%0 Journal Article %J Cell Mol Life Sci %D 2023 %T Molecular basis of retinal remodeling in a zebrafish model of retinitis pigmentosa. %A Santhanam, Abirami %A Shihabeddin, Eyad %A Wei, Haichao %A Wu, Jiaqian %A O'Brien, John %K Animals %K Disease Models, Animal %K Female %K Male %K Retina %K Retinal Degeneration %K Retinal Rod Photoreceptor Cells %K Retinitis Pigmentosa %K Zebrafish %X

A hallmark of inherited retinal degenerative diseases such as retinitis pigmentosa (RP) is progressive structural and functional remodeling of the remaining retinal cells as photoreceptors degenerate. Extensive remodeling of the retina stands as a barrier for the successful implementation of strategies to restore vision. To understand the molecular basis of remodeling, we performed analyses of single-cell transcriptome data from adult zebrafish retina of wild type AB strain (WT) and a P23H mutant rhodopsin transgenic model of RP with continuous degeneration and regeneration. Retinas from both female and male fish were pooled to generate each library, combining data from both sexes. We provide a benchmark atlas of retinal cell type transcriptomes in zebrafish and insight into how each retinal cell type is affected in the P23H model. Oxidative stress is found throughout the retina, with increases in reliance on oxidative metabolism and glycolysis in the affected rods as well as cones, bipolar cells, and retinal ganglion cells. There is also transcriptional evidence for widespread synaptic remodeling and enhancement of glutamatergic transmission in the inner retina. Notably, changes in circadian rhythm regulation are detected in cones, bipolar cells, and retinal pigmented epithelium. We also identify the transcriptomic signatures of retinal progenitor cells and newly formed rods essential for the regenerative process. This comprehensive transcriptomic analysis provides a molecular road map to understand how the retina remodels in the context of chronic retinal degeneration with ongoing regeneration.

%B Cell Mol Life Sci %V 80 %P 362 %8 2023 Nov 18 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/37979052?dopt=Abstract %R 10.1007/s00018-023-05021-1 %0 Journal Article %J Graefes Arch Clin Exp Ophthalmol %D 2022 %T EYS-Associated Sector Retinitis Pigmentosa. %A Marques, João Pedro %A Porto, Fernanda Belga Ottoni %A Carvalho, Ana Luísa %A Neves, Emmanuel %A Rui Chen %A Sampaio, Shirley Aparecida Madureira %A Murta, Joaquim %A Saraiva, Jorge %A Silva, Rufino %K Cone-Rod Dystrophies %K Cross-Sectional Studies %K DNA Mutational Analysis %K Eye Proteins %K Female %K Humans %K Mutation %K Retinitis Pigmentosa %X

PURPOSE: Sector retinitis pigmentosa (RP) is a rare form of rod-cone degeneration typically associated with mutations in the RHO gene. We describe six unrelated patients presenting with this atypical phenotype in association with biallelic mutations in EYS gene.

METHODS: Multinational, multicentre cross-sectional case series. Patients with biallelic disease-causing variants in EYS and a clinical diagnosis of sector RP were recruited from specialized centres in Portugal and Brazil. All patients underwent a comprehensive ophthalmologic examination complemented by deep phenotyping. Peripheral blood samples were collected from all probands and available relatives for genetic analysis. Genetic counselling was provided to all subjects.

RESULTS: Seven disease-causing variants (4 pathogenic; 3 likely pathogenic) were identified in 6 unrelated female patients. Best-corrected visual acuity ranged from 75 to 85 ETDRS letters. All eyes showed bilateral and symmetrical areas of outer retinal atrophy distributed along the inferior vascular arcades and extending temporally and/or nasally in a crescent-shaped pattern. On fundus autofluorescence (AF), a foveal-sparing curvilinear band of hyperAF encroaching the optic nerve head and extending temporally was seen in 4 patients. The remaining 2 presented bilateral and symmetrical patches of hypoAF inside crescent-shaped areas of hyperAF along the inferior temporal vascular arcade. Visual field testing revealed superior visual field defects of varying extents, always in close association with the fundus AF findings.

CONCLUSIONS: Even though EYS has only recently been listed as a cause of the sector RP phenotype, we believe that this presentation is not infrequent and should be considered an important differential for sector RP.

%B Graefes Arch Clin Exp Ophthalmol %V 260 %P 1405-1413 %8 2022 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/34568954?dopt=Abstract %R 10.1007/s00417-021-05411-w %0 Journal Article %J Genet Med %D 2022 %T Identification of autosomal recessive novel genes and retinal phenotypes in members of the solute carrier (SLC) superfamily. %A Millo, Talya %A Rivera, Antonio %A Obolensky, Alexey %A Marks-Ohana, Devora %A Xu, Mingchu %A Yumei Li %A Wilhelm, Enosh %A Gopalakrishnan, Prakadeeswari %A Gross, Menachem %A Rosin, Boris %A Hanany, Mor %A Webster, Andrew %A Tracewska, Anna Maria %A Koenekoop, Robert K %A Rui Chen %A Arno, Gavin %A Schueler-Furman, Ora %A Roosing, Susanne %A Banin, Eyal %A Sharon, Dror %K DNA Mutational Analysis %K Genes, Recessive %K Genetic Association Studies %K Humans %K Mutation %K Pedigree %K Phenotype %K Retinitis Pigmentosa %X

PURPOSE: This study aimed to investigate the clinical and genetic aspects of solute carrier (SLC) genes in inherited retinal diseases (IRDs).

