Autosomal dominant retinitis pigmentosa mapping to chromosome 7p exhibits variable expression

Genetic modifiers and oligogenic inheritance

Despite remarkable progress in the identification of mutations that drive genetic disorders, progress in understanding the effect of genetic background on the penetrance and expressivity of causal alleles has been modest, in part because of the methodological challenges in identifying genetic modifiers. Nonetheless, the progressive discovery of modifier alleles has improved both our interpretative ability and our analytical tools to dissect such phenomena. In this review, we analyze the genetic properties and behaviors of modifiers as derived from studies in patient populations and model organisms and we highlight conceptual and technological tools used to overcome some of the challenges inherent in modifier mapping and cloning. Finally, we discuss how the identification of these modifiers has facilitated the elucidation of biological pathways and holds the potential to improve the clinical predictive value of primary causal mutations and to develop novel drug targets.

Hypoxia-regulated components of the U4/U6.U5 tri-small nuclear riboprotein complex: possible role in autosomal dominant retinitis pigmentosa

PURPOSE

High oxygen consumption and cyclical changes related to dark-adaptation are characteristic of the outer retina. Oxygenation changes may contribute to the selective vulnerability of the retina in retinitis pigmentosa (RP) patients, especially for those forms involving genes with global cellular functions. Genes coding for components of the U4/U6.U5 tri small nuclear ribonucleoprotein (tri-snRNP) complex of the spliceosome stand out, because mutations in four genes cause RP, i.e., RP9 (PAP1), RP11 (PRPF31), RP13 (PRPF8), and RP18 (PRPF3), while there is no degeneration outside the retina despite global expression of these genes. With the assumption that variable oxygenation plays a role in RP forms related to pre-mRNA splicing and the retina and brain are similar, we searched a data collection of ischemia-hypoxia regulated genes of the brain for oxygen regulated genes of the U4/U6.U5 tri-snRNP complex.

METHODS

A database of ischemia-hypoxia response (IHR) genes in the brain was generated from gene expression profiling studies [n=24]. Public databases (NCBI) were searched for RP genes with global function that are expressed in the brain. From the IHR gene list, we extracted genes that were directly related to retinal degeneration through a listed mutation (OMIM, Retnet, RISN). The database was then examined for indirect links to RP forms affecting the U4/U6.U5 tri-snRNP complex by searching for IHR genes contributing to this complex. Potential expression of matched genes in the retina was ascertained using NEIBank. Immunohistochemistry was used to localize a selected protein of the U4/U6.U5 tri-snRNP complex in cynomolgus monkey and human retina specimens.

RESULTS

The approach identified genes that cause retinal degeneration (CNGB1, SEMA4A, RRG4) or developmental changes (SOX2) when mutated. One IHR gene, Pim1, is the immediate binding partner for PAP1 (RP9). Three IHR genes linked the U4/U6.U5 tri-snRNP complex to regulation by oxygenation: PRPF4; SART1, also known as 110 kDa SR-related protein of the U4/U6.U5 tri-snRNP or as hypoxia associated factor (HAF); and LSM8, U6 snRNA-associated Sm-like protein. The 110 kDa SR-related protein was localized in all retinal cells including photoreceptors.

CONCLUSIONS

Regulation by changes in oxygenation within the U4/U6.U5 tri-snRP complex could be particularly important for photoreceptors where oxygen consumption follows a circadian rhythm. If the U4/U6.U5 tri-snRP complex is already impaired by mutations in any of the four genes causing RP, it may be unable to follow properly the physiological demands of oxygenation which are mediated by the four hypoxia-regulated proteins emerging in this study. Selective vulnerability may involve complex combinations of widely expressed genes, specific cellular functions and local energy availability.

Pre-mRNA splicing and retinitis pigmentosa

Retinitis pigmentosa (RP) is a group of genetically and clinically heterogeneous retinal diseases and a common cause of blindness. Among the 12 autosomal dominant RP (adRP) genes identified, four encode ubiquitously expressed proteins involved in pre-mRNA splicing, demonstrating the important role that pre-mRNA splicing plays in the pathogenesis of retinal degeneration. This review focuses on recent progress in identifying adRP mutations in genes encoding pre-mRNA splicing factors and the potential underlying molecular mechanisms.

