Description of Research Expertise

RESEARCH INTERESTS
Molecular Genetics of Inherited Blindness
Inherited retinal degenerations such as retinitis pigmentosa (RP) are common causes of blindness. The overall goals of our research program are to improve our understanding of the molecular bases of inherited retinal degenerations and related cilia disorders so that rational therapies can be developed for these diseases.

Key words: Cilia, gene targeting, photoreceptor cells, macular degeneration, next generation sequencing, proteomic analysis, retinal degeneration, retinitis pigmentosa, RP1, RNA splicing

DESCRIPTION OF RESEARCH
1. The Biology and Diseases of Photoreceptor Sensory Cilia
Cilia are present on most cells in the human body. These structures are typically sensory organelles, and are involved in many critical aspects of cell biology and development. The photoreceptor sensory cilium (PSC) elaborated by each rod and cone photoreceptor cell of the retina is a classic example (Figure 1). Consistent with the importance of cilia in biology, mutations in genes that encode cilia components are common causes of disease. Mutations that cause inherited retinal degenerations, which are common causes of blindness, have been identified in genes encoding more than 40 PSC proteins to date. These disorders are characterized by PSC dysfunction, followed by degeneration and death of the photoreceptor cells, resulting in loss of vision.



We are interested in studying how photoreceptor sensory cilia are built and maintained, and how these processes are disrupted in disease. For example, while there has been notable progress identifying the genetic causes of inherited retinal degenerations and other cilia disorders, the genes that harbor mutations which cause disease in half of patients with inherited retinal degeneration remain to be identified. To help understand PSCs better, and facilitate identification of new retinal degeneration disease genes, we performed a series of proteomic analyses to identify all of the proteins in mouse photoreceptor sensory cilia. The results show that PSCs are made of almost 2000 proteins, including ~1500 proteins not detected in cilia from lower organisms. This database of PSC proteins has already proved to be very useful. For example, in the past year we have used the list of genes that encode novel PSC proteins to help identify one confirmed and four potential new retinal degeneration disease genes.

Retinitis Pigmentosa 1
Part of our work on PSCs is focused on the retinitis pigmentosa 1 (RP1) protein. Mutations in RP1 are a common cause of dominant RP, which is the most common form of inherited retinal degeneration. Work in our lab has found that the RP1 protein is a photoreceptor microtubule-associated protein that is required for the correct formation of PSCs. We are now working to identify proteins that interact with RP1 in order to further define how it participates in PSC formation, and study how its mutations lead to photoreceptor cell death. We are also beginning to test potential therapies for RP1 disease, including gene augmentation therapy, in point mutation Rp1 knockin mice.

2. RNA Splicing Factor Retinitis Pigmentosa
Mutations in genes that encode the RNA splicing factors are common causes retinitis pigmentosa (RP). Despite their prevalence, the pathogenesis of these disorders is not understood. The splicing factors affected, pre-mRNA processing factor (PRPF) 3, PRPF8, PRPF31 are highly conserved components of the spliceosome, the complex which excises introns from nascent RNA transcripts to generate mature mRNAs. Since RNA splicing is required in all cells, it is not clear how mutations in these ubiquitous proteins lead to retina-specific disease. We hypothesize that mutations in these RNA splicing factors disrupt RNA splicing and lead to the generation of aberrant transcripts and proteins in the retina and other tissues, one or more of which are pathogenic in the retina. We have generated Prpf3 and Prpf8 knockin mice to investigate the pathogenesis of the RNA splicing factor forms of RP. We are now using exon microarray and next generation sequencing based transcriptome analyses to identify aberrant mRNAs that may be pathogenic in these disorders.

3. Inherited Macular Degeneration
Age-related macular degeneration (AMD) is one of the most common cause of vision loss in developed countries. The most characteristic clinical finding in the retinas of patients with AMD is drusen, or extracellular deposits of protein, lipid and debris that accumulate underneath the retinal pigment epithelium (RPE). At present, the etiology of drusen in AMD is not known, and there are only limited treatments are available to prevent the progression of AMD. In order to gain insight into the pathogenesis of AMD, we are studying an inherited form of macular degeneration called Doyne honeycomb retinal dystrophy (DHRD)/Malattia Leventinese (ML). Both DHRD and ML are caused by a single mutation, Arg-345 to Trp (R345W), in the EFEMP1 or Fibulin-3 gene. We have used gene targeting techniques to introduce this mutation into the Efemp1 gene of mice. We have found that the Efemp1-R345W knockin mice develop AMD-like deposits under their retinas, and are now using proteomic analyses to study the pathogenesis of these lesions.

4. Oligonucleotide-Directed Gene Targeting and Gene Correction
The fundamental premise of this project that oligodeoxynucleotides (ODNs) can be used to introduce sequence-specific alterations into the genomic DNA of stem cells. In mouse embryonic stem (ES) cells, the goal of ODN-mediated gene targeting is to create knock-in mouse models of human disease. In adult and induced pluripotent stem cells (iPS), the use of ODNs is directed toward the therapeutic correction of pathogenic mutations in human disease genes. Results generated from our research and from other investigators in the past several years have demonstrated proof of principle for this approach. We are workinng to build on these successes to develop strategies for broad application of ODN-mediated gene correction for the treatment of human disease and ODN-mediated gene targeting for the generation of mouse models of disease.


Techniques
Molecular biology, cell biology, proteomics, next generation sequencing, gene targeting to generate mouse models of disease.


Rotation Projects for 2009-2010
1. Investigation of the roles of novel PSC proteins in the formation, maintenance and function of photoreceptor cilia.
2. Transcriptome analyses of RNA samples from RNA splicing factor knockin mice
3. Tandem affinity purification analyses to identify proteins that interact with RP1 in vivo
4. Proteomic analyses of AMD-like deposits in Efemp1 mutant mice


Lab personnel:
Donna Garland, Ph.D. – Senior Research Investigator
Mike Farkas, Ph.D. – Postdoctoral Researcher
Robert Jinks, Ph.D. – Visiting Associate Professor
Qin Liu, M.D., Ph.D. – Research Assistant Professor
Yun Liu – Research Specialist
Suzanne Pavluk – Lab Manager
Alex Saveliev – Research Specialist
Qi Zhang, Ph.D. – Senior Research Investigator


Lab Address
F.M. Kirby Center for Molecular Ophthalmology
304-306 Stellar-Chance Labs

Description of Clinical Expertise

Inherited Retinal Degenerations and Ophthalmic Genetics