METHODS: Exome sequencing data were filtered to identify pathogenic variants in SLC genes. Analysis of transcript and protein expression was performed on fibroblast cell lines and retinal sections.

RESULTS: Comprehensive analysis of 433 SLC genes in 913 exome sequencing IRD samples revealed homozygous pathogenic variants in 6 SLC genes, including 2 candidate novel genes, which were 2 variants in SLC66A1, causing autosomal recessive retinitis pigmentosa (ARRP), and a variant in SLC39A12, causing autosomal recessive mild widespread retinal degeneration with marked macular involvement. In addition, we present 4 families with ARRP and homozygous null variants in SLC37A3 that were previously suggested to cause retinitis pigmentosa, 2 of which cause exon skipping. The recently reported SLC4A7- c.2007dup variant was found in 2 patients with ARRP resulting in the absence of protein. Finally, variants in SLC24A1 were found in 4 individuals with either ARRP or congenital stationary night blindness.

CONCLUSION: We report on SLC66A1 and SLC39A12 as candidate novel IRD genes, establish SLC37A3 pathogenicity, and provide further evidence of SLC4A7 as IRD genes. We extend the phenotypic spectrum of SLC24A1 and suggest that its ARRP phenotype may be more common than previously reported.

%B Genet Med %V 24 %P 1523-1535 %8 2022 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/35486108?dopt=Abstract %R 10.1016/j.gim.2022.03.020 %0 Journal Article %J J Clin Invest %D 2019 %T A nonhuman primate model of inherited retinal disease. %A Moshiri, Ala %A Rui Chen %A Kim, Soohyun %A R. Alan Harris %A Yumei Li %A Raveendran, Muthuswamy %A Davis, Sarah %A Liang, Qingnan %A Pomerantz, Ori %A Wang, Jun %A Garzel, Laura %A Cameron, Ashley %A Yiu, Glenn %A Stout, J Timothy %A Huang, Yijun %A Murphy, Christopher J %A Roberts, Jeffrey %A Gopalakrishna, Kota N %A Boyd, Kimberly %A Artemyev, Nikolai O %A Jeffrey Rogers %A Thomasy, Sara M %K Amino Acid Substitution %K Animals %K Color Vision Defects %K Cone Dystrophy %K Cyclic Nucleotide Phosphodiesterases, Type 6 %K Disease Models, Animal %K Eye Proteins %K Female %K HEK293 Cells %K Humans %K Macaca mulatta %K Male %K Mutation, Missense %K Retinitis Pigmentosa %X

Inherited retinal degenerations are a common cause of untreatable blindness worldwide, with retinitis pigmentosa and cone dystrophy affecting approximately 1 in 3500 and 1 in 10,000 individuals, respectively. A major limitation to the development of effective therapies is the lack of availability of animal models that fully replicate the human condition. Particularly for cone disorders, rodent, canine, and feline models with no true macula have substantive limitations. By contrast, the cone-rich macula of a nonhuman primate (NHP) closely mirrors that of the human retina. Consequently, well-defined NHP models of heritable retinal diseases, particularly cone disorders that are predictive of human conditions, are necessary to more efficiently advance new therapies for patients. We have identified 4 related NHPs at the California National Primate Research Center with visual impairment and findings from clinical ophthalmic examination, advanced retinal imaging, and electrophysiology consistent with achromatopsia. Genetic sequencing confirmed a homozygous R565Q missense mutation in the catalytic domain of PDE6C, a cone-specific phototransduction enzyme associated with achromatopsia in humans. Biochemical studies demonstrate that the mutant mRNA is translated into a stable protein that displays normal cellular localization but is unable to hydrolyze cyclic GMP (cGMP). This NHP model of a cone disorder will not only serve as a therapeutic testing ground for achromatopsia gene replacement, but also for optimization of gene editing in the macula and of cone cell replacement in general.

