373 541
FK506 binding protein 4 1340 845 522 2053 1584 506 523 586 673 565 393 578
Table 4.
 
Hypothalamus Overexpressed Genes in RGCs
Table 4.
 
Hypothalamus Overexpressed Genes in RGCs
Cer Olf Am DR Trig Cort Stri Sp-u Sp-l Fro Hip Hyp
Nascent polypeptide–associated complex alpha 981 1040 953 884 1104 818 1179 1118 1043 930 854 1463
Ribosomal protein L6 1977 2170 2437 2206 2874 2323 2399 2456 2425 2363 2267 3230
Melanoma antigen D1 594 1448 1812 1259 1753 1262 1451 1196 1198 1366 1681 2721
Centrin 2 (Cetn2) 0 34 118 79 95 9 26 34 58 24 76 145
Necdin (Ndn) 1853 901 2188 1749 769 1624 1697 1317 1389 1304 1628 4602
Secretogranin 2 (Scg2) 333 1609 865 980 776 746 1098 872 725 611 418 2691
Riken cDNA 6330403K07 6 1535 1496 522 321 1422 1450 1014 1043 1271 985 4696
Paternally expressed 3 682 918 885 810 631 705 1100 943 1012 820 598 2074
Regulated endocrine-specific protein 18 187 256 665 569 816 469 426 1062 938 535 390 3109
Ras-like without CAAX 2 284 221 206 286 215 120 234 652 419 169 180 933
Chromobox homolog 5 313 384 435 356 246 404 524 423 366 414 359 617
Table 5.
 
Candidate Optic Neuropathy Genes Expressed by RGCs
Table 5.
 
