Candidate genes for chromosomes 6 and 10 quantitative trait loci for age-related retinal degeneration in mice.

PURPOSE: In a previous study, several quantitative trait loci (QTL) that influence age-related degeneration (ageRD) were identified in a cross between the albino strains B6(Cg)-Tyr(c-2J)/J (B6a) and BALB/cByJ (C). The Chromosome (Chr) 6 and Chr 10 QTL were the strongest and most highly significant loci and both involved B6a protective alleles. The QTL were responsible for 21% and 9% of the variance in phenotypes, respectively. We focused on these two QTL to identify candidate genes. METHODS: DNA microarrays were used for the two mouse strains at four and eight months of age to identify genes that are differentially regulated and map to either QTL. Gene Ontology (GO) analysis of the differentially expressed genes was performed to identify possible processes and pathways associated with ageRD. To identify additional candidates, database analyses (Positional Medline or PosMed) were used. Based on differential expression, PosMed, and the presence of reported polymorphisms, five genes per QTL were selected for further study by sequencing analysis and qRT-PCR. Tumor necrosis factor, alpha- induced protein 3 (Tnfaip3; on a C57BL/6J (B6) background) was phenotypically tested. Single nucleotide polymorphisms (SNPs) flanking this gene were correlated with outer nuclear layer thickness (ONL), and eight-month-old Tnfaip3(+/-) mice were tested for ageRD. RESULTS: Polymorphisms were found in the coding regions of eight genes. Changes in gene expression were identified by qRT-PCR for Hexokinase 2 (Hk2) and Docking protein 1 (Dok1) at four months and for Dok1 and Tnfaip3 at eight months. Tnfaip3 was selected for phenotypic testing due to differential expression and the presence of two nonsynonymous mutations. However, when ONL thickness was compared in eight-month-old congenic Tnfaip3(+/-) and Tnfaip3(+/+) mice, no differences were found, suggesting that Tnfaip3 is not the quantitative trait gene (QTG) for the Chr 10 QTL. The GO analysis revealed that GO terms associated with stress and cell remodeling are overrepresented in the ageRD-sensitive C strain compared with the B6a strain with age (eight months). In the ageRD-resistant B6a strain, compared with the C strain, GO terms associated with antioxidant response and the regulation of blood vessel size are overrepresented with age. CONCLUSIONS: The analyses of differentially expressed genes and the PosMed database yielded candidate genes for the Chr 6 and Chr 10 QTL. HtrA serine peptidase 2 (Htra2), Dok1, and Tnfaip3 were deemed most promising because of their known roles in apoptosis and our finding of nonsynonymous substitutions between B6a and C strains. While Tnfaip3 was excluded as the QTG for the Chr 10 QTL, Dok1 and Htra2 remain good candidates for the Chr 6 QTL. Finally, the GO term analysis further supports the general hypothesis that oxidative stress is involved in ageRD.

Loss of the metalloprotease ADAM9 leads to cone-rod dystrophy in humans and retinal degeneration in mice.

Cone-rod dystrophy (CRD) is an inherited progressive retinal dystrophy affecting the function of cone and rod photoreceptors. By autozygosity mapping, we identified null mutations in the ADAM metallopeptidase domain 9 (ADAM9) gene in four consanguineous families with recessively inherited early-onset CRD. We also found reduced photoreceptor responses in Adam9 knockout mice, previously reported to be asymptomatic. In 12-month-old knockout mice, photoreceptors appear normal, but the apical processes of the retinal pigment epithelium (RPE) cells are disorganized and contact between photoreceptor outer segments (POSs) and the RPE apical surface is compromised. In 20-month-old mice, there is clear evidence of progressive retinal degeneration with disorganized POS and thinning of the outer nuclear layer (ONL) in addition to the anomaly at the POS-RPE junction. RPE basal deposits and macrophages were also apparent in older mice. These findings therefore not only identify ADAM9 as a CRD gene but also identify a form of pathology wherein retinal disease first manifests at the POS-RPE junction.