%B J Clin Invest %V 129 %P 863-874 %8 2019 Feb 01 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/30667376?dopt=Abstract %R 10.1172/JCI123980 %0 Journal Article %J Exp Eye Res %D 2018 %T Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice. %A Eblimit, Aiden %A Agrawal, Smriti Akshay %A Thomas, Kandace %A Anastassov, Ivan Assenov %A Abulikemu, Tajiguli %A Moayedi, Yalda %A Mardon, Graeme %A Chen, Rui %K Animals %K Cytoskeletal Proteins %K Disease Models, Animal %K DNA-Binding Proteins %K Electroretinography %K Mice %K Mice, Knockout %K Proteins %K Retina %K Retinal Cone Photoreceptor Cells %K Retinal Degeneration %K Retinal Rod Photoreceptor Cells %K Retinitis Pigmentosa %K Rhodopsin %X

The mammalian retina consists of multiple cell layers including photoreceptor cells, which are light sensing neurons that play essential functions in the visual process. Previously, we identified mutations in SPATA7, encoding spermatogenesis associated protein 7, in families with Leber Congenital Amaurosis (LCA) and juvenile Retinitis Pigmentosa (RP), and showed that Spata7 null mice recapitulate the human disease phenotype of retinal degeneration. SPATA7 is expressed in the connecting cilium of photoreceptor (PR) cells in the mouse retina, as well as in retinal pigment epithelium (RPE) cells, but the functional role of Spata7 in the RPE remains unknown. To investigate whether Spata7 is required in PRs, the RPE, or both, we conditionally knocked out Spata7 in photoreceptors and RPE cells using Crx-Cre and Best1-Cre transgenic mouse lines, respectively. In Spata7 photoreceptor-specific conditional (cKO) mice, both rod and cone photoreceptor dysfunction and degeneration is observed, characterized by progressive thinning of the outer nuclear layer and reduced response to light; however, RPE-specific deletion of Spata7 does not impair retinal function or cell survival. Furthermore, our findings show that both Rhodopsin and RPGRIP1 are mislocalized in the Spata7; Crx-Cre cKO mice, suggesting that loss of Spata7 in photoreceptors alone can result in altered trafficking of these proteins in the connecting cilium. Together, our findings suggest that loss of Spata7 in photoreceptors alone is sufficient to cause photoreceptor degeneration, but its function in the RPE is not required for photoreceptor survival; therefore, loss of Spata7 in photoreceptors alters both rod and cone function and survival, consistent with the clinical phenotypes observed in LCA and RP patients with mutations in SPATA7.

%B Exp Eye Res %V 166 %P 120-130 %8 2018 Jan %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/29100828?dopt=Abstract %R 10.1016/j.exer.2017.10.015 %0 Journal Article %J Am J Med Genet A %D 2018 %T A heterozygous mutation in RPGR associated with X-linked retinitis pigmentosa in a patient with Turner syndrome mosaicism (45,X/46,XX). %A Zhou, Qi %A Yao, Fengxia %A Wang, Feng %A Li, Hui %A Rui Chen %A Sui, Ruifang %K Adult %K Eye Proteins %K Female %K Frameshift Mutation %K Genes, X-Linked %K Genomics %K Heterozygote %K Humans %K In Situ Hybridization, Fluorescence %K Male %K Mutation %K Pedigree %K Phenotype %K Retinitis Pigmentosa %K Sequence Analysis, DNA %K Turner Syndrome %X

Turner syndrome with retinitis pigmentosa (RP) is rare, with only three cases reported based on clinical examination alone. We summarized the 4-year follow-up and molecular findings in a 28-year-old patient with Turner syndrome and the typical features of short stature and neck webbing, who also had X-linked RP. Her main complaints were night blindness and progressive loss of vision since the age of 9 years. Ophthalmologic examination, optical coherent tomographic imaging, and visual electrophysiology tests showed classic manifestations of RP. The karyotype of peripheral blood showed mosaicism (45,X [72%]/46,XX[28%]). A novel heterozygous frameshift mutation (c.2403_2406delAGAG, p.T801fsX812) in the RP GTPase regulator (RPGR) gene was detected using next generation sequencing and validated by Sanger sequencing. We believe that this is the first report of X-linked RP in a patient with Turner syndrome associated with mosaicism, and an RPGR heterozygous mutation. We hypothesize that X-linked RP in this woman is not related to Turner syndrome, but may be a manifestation of the lack of a normal paternal X chromosome with intact but mutated RPGR.

%B Am J Med Genet A %V 176 %P 214-218 %8 2018 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29135076?dopt=Abstract %R 10.1002/ajmg.a.38501 %0 Journal Article %J Ophthalmic Genet %D 2018 %T Investigating the disease association of USH2A p.C759F variant by leveraging large retinitis pigmentosa cohort data. %A DuPont, Mariana %A Jones, Evan M %A Xu, Mingchu %A Chen, Rui %K Cohort Studies %K Extracellular Matrix Proteins %K Gene Frequency %K Genetic Variation %K Humans %K Mutation %K Retinitis Pigmentosa %K RNA, Messenger %X

Retinitis pigmentosa (RP) is an inherited retinal disease with a prevalence of 1/4,000. RP is highly genetically heterogeneous and there are over 80 genes associated with RP to date. One particular variant, p.C759F, has long been reported in RP cases but its pathogenicity was questioned by a recent study. Here, by leveraging large scale next-generation sequencing data from 982 non-Asian RP probands, we used binomial tests to evaluate the enrichment of this allele in RP cohort. We observed significant enrichment of this allele both in homozygous state and in compound heterozygous state with another protein-truncating allele. The results highlighted the clinical significance of the p.C759F allele in RP cases, which is important for accurate molecular diagnosis.