[Genetics of retinitis pigmentosa: metabolic classification and phenotype/genotype correlations]

Retinitis pigmentosa (RP, prevalence 1/4000) is a set of hereditary retinal dystrophies characterized by pigment deposits in fundus and progressive death of photoreceptors, always associated with the alteration of retinal pigment epithelium. Genetic heterogeneity of the typical nonsyndromic form (rod cone dystrophy) is extensive: 11 genes and one locus were reported for autosomal dominant RP, 17 genes and five loci for autosomal recessive RP, and two genes and two loci for X-linked RP. A survey of mutation screening reports in large series of patients indicates that the frequency of mutations for all cloned genes varies from 40% to 54% of cases in autosomal dominant RP, from 17% to 24% in autosomal recessive RP (excluding the USH2A gene for which the values remain uncertain) and from 61% to 89% in X-linked RP. Very few studies report on sporadic cases except for the two X-linked genes, RP2 and RPGR, which account for 29% of sporadic cases in males. Altogether, the two most frequently involved genes are RPGR (13% of all RP cases) and RHO (4%), an important consideration for molecular diagnosis. Finally, we roughly estimate that currently known genes do not represent more than 50% of RP cases, suggesting that many genes remain to be discovered. The known genes can be classified into metabolic groups according to the encoded protein: visual transduction, visual cycle, transcription factors, structural proteins, spliceosome complex and cellular traffic, indicating the high level of specialization of photoreceptors and of the retinal pigment epithelium. In parallel with this classification, genotype/phenotype correlations have been established that will help ophthalmologists to suspect particular genes, and thereby mechanisms. This approach will provide better informations to patients and will orient the choice of future therapies.

ENU-induced late-onset night blindness associated with rod photoreceptor cell degeneration in zebrafish

We describe a dominant mutation, night blindness d (nbd), that causes late-onset rod photoreceptor cell degeneration in zebrafish. The mutation was induced by treating male zebrafish with N-ethyl-N-nitrosourea (ENU). Visual sensitivity was tested using a behavioral assay based on a visually mediated escape response. At a young age, the heterozygous (nbd+/-) fish did not show any signs of night blindness or retinal degeneration. At 2 years, their behaviorally assessed visual sensitivity was decreased, albeit no alterations in the electroretinogram (ERG) were detected. Histology revealed that in the mutant retinas the rod photoreceptor cell outer segments (ROS) were thinned out. In homozygous larvae (nbd-/-), mass neural degeneration was detectable at about 2 days post fertilization (dpf). They died at an early age, usually no later than 8 dpf. In conclusion, nbd is a dominant mutation that causes late-onset night blindness with slow progression. However, nbd is not photoreceptor cell-specific, as becomes clear from the systemic dysfunctions of the homozygous larvae.

PROGRESSTOWARDUNDERSTANDING THEGENETIC ANDBIOCHEMICALMECHANISMS OFINHERITEDPHOTORECEPTORDEGENERATIONS

More than 80 genes associated with human photoreceptor degenerations have been identified. Attention must now turn toward defining the mechanisms that lead to photoreceptor death, which occurs years to decades after the birth of the cells. Consequently, this review focuses on topics that offer insights into such mechanisms, including the one-hit or constant risk model of photoreceptor death; topological patterns of photoreceptor degeneration; mutations in ubiquitously expressed splicing factor genes associated only with photoreceptor degeneration; disorders of the retinal pigment epithelium; modifier genes; and global gene expression analysis of the retina, which will greatly increase our understanding of the downstream events that occur in response to a mutation.

Clinical characterization, linkage analysis, and PRPC8 mutation analysis of a family with autosomal dominant retinitis pigmentosa type 13 (RP13)

A Dutch family with autosomal dominant retinitis pigmentosa (adRP) displayed a phenotype characterized by an early age of onset, a diffuse loss of rod and cone sensitivity, and constricted visual fields (type I). One male showed a mild progression of the disease. Linkage analysis showed cosegregation of the genetic defect with markers from chromosome 17p13.1-p13.3, a region overlapping the RP13 locus. The critical interval of the RP locus as defined in this family was flanked by D17S926 and D17S786, with a maximal lod score of 4.2 (theta = 0.00) for marker D17S1529. Soon after the mapping of the underlying defect to the 17p13 region, a missense mutation (6970G>A; R2310K) was identified in exon 42 of the splicing factor gene PRPC8 in one patient of this family. Diagnostic restriction enzyme digestion of exon 42 amplified from genomic DNA of all family members revealed that the R2310K mutation segregated fully with the disease. The type I phenotype observed in this family is similar to that described for three other RP13 families with mutations in PRPC8.

A human homolog of yeast pre-mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11)

We report mutations in a gene (PRPF31) homologous to Saccharomyces cerevisiae pre-mRNA splicing gene PRP31 in families with autosomal dominant retinitis pigmentosa linked to chromosome 19q13.4 (RP11; MIM 600138). A positional cloning approach supported by bioinformatics identified PRPF31 comprising 14 exons and encoding a protein of 499 amino acids. The level of sequence identity to the yeast PRP31 gene indicates that PRPF31 is also likely to be involved in pre-mRNA splicing. Mutations that include missense substitutions, deletions, and insertions have been identified in four RP11-linked families and three sporadic RP cases. The identification of mutations in a pre-mRNA splicing gene implicates defects in the splicing process as a novel mechanism of photoreceptor degeneration.