A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

PURPOSE: To investigate the genetic basis of autosomal recessive retinal degeneration in a large consanguineous family from Pakistan. METHODS: Ophthalmic examinations were conducted on family members to establish their diagnosis. Genomic DNA extracted from peripheral blood was used for homozygosity mapping to discover the chromosomal region that harbors the defective gene. Direct sequence analysis and restriction enzyme digestion were used to identify and confirm the defect in the gene. RESULTS: There were three affected siblings in the family, each with limited peripheral vision and impaired visual acuity. We established linkage to a region on chromosome 2 that encompasses the RP26 locus. Upon sequencing the ceramide kinase-like (CERKL) gene, which is mutated in the original RP26 family, we identified a C>A transversion in exon 2 (c.316C>A) that substitutes an arginine residue with a serine (p.R106S) in the conserved nuclear localization signal sequence (KLKRR) of the protein. This mutation segregated with retinal degeneration in the Pakistani family and was not observed in the DNA of 174 ethnically matched unaffected controls. CONCLUSIONS: This is the third reported mutation in CERKL causing retinal degeneration but is the first report to show that a single amino acid change in CERKL, rather than a null mutation, can cause retinal disease. Although the function of CERKL is still unknown, the mutation described herein confirms that the nuclear localization signal sequence is important in the physiologic function of the protein.

Genetic modifiers of retinal degeneration in the rd3 mouse.

PURPOSE: In previous studies of light-induced (LRD) and age-related (ageRD) retinal degeneration (RD) between the BALB/cByJ (BALB) and B6(Cg)-Tyr(c-2J)/J (B6a) albino mouse strains, RD-modifying quantitative trait loci (QTLs) were identified. After breeding BALB- and B6a-rd3/rd3 congenic strains and finding significant differences in RD, an F1 intercross to determine rd3 QTLs that influence this inherited RD was performed. METHODS: N10, F2 BALB- and B6a-rd3/rd3 strains were measured for retinal outer nuclear layer (ONL) thickness from 5 to 12 weeks of age. Since 10 weeks showed significant differences in the ONL, F2 progeny from an F1 intercross were measured for ONL thickness. F2 DNAs were genotyped for SNPs by the Center for Inherited Disease Research. Correlation of genotype with phenotype was made with Map Manager QTX. RESULTS: One hundred forty-eight SNPs approximately 10 cM apart were typed in the F2 progeny and analyzed. Significant QTLs were identified on chromosomes (Chrs) 17, 8, 14, and 6 (B6a alleles protective) and two on Chr 5 (BALB alleles protective). Suggestive QTLs were found as well. For the strongest QTLs, follow-up SNPs were analyzed to narrow the critical intervals. Additional studies demonstrated that rd3 disease is exacerbated by light but not protected by the absence of rhodopsin regeneration. CONCLUSIONS: QTLs were identified that modulate rd3-RD. These overlapped some QTLs from previous ageRD and LRD studies. The presence of some of the same QTLs in several studies suggests partial commonality in RD pathways. Identifying natural gene/alleles that modify RDs opens avenues of study that may lead to therapies for RD diseases.

Influence of a quantitative trait locus on mouse chromosome 19 to the light-adapted electroretinogram.

PURPOSE: Both implicit time and amplitude of the cone-mediated electroretinographic (ERG) b-wave differ significantly between the C57BL/6JOlaHsd and 129S2/SvHsd inbred mouse strains. The purpose of this work was to undertake a quantitative genetics study to localize the gene or genes involved. METHODS: Implicit time and amplitude of the a- and b-waves of the single-flash and flicker cone-mediated ERG were recorded as the quantitative traits in reciprocal backcrossed populations. A genome-wide scan was performed with 106 polymorphic markers. Map Manager (release QTXb20) was used to analyze the data and make phenotype-genotype correlations. RESULTS: A quantitative trait locus (QTL) of major effect in controlling variation in both implicit time and amplitude of the cone-mediated ERG localized to the middle of chromosome 19. CONCLUSIONS: Mapping of a QTL influencing both implicit time and b-wave amplitude of the light-adapted ERG represents an initial step toward identifying the gene(s) responsible for this phenotypic variation.

Association of the Asn306Ser variant of the SP4 transcription factor and an intronic variant in the beta-subunit of transducin with digenic disease.