%B Ophthalmic Genet %V 39 %P 291-292 %8 2018 Apr %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/29283788?dopt=Abstract %R 10.1080/13816810.2017.1418388 %0 Journal Article %J PLoS Genet %D 2018 %T Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa. %A Li, Lin %A Jiao, Xiaodong %A D'Atri, Ilaria %A Ono, Fumihito %A Nelson, Ralph %A Chan, Chi-Chao %A Nakaya, Naoki %A Ma, Zhiwei %A Ma, Yan %A Cai, Xiaoying %A Zhang, Longhua %A Lin, Siying %A Hameed, Abdul %A Chioza, Barry A %A Hardy, Holly %A Arno, Gavin %A Hull, Sarah %A Khan, Muhammad Imran %A Fasham, James %A Harlalka, Gaurav V %A Michaelides, Michel %A Moore, Anthony T %A Coban Akdemir, Zeynep Hande %A Jhangiani, Shalini %A James R Lupski %A Cremers, Frans P M %A Qamar, Raheel %A Salman, Ahmed %A Chilton, John %A Self, Jay %A Ayyagari, Radha %A Kabir, Firoz %A Naeem, Muhammad Asif %A Ali, Muhammad %A Akram, Javed %A Sieving, Paul A %A Riazuddin, Sheikh %A Baple, Emma L %A Riazuddin, S Amer %A Crosby, Andrew H %A Hejtmancik, J Fielding %K Animals %K Asian People %K Cell Line %K Chloride Channels %K Cytoplasm %K Eye Proteins %K HEK293 Cells %K Homozygote %K Humans %K Mice %K Mice, Knockout %K Mutation, Missense %K Pakistan %K Retina %K Retinal Cone Photoreceptor Cells %K Retinal Rod Photoreceptor Cells %K Retinitis Pigmentosa %K Zebrafish %X

We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post fertilization. The depressed electroretinogram (ERG) cone response and cone spectral sensitivity of 5 dpf KO zebrafish and reduced eye size, retinal thickness, and expression of rod and cone opsins could be rescued by injection of wild type CLCC1 mRNA. Clcc1+/- KO mice showed decreased ERGs and photoreceptor number. Together these results strongly suggest that intracellular chloride transport by CLCC1 is a critical process in maintaining retinal integrity, and CLCC1 is crucial for survival and function of retinal cells.

%B PLoS Genet %V 14 %P e1007504 %8 2018 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/30157172?dopt=Abstract %R 10.1371/journal.pgen.1007504 %0 Journal Article %J Ophthalmology %D 2018 %T Pigmentary Maculopathy Associated with Chronic Exposure to Pentosan Polysulfate Sodium. %A Pearce, William A %A Rui Chen %A Jain, Nieraj %K Adult %K Anticoagulants %K Cystitis, Interstitial %K Dyslexia %K Electroretinography %K Female %K Fluorescein Angiography %K Genetic Testing %K High-Throughput Nucleotide Sequencing %K Humans %K Middle Aged %K Multimodal Imaging %K Pentosan Sulfuric Polyester %K Retinal Pigment Epithelium %K Retinitis Pigmentosa %K Retrospective Studies %K Tomography, Optical Coherence %K Vision Disorders %K Visual Acuity %X

PURPOSE: To describe the clinical features of a unique pigmentary maculopathy noted in the setting of chronic exposure to pentosan polysulfate sodium (PPS), a therapy for interstitial cystitis (IC).

DESIGN: Retrospective case series.

PARTICIPANTS: Six adult patients evaluated by a single clinician between May 1, 2015, and October 1, 2017.

METHODS: Patients were identified by query of the electronic medical record system. Local records were reviewed, including results of the clinical examination, retinal imaging, and visual function assessment with static perimetry and electroretinography. Molecular testing assessed for known macular dystrophy and mitochondrial cytopathy genotypes.

MAIN OUTCOME MEASURES: Mean best-corrected visual acuity (BCVA; in logarithm of the minimum angle of resolution units), median cumulative PPS exposure, subjective nature of the associated visual disturbance, qualitative examination and imaging features, and molecular testing results.