Candidate Optic Neuropathy Genes Expressed by RGCs
GLC1B
 NM_031100.1 Ribosomal protein L10 (Rpl10)
 NM_025379.1 Cytochrome c oxidase subunit VIIb (Cox7b)
 NM_175838.1 Eukaryotic translation elongation factor 1 alpha 1 (Eef1a1)
 NM_016774.1 ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit (Atp5b)
 NM_021261.1 Thymosin, beta 10 (Tmsb10)
 NM_017101.1 Peptidylprolyl isomerase A (cyclophilin A) (Ppia)
 NM_031099.1 Ribosomal protein L5 (Rpl5)
GLC1C
 NM_024351.1 Heat shock protein 8 (Hspa8)
 Rn.3357 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c, isoform 1
 NM_007951.1 Enhancer of rudimentary homologue (Drosophila) (Erh),
 Rn.1425 RAB7, member RAS oncogene family
 NM_053330.1 Ribosomal protein L21 (Rpl21)
 NM_012497.1 Aldolase C, fructose-biphosphate (Aldoc)
 NM_012963.1 High mobility group box 1 (Hmgb1)
 NM_030873.1 Profilin II (Pfn2)
 Rn.82741 Actin, beta
 NM_013067.1 Ribophorin I (Rpn1)
GLC1F
 CF978681 EST
 Rn.1463 Peptidylprolyl isomerase A (cyclophilin A)
 CF978691 EST
 NM_031113.1 Ribosomal protein S27a (Rps27a)
 NM_013216.1 Ras homologue enriched in brain (Rheb)
GLC1D
 NM_021697.1 Neuronal potassium channel alpha subunit (Kv8.1)
WFS2
 CF978606 EST
 NM_007410.1 Alcohol dehydrogenase 5 (class III), chi polypeptide (Adh5)
 NM_008015.1 Fibroblast growth factor inducible 14 (Fin14)
 NM_175838.1 Eukaryotic translation elongation factor 1 alpha 1 (Eef1a1)
 NM_145455.1 Similar to transcription factor BTF3 (RNA polymerase B transcription factor 3) (LOC218490)
SCABD
 NM_013226.1 Ribosomal protein L32 (Rpl32)
 Rn.999 Laminin receptor 1 (67kD, ribosomal protein SA)
 Rn.37758 Putative protein phosphatase 1 nuclear targeting subunit
 NM_008210.1 H3 histone, family 3A (H3f3a)
 NM_031100.1 Ribosomal protein L10 (Rpl10)
 Rn.2458 Class 1 beta-tubulin, complete cds
 Rn.82741 Actin, beta
 Mm.66 Ribosomal protein S4, X-linked
 NM_027148.1 RIKEN cDNA 2310032N20 gene (2310032N20Rik)
 NM_022891.1 Ribosomal protein L23 (Rpl23)
 NM_019678.1 Trk-fused gene (Tfg)
 NM_173119.1 Heat shock factor binding protein 1 (Hsbp1)
 NM_025592.2 Ribosomal protein L35 (Rpl35)
 Rn.880 Cytochrome c oxidase subunit Vla (liver)
 NM_029632.1 Protein phosphatase 1, regulatory (inhibitor) subunit 11 (Ppp1r11)
 NM_173102.1 Tubulin, beta 5 (Tubb5)
 NM_130823.1 ATPase, H+ transporting, lysosomal (vacuolar proton pump) 16 kDa (Atp6l)
 NM_017101.1 Peptidylprolyl isomerase A (cyclophilin A) (Ppia)
 NM_013663.2 Splicing factor, arginine/serine-rich 3 (SRp20) (Sfrs3)
 NM_031099.1 Ribosomal protein L5 (Rpl5)
 NM_013762.1 Ribosomal protein L3 (Rpl3)
 NM_000984.2 Homo sapiens ribosomal protein L23a (RPL23A)
 CF979103 EST
OPA4
 Mm.5163 Ras-like without CAAX/Rin
 NM_013721.1 Ribosomal protein L7a (Rpl7a)
 Rn.23878 ESTs, Weakly similar to elav-type RNA-binding protein 3
OPA2
 NM_031144.1 Actin, beta (Actb)
 NM_029814.1 RIKEN cDNA 2210412K09 gene (2210412K09Rik)
 NM_013226.1 Ribosomal protein L32 (Rpl32)
 Rn.999 Laminin receptor 1 (67kD, ribosomal protein SA)
 NM_012963.1 High mobility group box 1 (Hmgb1)
 NM_031683.1 SMC-like 1 (yeast) (Smc1l1)
 NM_008015.1 Fibroblast growth factor inducible 14 (Fin14)
 NM_013721.1 Ribosomal protein L7a (Rpl7a)
 NM_025449.1 Nicolin 1 (Nicn1)
 Rn.2890 Ribosomal protein S15a
 NM_027439.1 ATPase, H+ transporting, lysosomal interacting protein 1 (Atp6ip2)
 NM_172372.1 DNA segment, Chr X, Immunex 38, expressed (DXlmx38e)
 NM_000984.2 Homo sapiens ribosomal protein L23a (RPL23A)
ARTS
 NM_027870.1 ALEX3 protein (Alex3-pending)
 NM_139254.1 Tubulin, beta 3 (Tubb3)
 NM_008210.1 H3 histone, family 3A (H3f3a)
 NM_022934.1 DnaJ-like protein (Hsj2)
 NM_031119.1 Sjogren syndrome antigen B (Ssb)
 NM_022298.1 Alpha-tubulin (Tuba1)
 NM_012497.1 Aldolase C, fructose-biphosphate (Aldoc)
 NM_021766.1 Progesterone receptor membrane component 1 (Pgrmc1)
 NM_019979.1 Selenoprotein K (Selk-pending)
 NM_145629.1 Expressed sequence Al115446 (Al115446)
 Rn.1463 Peptidylprolyl isomerase A (cyclophilin A)
 NM_026007.2 RIKEN cDNA 2610301D06 gene (2610301D06Rik)
 NM_012570.1 Glutamate dehydrogenase 1 (Glud1)
 NM_024351.1 Heat shock protein 8 (Hspa8)
 Rn.2605 Thymosin beta-4
 NM_007951.1 Enhancer of rudimentary homologue (Drosophila) (Erh)
 NM_173119.1 Heat shock factor binding protein 1 (Hsbp1)
 Rn.1463 Peptidylprolyl isomerase A (cyclophilin A)
 NM_007451.2 Solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 (Slc25a5)
 CF978610 EST
 NM_053297.1 Pyruvate kinase, muscle (Pkm2)
 NM_023716.1 RIKEN cDNA 2410129E14 gene (2410129E14Rik)
 NM_017101.1 Peptidylprolyl isomerase A (cyclophilin A) (Ppia)
 NM_013762.1 Ribosomal protein L3 (Rpl3)
 NM_001696.2 Homo sapiens ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 1 (ATP6V1E1)
Supplemental Table 1
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