Abstract
BackgroundThe optic nerve is a pure white matter central nervous system (CNS) tract with an isolated blood supply, and is widely used in physiological studies of white matter response to various insults. We examined the gene expression profile of human optic nerve (ON) and, through the NEIBANK online resource, to provide a resource of sequenced verified cDNA clones. An un-normalized cDNA library was constructed from pooled human ON tissues and was used in expressed sequence tag (EST) analysis. Location of an abundant oligodendrocyte marker was examined by immunofluorescence. Quantitative real time polymerase chain reaction (qRT-PCR) and Western analysis were used to compare levels of expression for key calcium channel protein genes and protein product in primate and rodent ON.ResultsOur analyses revealed a profile similar in many respects to other white matter related tissues, but significantly different from previously available ON cDNA libraries. The previous libraries were found to include specific markers for other eye tissues, suggesting contamination. Immune/inflammatory markers were abundant in the new ON library. The oligodendrocyte marker QKI was abundant at the EST level. Immunofluorescence revealed that this protein is a useful oligodendrocyte cell-type marker in rodent and primate ONs. L-type calcium channel EST abundance was found to be particularly low. A qRT-PCR-based comparative mammalian species analysis reveals that L-type calcium channel expression levels are significantly lower in primate than in rodent ON, which may help account for the class-specific difference in responsiveness to calcium channel blocking agents. Several known eye disease genes are abundantly expressed in ON. Many genes associated with normal axonal function, mRNAs associated with axonal transport, inflammation and neuroprotection are observed.ConclusionWe conclude that the new cDNA library is a faithful representation of human ON and EST data provide an initial overview of gene expression patterns in this tissue. The data provide clues for tissue-specific and species-specific properties of human ON that will help in design of therapeutic models.
Highlights
The optic nerve is a pure white matter central nervous system (CNS) tract with an isolated blood supply, and is widely used in physiological studies of white matter response to various insults
A total of 4651 quality 5' reads from the library yielded 4269 clones after removal of contaminants and very short sequences and masking of repetitive sequences. Analysis of these clones using GRIST [10] resulted in identification of 2789 groups of clones, each potentially representing individual optic nerve (ON) expressed genes. 375 of these groups contained two or more clones. These results enable us to generate a 'first pass' analysis of about the relative expression of the more common genes, and allow us to compare characteristics of different CNS white matter libraries
The remainder consists of singleton clones, many of which represent longer 3' UTRs of known genes, sequences not include in RefSeq, sequences with high Phred quality scores that have insufficiently good sequence to give a reliable match, and clones from intron and intergenic regions
Summary
The optic nerve is a pure white matter central nervous system (CNS) tract with an isolated blood supply, and is widely used in physiological studies of white matter response to various insults. We examined the gene expression profile of human optic nerve (ON) and, through the NEIBANK online resource, to provide a resource of sequenced verified cDNA clones. An unnormalized cDNA library was constructed from pooled human ON tissues and was used in expressed sequence tag (EST) analysis. The optic nerve (ON) is an isolated CNS tract, supplied by a separate vasculature, that connects the eye to the rest of the central nervous system (CNS). The ON is one of the few areas that a pure CNS white matter tract is readily available for analysis, providing a window into in-vivo CNS axonal function. The ON provides a near-ideal tool for identifying axonally transported mRNAs; a newly described neuronal function [4,5]
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