RESULTS: The median age at presentation was 60 years (range, 37-62 years). All patients received PPS for a diagnosis of IC, with a median cumulative exposure of 2263 g (range, 1314-2774 g), over a median duration of exposure of 186 months (range, 144-240 months). Most patients (4 of 6) reported difficulty reading as the most bothersome symptom. Mean BCVA was 0.1±0.18 logarithm of the minimum angle of resolution. On fundus examination, nearly all eyes showed subtle paracentral hyperpigmentation at the level of the retinal pigment epithelium (RPE) with a surrounding array of vitelliform-like deposits. Four eyes of 2 patients showed paracentral RPE atrophy, and no eyes demonstrated choroidal neovascularization. Multimodal retinal imaging demonstrated abnormality of the RPE generally contained in a well-delineated area in the posterior pole. None of the 4 patients who underwent molecular testing of nuclear DNA returned a pathogenic mutation. Additionally, all 6 patients showed negative results for pathogenic variants in the mitochondrial gene MTTL1.

CONCLUSIONS: We describe a novel and possibly avoidable maculopathy associated with chronic exposure to PPS. Patients reported symptoms of difficulty reading and prolonged dark adaptation despite generally intact visual acuity and subtle funduscopic findings. Multimodal imaging and functional studies are suggestive of a primary RPE injury. Additional investigation is warranted to explore causality further.

%B Ophthalmology %V 125 %P 1793-1802 %8 2018 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/29801663?dopt=Abstract %R 10.1016/j.ophtha.2018.04.026 %0 Journal Article %J Hum Mol Genet %D 2018 %T Whole-exome sequencing revealed HKDC1 as a candidate gene associated with autosomal-recessive retinitis pigmentosa. %A Zhang, Lin %A Sun, Zixi %A Zhao, Peiquan %A Huang, Lulin %A Xu, Mingchu %A Yang, Yeming %A Chen, Xue %A Lu, Fang %A Zhang, Xiang %A Wang, Hui %A Zhang, Shanshan %A Liu, Wenjing %A Jiang, Zhilin %A Ma, Shi %A Rui Chen %A Zhao, Chen %A Yang, Zhenglin %A Sui, Ruifang %A Zhu, Xianjun %K Animals %K Disease Models, Animal %K Exome %K Exome Sequencing %K Female %K Genetic Association Studies %K Hexokinase %K Homozygote %K Humans %K Male %K Mice, Knockout %K Mutation %K Pedigree %K Retina %K Retinal Degeneration %K Retinitis Pigmentosa %X

Retinitis pigmentosa (RP) is an inheritable retina degenerative disease leading to blindness. Despite the identification of 70 genes associated with RP, the genetic cause of ∼40% of RP patients remains to be elucidated. Whole-exome sequencing was applied on the probands of a RP cohort of 68 unsolved cases to identify candidate genetic mutations. A homozygous missense variant (c.173C > T, p.T58 M) was found in HKDC1 in two unrelated families presenting late-onset retinal degeneration. This variant affects highly conserved amino acid residue and is very rare in several databases and absent in 4000 ethnic-matched controls. Mutant HKDC1 protein partially lost hexokinase activity. Hkdc1 is expressed in the mouse retina and localized to photoreceptor inner segments. To elucidate the in vivo roles of Hkdc1 in the retina, we generated Hkdc1 knockout (KO) mouse models using CRISPR/Cas9 technique. Two independent alleles were identified and backcrossed to C57BL/6 J for 6 generations. Absence of HKDC1 expression in the Hkdc1 KO retina was confirmed by western blot and immunostaning using HKDC1 antibody. Hkdc1 KO mice exhibited reduced scotopic electroretinogram response and thinner outer nuclear layer, similar to some of the human patient phenotypes. Loss of Hkdc1 led to mislocalization of rhodopsin to the inner segments and cell bodies of rods in some regions in the retina. Taken together, our data demonstrated that HKDC1 is associated with autosomal recessively inherited RP.

%B Hum Mol Genet %V 27 %P 4157-4168 %8 2018 Dec 01 %G eng %N 23 %1 https://www.ncbi.nlm.nih.gov/pubmed/30085091?dopt=Abstract %R 10.1093/hmg/ddy281 %0 Journal Article %J J Med Genet %D 2017 %T is mutated in a distinct type of Usher syndrome. %A Fu, Qing %A Xu, Mingchu %A Chen, Xue %A Sheng, Xunlun %A Yuan, Zhisheng %A Liu, Yani %A Li, Huajin %A Sun, Zixi %A Li, Huiping %A Yang, Lizhu %A Wang, Keqing %A Zhang, Fangxia %A Li, Yumei %A Zhao, Chen %A Sui, Ruifang %A Chen, Rui %K Adult %K Cell Cycle Proteins %K Child %K Consanguinity %K Exome %K Female %K Frameshift Mutation %K Genome, Human %K Hair Cells, Auditory, Inner %K High-Throughput Nucleotide Sequencing %K Homozygote %K Humans %K Male %K Pedigree %K Retinitis Pigmentosa %K Usher Syndromes %X

BACKGROUND: Usher syndrome is a genetically heterogeneous disorder featured by combined visual impairment and hearing loss. Despite a dozen of genes involved in Usher syndrome having been identified, the genetic basis remains unknown in 20-30% of patients. In this study, we aimed to identify the novel disease-causing gene of a distinct subtype of Usher syndrome.