PURPOSE: SP4 is a transcription factor abundantly expressed in retina that binds to the GC promoter region of photoreceptor signal transduction genes. We have previously shown that SP4 may be involved in the transcriptional activation of these genes alone or together with other transcription factors such as SP1, neural retina leucine zipper protein (NRL), and cone-rod homeobox gene (CRX). Since mutations in NRL and CRX are involved in inherited retinal degenerations, SP4 was considered a good candidate for mutation screening in patients with this type of diseases. The purpose of this work, therefore, was to investigate possible mutations in SP4 in a cohort of patients affected with different forms of retinal degenerations. METHODS: 270 unrelated probands with various forms of retinal degeneration including autosomal dominant and autosomal recessive retinitis pigmentosa (RP), autosomal dominant and autosomal recessive cone-rod dystrophy (CRD), and Leber's congenital amaurosis (LCA), were screened for mutations in the SP4 gene. Single strand conformation polymorphism (SSCP) analysis was performed on the six SP4 gene exons including flanking regions followed by direct sequencing of SSCP variants. RESULTS: Nine different sequence variants were found in 29 patients, four in introns and five in exons. Many of the probands were previously screened for mutations in the genes encoding the alpha-, beta- and gamma-subunits of rod-specific cGMP phosphodiesterase (PDE6A, PDE6B, PDE6G), the beta-subunit of rod-specific transducin (GNB1), and peripherin/rds (RDS). One group of seven probands of Hispanic background that included five with arRP, one with RP of unknown inheritance (isolate) and 1 with arCRD carried an Asn306Ser mutation in SP4. Of the seven, the isolate case was homozygous and the other 6 heterozygous for the variant. Two arRP and the arCRD probands carried an additional intronic GNB1 variant. DNA from the family members of the arCRD proband could not be obtained, but for the other two families, all affected members and none of the unaffected carried both the SP4 Asn306Ser allele and the GNB1 intronic variant. CONCLUSIONS: If mutations in SP4 do cause retinal degenerative disease, their frequency would be low. While digenic disease with the SP4 Asn306Ser and the GNB1 intronic variant alleles has not been established, neither has it been ruled out. This leaves open the possibility of a cooperative involvement of SP4 and GNB1 in the normal function of the retina.

Disruption of the gene encoding the beta1-subunit of transducin in the Rd4/+ mouse.

PURPOSE: The Rd4/+ mouse inherits an autosomal dominant retinal degeneration that cosegregates with a large inversion spanning nearly all of mouse chromosome 4 (Chr 4). This inversion is homozygous lethal. The hypothesis for the study was that disruption of a gene at one of the two breakpoints in the Rd4 chromosome is responsible for the retinal degeneration. The purpose was to identify the disrupted gene. METHODS: Genotyping was performed by PCR and gel electrophoresis. The Rd4/+ phenotype was confirmed by ERG. Fluorescence in situ hybridization (FISH) analysis was performed with bacterial artificial chromosome (BAC) probes. Northern and quantitative PCR procedures were used to evaluate Gnb1 mRNA expression. Protein expression was measured by Western blot. RESULTS: To identify the Rd4 gene defect, the breakpoints were first localized with a testcross and the locus refined by using FISH. Genetic testcross data revealed that the inversion breakpoints are located within a few centimorgans of both the telomeric and centromeric ends of Chr 4. Initial FISH analysis showed the proximal breakpoint of the inversion to be in the centromere itself. Therefore, we focused on the distal breakpoint and found that it lies in the second intron of the gene Gnb1, coding for the transducin beta1-subunit (Tbeta1) protein that is directly involved in the response to light of rod photoreceptors. Before the beginning of retinal degeneration in Rd4/+ retina, the levels of Gnb1 mRNA and Tbeta1 protein are 50% of those in wild-type retina. CONCLUSIONS: The results suggest that disruption of the Gnb1 gene is responsible for Rd4 retinal disease.

Constant light-induced retinal damage and the RPE65-MET450 variant: assessment of the NZW/LacJ mouse.

