Of all the maladies known to man (and woman), from A to Z — abscess to zygomycosis — the gold standard Metabolic Basis for Inherited Diseases describes a good 11,000 of them. Several hundred of these condemn the human retina to diminished vision or outright blindness. The mutated genes that cause these diseases are mostly mysteries.

Best known, and most dreaded, of these sight-attacking entities are diabetic retinopathy — a leading cause of blindness — retinitis pigmentosa and age-related macular degeneration, which slowly destroys the central dimple, or fovea, in the retina, causing loss of visual acuity. So does Leber’s hereditary optic atrophy, a mitochondrial inheritance that strikes retinas in young male adults.

“There are two major layers to the retina,” explained research ophthalmologist and molecular geneticist Thaddeus Dryja. “One, the neural retina, has all the neurons that receive photons and process them into brain-directed signals. A neighboring retinal layer, the pigment epithelium, also in the central nervous system, occupies a support role. Some eye diseases,” Dryja went on, “preferentially affect the neural retina; others, the pigment epithelium.

“Certain eye diseases,” he continued, “impair central vision, which provides high visual acuity. Others reduce peripheral vision by altering the retina’s periphery. Genes already known are exclusively implicated in one or the other tissues that cause these diseases. An estimated 50,000 to 100,000 people in the U.S., one in 4,000, suffer from the progressive deteriorated vision of retinitis pigmentosa. Worldwide, the number is 1.5 million.”

Dryja directs the Ocular Molecular Genetics Institute at the Harvard-affiliated Massachusetts Eye and Ear Infirmary in Boston. He is senior author of a paper in the current Proceedings of the National Academy of Sciences (PNAS) dated Jan. 8, 2002. It’s titled: “Profile of the genes expressed in the human peripheral retina, macula and retinal pigment epithelium determined through serial analysis of gene expression (SAGE).”

Genzyme Molecular Oncology, of Framingham, Mass., owns the SAGE technology.

“The single overall advance reported in this article,” Dryja told BioWorld Today, “is that we now have for the first time a catalogue or library of the genes, their relevant expression levels in the retina, and separately in the retinal pigment epithelium.”

SAGE — Gene-Scanning Springboard’

“We’re finding more and more uses for this SAGE-derived data,” he continued, “which complements gene linkage analysis. In my own lab it’s a help to finding the genes that cause hereditary diseases of the retina. Most often they are expressed exclusively by the retinal tissue. This is a springboard to start scanning many of the genes we’ve identified. Many of them are genes we’ve never even known to be expressed in the retina. We don’t even know what they do, so there are lots of new pathways and functions there that are worth investigating about how the retina works.”

Dryja recounted how he and his co-authors conducted gene analysis on the healthy eyeballs of two patients, an 88-year-old woman and a man of 44, about to undergo surgery for cancer of the eye: “These cases had cancers that were surrounding their eyes, so the eyeballs had to come out. This gave us an opportunity to obtain very fresh tissues.

“As we reported in PNAS,” Dryja continued, “we analyzed two eyes of different ages, and saw some differences in gene expression. But with only two specimens it was hard to know if these were due to age differences or just two different individuals. So we’ll have to look at more eyes as we get them, to see which one of those possibilities proves valid.

“Another of the puzzles we were trying to figure out,” he added, “is why some disease hits one region worse than another site, and we figured if we had libraries of genes that are preferentially expressed in one region or another that could give us some clues. So that’s why we looked at SAGE.

“That entailed dissecting away the different regions of the retina from each other, making libraries of the tissues that we got from these different dissections, then cataloging the genes we found. It allowed us to enumerate and quantitate the messenger RNAs in those tissues. Of the 23,112 that were in the retina, we could assign 18,119 — 78 percent of them. Then when we went to the retinal pigment epithelium, which starts with 10,404, we could assign only 6,401 — 62 percent. What this meant was that 38 percent are genes no one has ever seen before.

“That’s just the messenger RNA transcripts,” Dryja pointed out. “We were able to assign most of them to known genes — uniGenes that are in a catalogue on the Internet. If we just count the ones we can definitely assign to uniGenes, in the retina we netted 18,119 of the 23,112, which we could definitely assign to known genes.”

How does Dryja square his gross number of 23,112 retinal genes with the 30,000 to 40,000 grand total of genes in the formally sequenced human genome?

“Other SAGE libraries, not just ours,” he noted, “are finding so many genes in a specialized tissue like the retina, that we wonder whether that estimate of 30,000 is correct. Whether it’s that our catalogues of the SAGE tags are overestimating the number of genes, or whether the master genome sequence analysis is underestimating — I don’t know which way it goes, but there seems to be discrepancy.” (See BioWorld Today, Dec. 19, 2001, p. 1.)

Biochemical Approach Or Gene Therapy?

“I’ve been studying diseased genes that affect the retina,” Dryja observed, “but there are hereditary diseases that affect other parts of the eye — cornea, lens, trabecular meshwork — that’s a tissue important in glaucoma — and the choroid. It will be valuable to have separate kinds of catalogues for these genes.

“As for potential clinical applications of this work,” he stated, “right now it’s disease-genes identification. Many retinal diseases are still unidentified. There could be 100 or 200 of them, and the key focus of my lab is to find them. That’s the main clinical value. We’re faced with either many years of study,” he concluded, “trying to figure out the biochemical mechanisms by which the gene defects cause these diseases, or with gene therapy approaches that are starting to show some success in the eyes of animal models.”