METHODS: Ophthalmic examinations and hearing tests were performed on patients with Usher syndrome in two consanguineous families. Target capture sequencing was initially performed to screen causative mutations in known retinal disease-causing loci. Whole exome sequencing (WES) and whole genome sequencing (WGS) were applied for identifying novel disease-causing genes. RT-PCR and Sanger sequencing were performed to evaluate the splicing-altering effect of identified variants.

RESULTS: Patients from the two independent families show a mild Usher syndrome phenotype featured by juvenile or adult-onset cone-rod dystrophy and sensorineural hearing loss. WES and WGS identified two homozygous rare variants that affect mRNA splicing of a ciliary gene . RT-PCR confirmed that the two variants indeed lead to abnormal splicing, resulting in premature stop of protein translation due to frameshift.

CONCLUSIONS: Our results provide evidence that is a novel disease-causing gene for Usher syndrome, demonstrating an additional link between ciliopathy and Usher protein network in photoreceptor cells and inner ear hair cells.

%B J Med Genet %V 54 %P 190-195 %8 2017 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/27627988?dopt=Abstract %R 10.1136/jmedgenet-2016-104166 %0 Journal Article %J Hum Mutat %D 2016 %T ADIPOR1 Is Mutated in Syndromic Retinitis Pigmentosa. %A Xu, Mingchu %A Eblimit, Aiden %A Wang, Jing %A Li, Jianli %A Wang, Feng %A Zhao, Li %A Wang, Xia %A Xiao, Ningna %A Li, Yumei %A Wong, Lee-Jun C %A Lewis, Richard A %A Chen, Rui %K Adult %K Animals %K Exome %K Female %K Frameshift Mutation %K Humans %K Male %K Mice %K Mutation %K Receptors, Adiponectin %K Retinitis Pigmentosa %K Young Adult %X

Retinitis pigmentosa (RP) is a genetically heterogeneous retinal disorder. Despite the numerous genes associated with RP already identified, the genetic basis remains unknown in a substantial number of patients and families. In this study, we performed whole-exome sequencing to investigate the molecular basis of a syndromic RP case that cannot be solved by mutations in known disease-causing genes. After applying a series of variant filtering strategies, we identified an apparently homozygous frameshift mutation, c.31delC (p.Q11Rfs*24) in the ADIPOR1 gene. The reported phenotypes of Adipor1-null mice contain retinal dystrophy, obesity, and behavioral abnormalities, which highly mimic those in the syndromic RP patient. We further confirmed ADIPOR1 retina expression by immunohistochemistry. Our results established ADIPOR1 as a novel disease-causing gene for syndromic RP and highlight the importance of fatty acid transport in the retina.

%B Hum Mutat %V 37 %P 246-9 %8 2016 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26662040?dopt=Abstract %R 10.1002/humu.22940 %0 Journal Article %J Hum Mol Genet %D 2016 %T Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa. %A Xu, Mingchu %A Yamada, Takeyuki %A Sun, Zixi %A Eblimit, Aiden %A Lopez, Irma %A Wang, Feng %A Manya, Hiroshi %A Xu, Shan %A Zhao, Li %A Li, Yumei %A Kimchi, Adva %A Sharon, Dror %A Sui, Ruifang %A Endo, Tamao %A Koenekoop, Robert K %A Chen, Rui %K Adult %K Aged %K Animals %K Cells, Cultured %K Exome %K Female %K Genes, Recessive %K Genetic Predisposition to Disease %K Glycosylation %K Humans %K Male %K Mice %K Middle Aged %K Mutation %K N-Acetylglucosaminyltransferases %K Pedigree %K Photoreceptor Cells, Vertebrate %K Retinitis Pigmentosa %K Sequence Analysis, DNA %X

A growing number of human diseases have been linked to defects in protein glycosylation that affects a wide range of organs. Among them, O-mannosylation is an unusual type of protein glycosylation that is largely restricted to the muscular and nerve system. Consistently, mutations in genes involved in the O-mannosylation pathway result in infantile-onset, severe developmental defects involving skeleton muscle, brain and eye, such as the muscle-eye-brain disease (MIM no. 253280). However, the functional importance of O-mannosylation in these tissues at later stages remains largely unknown. In our study, we have identified recessive mutations in POMGNT1, which encodes an essential component in O-mannosylation pathway, in three unrelated families with autosomal recessive retinitis pigmentosa (RP), but without extraocular involvement. Enzymatic assay of these mutant alleles demonstrate that they greatly reduce the POMGNT1 enzymatic activity and are likely to be hypomorphic. Immunohistochemistry shows that POMGNT1 is specifically expressed in photoreceptor basal body. Taken together, our work identifies a novel disease-causing gene for RP and indicates that proper protein O-mannosylation is not only essential for early organ development, but also important for maintaining survival and function of the highly specialized retinal cells at later stages.