PURPOSE: In a previous constant light-induced retinal damage (CLD) quantitative genetics study between the albino C57BL/6J-c2J (B6al) and BALB/c mouse strains, we identified a very strong and highly significant quantitative trait locus (QTL) on distal Chr 3 that we associated with a variant of the Rpe65 gene. The B6al strain carries the MET450 variant of RPE65 and is resistant to CLD while the BALB/c strain carries the LEU450 variant and is sensitive. Since then, we have discovered that the NZW/LacJ (NZW) albino mouse strain is sensitive to CLD but carries the MET450 variant of RPE65. The purpose of this study was to determine if the NZW mouse disproves the hypothesis that the MET450 variant of RPE65 protects the mouse retina against constant light-induced retinal damage. METHODS: F2 progeny were bred from an intercross between the NZW/LacJ and B6al mouse strains. After a prolonged exposure to moderate constant light, F2 mice were phenotyped for retinal outer nuclear layer thickness as the quantitative trait. A subset of 156 of the 201 F2 mice was genotyped for a set of markers spanning the genome, and any marker with a significant association with the quantitative trait was genotyped in the remaining 45 F2s. Data were analyzed for QTL by the Map Manager QTX software. RESULTS: No QTL was identified at distal Chr 3, although several QTL on Chrs 1 (two), 10, 13, 14, 16, and X were detected. One QTL on middle Chr 1 (LOD 5.22) mapped to the same location of a QTL (LOD 6.8) in a previous intense, short exposure light-induced retinal damage study conducted with an intercross between the 129S1/SvImJ and BALB/c strains. QTL on Chrs 1 (distal), 10, and 14 also appeared in other retinal damage quantitative genetics studies. Three pairs of genes exhibited significant epistatic effects. Two of the pairs involved synergistic interactions between NZW and B6al alleles, and the third between two B6al alleles. CONCLUSIONS: If another gene besides Rpe65 was responsible for the QTL in the original BALB/c x B6al study, and the NZW mouse carried a light sensitive allele of this gene, a QTL should have been present in this study. Since a QTL on Chr 3 was not found, the hypothesis that RPE65-MET450 protects the retina from constant light-induced damage is left intact. The explanation for the NZW mouse being sensitive to constant light while carrying the RPE65-MET450 variant is that other light sensitive QTL (gene alleles) negate the protective effect.

A substitution of G to C in the cone cGMP-phosphodiesterase gamma subunit gene found in a distinctive form of cone dystrophy.

OBJECTIVE: To identify genes responsible for cone dystrophies and determine the functional consequences of their underlying mutations. DESIGN: Case-control study. PARTICIPANTS: Two hundred forty unrelated patients diagnosed with cone dystrophy, cone-rod dystrophy, macular dystrophy, macular degeneration, or Stargardt disease, 95 control individuals, and 2 unrelated families with a distinctive type of cone dystrophy. METHODS: The DNAs of the 240 probands were screened for sequence variants in the PDE6H gene (that encodes the inhibitory gamma-subunit of cone cyclic guanosine monophosphate [cGMP]-phosphodiesterase [PDE]) by single-strand conformation polymorphism electrophoresis. The effect of a nucleotide substitution in the DNA of a patient on gene expression efficiency was analyzed by in vitro transcription/translation. MAIN OUTCOME MEASURES: Cone-specific gene variants, fundus, visual field and electroretinogram (ERG) findings, and protein synthesis efficiency. RESULTS: We found a heterozygous G to C substitution in the 5' untranslated region (UTR) of the PDE6H gene in the DNA of a patient with a distinctive form of cone dystrophy, her sibling, and their father. This rare form of disease is very different in manifestation from other cone dystrophies and has been described as "cone dystrophy with nyctalopia and supernormal rod responses," "cone dystrophy with supernormal scotopic ERGs" and "supernormal and delayed rod ERG syndrome." Among the 240 patients that we studied, only 1 proband had the G to C variant. Furthermore, none of the 95 controls used in this study had this nucleotide change. We also determined that the PDE6H variant was not present in another family affected with this particular type of cone dystrophy. Because the 5' UTR of mRNAs plays a critical role in the regulation of protein synthesis, we determined the effect of the G to C change in this process. By use of in vitro transcription/translation experiments, we demonstrated that this substitution could lead to an increase in PDE6H gene expression. CONCLUSIONS: Our results indicate that mutations in the PDE6H gene are not common, because only 1 of 240 patients with cone dystrophy showed a single nucleotide substitution in the 5' UTR of PDE6H mRNA that could be associated with the disease. If the effect of the G to C substitution we observed in vitro also occurs in vivo, it will lead to PDE6H overexpression in the photoreceptors. Excess of PDEgamma may affect normal cone cGMP-PDE function by inhibiting the catalytic PDEalpha,beta activity and lead to pathogenic elevation of cGMP and eventual degeneration of cone photoreceptors.

New retinal light damage QTL in mice with the light-sensitive RPE65 LEU variant.

