Leber Congenital Amaurosis Type 18 Gene Identified

Ricki Lewis, PhD

August 01, 2012

August 1, 2012 — Four independent research teams have described mutations in a gene known for its role in energy metabolism as the cause of the 18th recognized form of Leber congenital amaurosis (LCA), the most common type of childhood blindness.

The discovery, described in 4 articles published online July 29 in Nature Genetics, provides a starting point for developing treatments. Another form of LCA, caused by mutation in the RPE65 gene, has responded well to 2 approaches: gene therapy and administration of 9-cis-retinal to bypass the metabolic block.

From 30% to 50% of families with members clinically diagnosed with LCA have not been helped by genetic testing because their mutations have not yet been discovered, but the newly described form of LCA is distinctive: In addition to causing profound visual impairment from birth, the phenotype includes an apparently characteristic absence of photoreceptors, ganglion cells, and bipolar cells in the fovea, a condition called macular coloboma.

"Identifying this new gene whittles down the list of unknown inherited causes of LCA. This gene accounts for about 3% of cases of LCA," Jean Bennett, MD, PhD, professor of ophthalmology, cell and developmental biology at the University of Pennsylvania, Philadelphia, told Medscape Medical News. She led one of the LCA gene therapy trials and is already thinking about the approach for number 18. "We need to identify the retinal cell types in which NMNAT1 is expressed, and the level of expression, so that we can deliver the correct cDNA to the appropriate cells and at the appropriate levels."

LCA in total affects 2 or 3 children per 100,000 newborns. The mutations that cause the 17 other forms are in genes that affect development of the photoreceptors or the biochemical reactions of the visual cycle, including ciliary transport, phototransduction, and retinoid cycling.

Unlike the other LCA genes, the newly identified gene (nicotinamide adenine dinucleotide synthase [NMNAT1]) is widely expressed. It encodes nicotinamide mononucleotide adenylyltransferase 1, which catalyzes the reaction of nicotinamide mononucleotide with ATP to form NAD+. The enzyme is therefore a key component of the cellular respiration pathway.

Next-generation DNA and whole-exome sequencing made the discovery possible, with a large hint: In 2003, researchers had mapped the gene to part of chromosome 1 holding more than 50 genes.

A similar multistep strategy led the 4 separate research groups to the same gene. They began by sequencing the exomes of 1 or 2 probands who had had negative results on all mutation screens. Then the researchers deduced and narrowed down candidate genes, a task eased when 1 of the genes hailed from the previously highlighted chromosome 1 region.

The authors of the first article, led by Pei-Wen Chiang, PhD, director of the Molecular Diagnostic Laboratory at the Casey Eye Institute in Portland, Oregon, for example, sorted through 2460 DNA variations in the exome of the proband, then applied certain criteria. "It's rare, so variations must be novel. Secondly, because the boy is very severely affected, he must have at least 1 nonsense mutation. The third criterion is that it is recessive," Dr. Chiang told Medscape Medical News. That individuals with 2 nonsense mutations are not seen and that mouse knockouts are lethal indicate that it is a vital gene, he added.

The researchers in all 4 groups then identified mutations in affected relatives of the probands, identified the mutations in unrelated cases, and demonstrated absence of the mutations in control patients. The crystal structure of the protein revealed ways that specific mutations might disrupt function.

All 55 individuals studied had either 2 missense mutations (many compound heterozygotes) or 1 missense and 1 nonsense mutation. As expected because of the importance of the gene in cellular metabolism, cells of the patients have residual enzymatic activity. The fact that the retina has the highest metabolic rate in the body may make it especially sensitive to the enzyme deficit.

One mutation, Glu257Lys, is especially common and may indicate a European founder effect, based on analysis of the surrounding DNA.

In addition to its enzymatic role, the protein product of NMNAT1 appears to be a neuroprotectant. In mice, it is part of a fusion protein that prevents axonal degeneration after injury. This dual function may mean that supplementing NAD+ may not be sufficient. Supplementing NAD+ is a possible treatment mentioned in the article by Robert K. Koenekoop, MD, PhD, from the McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada, and colleagues, but another article, by Isabelle Perrault, MD, from the Department of Genetics, Institut National de la Sante et de la Recherche Medicale, Université Paris Descartes–Sorbonne Paris Cité, Imagine Institute, France, and colleagues expressed skepticism about the value of this approach.

The fourth article was by Marni Falk, MD, from the Department of Pediatrics, Division of Human Genetics and Division of Child Development and Metabolic Disease, Children’s Hospital of Philadelphia, and the University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, and colleagues

"These elegant studies extend our understanding of the causes of LCA. Clinicians caring for children with LCA and related diseases can now look forward to the development of genetic tests for early diagnosis," Shalom J. Kieval, MD, MBA, from RetinaCare Consultants in Albany, New York, told Medscape Medical News. Dr. Kieval was not involved in any of the studies published in Nature Genetics.

Full conflict of interest information is provided in the articles on the journal's Web site. Dr. Kieval has disclosed no relevant financial relationships.

Nat Genet. Published online July 29, 2012. Chiang abstract, Koenekoop abstract, Perrault abstract, Falk abstract