%B Hum Mol Genet %V 25 %P 1479-88 %8 2016 Apr 15 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/26908613?dopt=Abstract %R 10.1093/hmg/ddw022 %0 Journal Article %J Am J Hum Genet %D 2016 %T Mutations in REEP6 Cause Autosomal-Recessive Retinitis Pigmentosa. %A Arno, Gavin %A Agrawal, Smriti A %A Eblimit, Aiden %A Bellingham, James %A Xu, Mingchu %A Wang, Feng %A Chakarova, Christina %A Parfitt, David A %A Lane, Amelia %A Burgoyne, Thomas %A Hull, Sarah %A Carss, Keren J %A Fiorentino, Alessia %A Hayes, Matthew J %A Munro, Peter M %A Nicols, Ralph %A Pontikos, Nikolas %A Holder, Graham E %A Asomugha, Chinwe %A Raymond, F Lucy %A Moore, Anthony T %A Plagnol, Vincent %A Michaelides, Michel %A Hardcastle, Alison J %A Li, Yumei %A Cukras, Catherine %A Webster, Andrew R %A Cheetham, Michael E %A Chen, Rui %K Adolescent %K Alleles %K Animals %K Child %K Child, Preschool %K Eye Proteins %K Female %K Genes, Recessive %K Humans %K Induced Pluripotent Stem Cells %K Male %K Membrane Proteins %K Membrane Transport Proteins %K Mice %K Mutation %K Mutation, Missense %K Phenotype %K Photoreceptor Cells, Vertebrate %K Retinitis Pigmentosa %K Young Adult %X

Retinitis pigmentosa (RP) is the most frequent form of inherited retinal dystrophy. RP is genetically heterogeneous and the genes identified to date encode proteins involved in a wide range of functional pathways, including photoreceptor development, phototransduction, the retinoid cycle, cilia, and outer segment development. Here we report the identification of biallelic mutations in Receptor Expression Enhancer Protein 6 (REEP6) in seven individuals with autosomal-recessive RP from five unrelated families. REEP6 is a member of the REEP/Yop1 family of proteins that influence the structure of the endoplasmic reticulum but is relatively unstudied. The six variants identified include three frameshift variants, two missense variants, and a genomic rearrangement that disrupts exon 1. Human 3D organoid optic cups were used to investigate REEP6 expression and confirmed the expression of a retina-specific isoform REEP6.1, which is specifically affected by one of the frameshift mutations. Expression of the two missense variants (c.383C>T [p.Pro128Leu] and c.404T>C [p.Leu135Pro]) and the REEP6.1 frameshift mutant in cultured cells suggest that these changes destabilize the protein. Furthermore, CRISPR-Cas9-mediated gene editing was used to produce Reep6 knock-in mice with the p.Leu135Pro RP-associated variant identified in one RP-affected individual. The homozygous knock-in mice mimic the clinical phenotypes of RP, including progressive photoreceptor degeneration and dysfunction of the rod photoreceptors. Therefore, our study implicates REEP6 in retinal homeostasis and highlights a pathway previously uncharacterized in retinal dystrophy.

%B Am J Hum Genet %V 99 %P 1305-1315 %8 2016 Dec 01 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/27889058?dopt=Abstract %R 10.1016/j.ajhg.2016.10.008 %0 Journal Article %J Sci Rep %D 2016 %T Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. %A Zhang, Qi %A Xu, Mingchu %A Verriotto, Jennifer D %A Li, Yumei %A Wang, Hui %A Gan, Lin %A Lam, Byron L %A Chen, Rui %K Alleles %K Eye Proteins %K Female %K High-Throughput Nucleotide Sequencing %K Hispanic or Latino %K Humans %K Male %K Mutation %K Pedigree %K Retinitis Pigmentosa %K RNA Splicing %X

Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. The prevalence of RP and the mutation spectrum vary across populations. Hispanic people account for approximately 17% of the United States population, and the genetic etiologies of RP of this ethnic group still remain not well defined. Utilizing next-generation sequencing (NGS), we screened mutations in known retinal disease-causing genes in an RP cohort of 35 unrelated Hispanic probands from the Miami area. We achieved a solving rate of 66% and identified 15 novel putative pathogenic mutations, including a frequent founder mutation disrupting PRPF31 splicing. Our data show that the mutation spectrum of Hispanic RP receives a significant impact from disease-causing alleles of Spanish origin and may also contain population-specific alleles.