Retinitis pigmentosa: defined from a molecular point of view

Retinitis pigmentosa (RP) denotes a group of hereditary retinal dystrophies, characterized by the early onset of night blindness followed by a progressive loss of the visual field. The primary defect underlying RP affects the function of the rod photoreceptor cell, and, subsequently, mostly unknown molecular and cellular mechanisms trigger the apoptotic degeneration of these photoreceptor cells. Retinitis pigmentosa is very heterogeneous, both phenotypically and genetically. In this review we propose a tentative classification of RP based on the functional systems affected by the mutated proteins. This classification connects the variety of phenotypes to the mutations and segregation patterns observed in RP. Current progress in the identification of the molecular defects underlying RP reveals that at least three distinct functional mechanisms may be affected: 1) the daily renewal and shedding of the photoreceptor outer segments, 2) the visual transduction cascade, and 3) the retinol (vitamin A) metabolism. The first group includes the rhodopsin and peripherin/RDS genes, and mutations in these genes often result in a dominant phenotype. The second group is predominantly associated with a recessive phenotype that results, as we argue, from continuous inactivation of the transduction pathway. Disturbances in the retinal metabolism seem to be associated with equal rod and cone involvement and the presence of deposits in the retinal pigment epithelium.

Evidence that the penetrance of mutations at the RP11 locus causing dominant retinitis pigmentosa is influenced by a gene linked to the homologous RP11 allele

A subset of families with autosomal dominant retinitis pigmentosa (RP) display reduced penetrance with some asymptomatic gene carriers showing no retinal abnormalities by ophthalmic examination or by electroretinography. Here we describe a study of three families with reduced-penetrance RP. In all three families the disease gene appears to be linked to chromosome 19q13.4, the region containing the RP11 locus, as defined by previously reported linkage studies based on five other reduced-penetrance families. Meiotic recombinants in one of the newly identified RP11 families and in two of the previously reported families serve to restrict the disease locus to a 6-cM region bounded by markers D19S572 and D19S926. We also compared the disease status of RP11 carriers with the segregation of microsatellite alleles within 19q13.4 from the noncarrier parents in the newly reported and the previously reported families. The results support the hypothesis that wild-type alleles at the RP11 locus or at a closely linked locus inherited from the noncarrier parents are a major factor influencing the penetrance of pathogenic alleles at this locus.

Evidence for a major retinitis pigmentosa locus on 19q13.4 (RP11) and association with a unique bimodal expressivity phenotype

Retinitis pigmentosa (RP) is the name given to a heterogeneous group of retinal degenerations mapping to at least 16 loci. The autosomal dominant form (ARP), accounting for approximately 25% of cases, can be caused by mutations in two genes, rhodopsin and peripherin/RDS, and by at least six other loci identified by linkage analysis. The RP11 locus for adRP has previously been mapped to chromosome 19q13.4 in a large English family. This linkage has been independently confirmed in a Japanese family, and we now report three additional unrelated linked U.K. families, suggesting that this is a major locus for RP. Linkage analysis in the U.K. families refines the RP11 interval to 5 cM between markers D19S180 and AFMc001yb1. All linked families exhibit incomplete penetrance; some obligate gene carriers remain asymptomatic throughout their lives, whereas symptomatic individuals experience night blindness and visual field loss in their teens and are generally registered as blind by their 30s. This "bimodal expressivity" contrasts with the variable-expressivity RP mapping to chromosome 7p (RP9) in another family, which has implications for diagnosis and counseling of RP11 families. These results may also imply that a proportion of sporadic RP, previously assumed to be recessive, might result from mutations at this locus.

Retinal photoreceptor dystrophies LI. Edward Jackson Memorial Lecture

PURPOSE

To assess the state of knowledge of photoreceptor dystrophies.

METHODS

The current literature concerning photoreceptor dystrophies is reviewed, and their potential impact on concepts of pathogenesis of disease and clinical practice is assessed.

RESULTS

As a result of cooperative investigative work between researchers in various disciplines, major advances in the classification of retinal photoreceptor dystrophies have been made. Until recently, classification of retinal dystrophies was based on clinical observation alone, and it was evident that this method was imprecise and of limited value. Largely through the work of molecular biologists, it has been shown that diseases clinically indistinguishable from one another may be a result of mutations on a variety of genes; conversely, different mutations on a single gene may give rise to a variety of phenotypes. It is reassuring that it is possible to generate concepts as to potential pathogenetic mechanisms that exist in retinal dystrophies in light of this new knowledge. More important for the clinician is the potential impact on clinical practice. There is as yet no therapy by which the course of most of these disorders can be modified. However, there is a considerable body of work in which therapeutic intervention is being explored, and many researchers now see treatment as a justifiable objective of their work.

CONCLUSIONS

Knowledge of the causative mutation is of value to the clinician in that it provides a precise diagnosis and allows the distribution of the abnormal gene to be documented fully within a family. To take full advantage of the opportunities provided by current research, clinical practice will have to be modified, particularly if therapy can be justified.