The purpose of this study was to determine the QTL that influence acute, light-induced retinal degeneration differences between the BALB/cByJ and 129S1/SvImJ mouse strains. Five- to 6-week-old F(2) progeny of an intercross between the two strains were exposed to 15,000 LUX of white light for 1 h after their pupils were dilated, placed in the dark for 16 h, and kept for 10-12 days in dim cyclic light before retinal rhodopsin was measured spectrophotometrically. This was used as the quantitative trait for retinal degeneration. Neither gender nor pigmentation had a significant influence on the amount of rhodopsin after light exposure in the F(2) progeny. For genetic study, DNAs of the 27-36 F(2) progeny with the highest and 27-36 F(2) with the lowest levels of rhodopsin after light exposure were genotyped with 71 dinucleotide repeat markers spanning the genome. Any marker with a 95% probability of being associated with phenotype was tested in all 289 F(2) progeny. Data were analyzed with Map Manager QTX. Significant QTL were found on mouse Chrs 1 and 4, and suggestive QTL on Chrs 6 and 2. The four QTL together equal an estimated 78% of the total genetic effect, and each of the QTL represents a gene with BALB/c susceptible alleles. The Chr 6 QTL is in the same region as a highly significant age-related retinal degeneration QTL found previously. Identification of these QTL is a first step toward identifying the modifier genes/alleles they represent, and identification of the modifiers may provide important information for human retinal diseases that are accelerated by light exposure.

Electroretinographic evidence for altered phototransduction gain and slowed recovery from photobleaches in albino mice with a MET450 variant in RPE65.

Our purpose was to investigate the physiological phenotype of albino mice with a variation in the Rpe65 gene encoding either methionine or leucine at amino acid #450. Full-field electroretinograms (ERGs) were recorded from C57BL/6J-c(2J) albino mice with MET450 and BALB/cByJ albino mice with LEU450. Recordings from pigmented mice (C57BL/6J) served as controls. Rod ERG a-waves were fitted with a model to estimate parameters of activation. Recovery of function following a photobleach was studied by monitoring the return to pre-bleach a- or b-wave amplitudes of the dark-adapted electroretinogram. The parameter, S, derived from the fit of the rod model, was significantly higher for albino mice compared to pigmented controls. Between the albino mice, S was highest for BALB/cByJ compared to C57BL/6J-c(2J). The parameters t(d) and Rm(P3) were not different across the three strains. The difference in S between the BALB/cByJ and C57BL/6J-c(2J) albino strains is interpreted to reflect differences in intrinsic phototransduction gain. Recovery from a photobleach was also slower for the C57BL/6J-c(2J) albino mice compared with BALB/cByJ albino mice, consistent with prior studies showing slowed rhodopsin regeneration in mice with the RPE65-METH450 variant. ERG recordings show that C57BL/6J-c(2J) albino mice with the MET450 variant of the RPE65 protein have a lower gain of activation and slower recovery from photobleach than do the BALB/cByJ albino mice with LEU450. Both the slower recovery from photobleach and lower gain of activation characteristic of the C57BL/6J-c(2J) strain may contribute to the mechanism by which it is protected from light-induced photoreceptor death relative to BALB/c.

A strong and highly significant QTL on chromosome 6 that protects the mouse from age-related retinal degeneration.

PURPOSE: BALB/cByJ (C) albino mice have significantly more retinal degeneration as they age than C57BL/6J-c(2J) (B6) albinos. To discover the genetic loci that influence age-related retinal degeneration (ARD), a quantitative genetics study was performed with 8-month-old progeny from an intercross between these two strains. METHODS: The thickness of the outer nuclear layer of the retina was used as the quantitative trait. A genome-wide scan was performed with 86 genetic markers at an average distance of 15.7 cM. Map Manager QTX was used to analyze the data. RESULTS: Three highly significant quantitative trait loci (QTLs) were detected on mouse chromosomes (Chrs) 6, 10, and 16. The B6 alleles were protective against ARD in the first two, and the C allele was protective in the third. Several suggestive, weak QTLs were also found, along with a gender-related effect. The strongest and most highly significant QTL on Chr 6 accounted for 30% of the total genetic effect with a LOD score of 13.5. The RPE65/MET450 variant of major influence on constant light-induced retinal degeneration (LRD) in a previous study of these same two mouse strains had no influence on ARD, and only some of the weak, suggestive QTLs influencing ARD were also observed in LRD. CONCLUSIONS: Because none of the ARD QTLs was homologous to human chromosomal loci so far implicated in age-related macular degeneration, each represents a new candidate gene for potential study. The gene represented by the Chr 6 QTL is of particular interest because it has broad influence, very high significance, and a B6 allele that protects against ARD.