%B Sci Rep %V 6 %P 32792 %8 2016 Sep 06 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/27596865?dopt=Abstract %R 10.1038/srep32792 %0 Journal Article %J Gene Ther %D 2015 %T AAV8(Y733F)-mediated gene therapy in a Spata7 knockout mouse model of Leber congenital amaurosis and retinitis pigmentosa. %A Zhong, H %A Eblimit, A %A Moayedi, Y %A Boye, S L %A Chiodo, V A %A Chen, Y %A Li, Y %A Nichols, R M %A Hauswirth, W W %A Chen, R %A Mardon, G %K Animals %K Dependovirus %K Disease Models, Animal %K DNA-Binding Proteins %K Genetic Therapy %K Genetic Vectors %K Leber Congenital Amaurosis %K Mice, Inbred C57BL %K Mice, Knockout %K Retinal Cone Photoreceptor Cells %K Retinal Rod Photoreceptor Cells %K Retinitis Pigmentosa %X

Loss of SPATA7 function causes the pathogenesis of Leber congenital amaurosis and retinitis pigmentosa. Spata7 knockout mice mimic human SPATA7-related retinal disease with apparent photoreceptor degeneration observed as early as postnatal day 15 (P15). To test the efficacy of adeno-associated virus (AAV)-mediated gene therapy for rescue of photoreceptor survival and function in Spata7 mutant mice, we employed the AAV8(Y733F) vector carrying hGRK1-driven full-length FLAG-tagged Spata7 cDNA to target both rod and cone photoreceptors. Following subretinal injection of this vector, FLAG-tagged SPATA7 was found to colocalize with endogenous SPATA7 in wild-type mice. In Spata7 mutant mice initially treated at P15, we observed improvement of photoresponse, photoreceptor ultrastructure and significant alleviation of photoreceptor degeneration. Furthermore, we performed treatments at P28 and P56 and found that all treatments (P15-P56) can ameliorate rod and cone loss in the long term (1 year); however, none efficiently protect photoreceptors from degeneration by 86 weeks of age as only a small amount of treated photoreceptors can survive to this time. This study demonstrates long-term improvement of photoreceptor function by AAV8(Y733F)-introduced Spata7 expression in a mouse model as potential treatment of the human disease, but also suggests that treated mutant photoreceptors still undergo progressive degeneration.

%B Gene Ther %V 22 %P 619-27 %8 2015 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/25965394?dopt=Abstract %R 10.1038/gt.2015.42 %0 Journal Article %J Hum Genet %D 2015 %T Mutations in human IFT140 cause non-syndromic retinal degeneration. %A Xu, Mingchu %A Yang, Lizhu %A Wang, Feng %A Li, Huajin %A Wang, Xia %A Wang, Weichen %A Ge, Zhongqi %A Wang, Keqing %A Zhao, Li %A Li, Hui %A Li, Yumei %A Sui, Ruifang %A Chen, Rui %K Adult %K Amino Acid Sequence %K Carrier Proteins %K Child %K Female %K Genetic Association Studies %K Humans %K Leber Congenital Amaurosis %K Male %K Middle Aged %K Mutation, Missense %K Pedigree %K Retinitis Pigmentosa %X

Leber congenital amaurosis (LCA) and retinitis pigmentosa (RP) are two genetically heterogeneous retinal degenerative disorders. Despite the identification of a number of genes involved in LCA and RP, the genetic etiology remains unknown in many patients. In this study, we aimed to identify novel disease-causing genes of LCA and RP. Retinal capture sequencing was initially performed to screen mutations in known disease-causing genes in different cohorts of LCA and RP patients. For patients with negative results, we performed whole exome sequencing and applied a series of variant filtering strategies. Sanger sequencing was done to validate candidate causative IFT140 variants. Exome sequencing data analysis led to the identification of IFT140 variants in multiple unrelated non-syndromic LCA and RP cases. All the variants are extremely rare and predicted to be damaging. All the variants passed Sanger validation and segregation tests provided that the family members' DNA was available. The results expand the phenotype spectrum of IFT140 mutations to non-syndromic retinal degeneration, thus extending our understanding of intraflagellar transport and primary cilia biology in the retina. This work also improves the molecular diagnosis of retinal degenerative disease.

%B Hum Genet %V 134 %P 1069-78 %8 2015 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/26216056?dopt=Abstract %R 10.1007/s00439-015-1586-x %0 Journal Article %J JAMA Ophthalmol %D 2015 %T New mutations in the RAB28 gene in 2 Spanish families with cone-rod dystrophy. %A Riveiro-Álvarez, Rosa %A Xie, Yajing Angela %A López-Martínez, Miguel-Ángel %A Gambin, Tomasz %A Pérez-Carro, Raquel %A Ávila-Fernández, Almudena %A López-Molina, María-Isabel %A Zernant, Jana %A Jhangiani, Shalini %A Muzny, Donna %A Yuan, Bo %A Boerwinkle, Eric %A Gibbs, Richard %A Lupski, James R %A Ayuso, Carmen %A Allikmets, Rando %K Adolescent %K Adult %K Child %K Diagnosis, Differential %K DNA Mutational Analysis %K Female %K Follow-Up Studies %K Genetic Predisposition to Disease %K Hispanic or Latino %K Humans %K Male %K Microscopy, Acoustic %K Mutation %K Pedigree %K Phenotype %K rab GTP-Binding Proteins %K Retinitis Pigmentosa %K Retrospective Studies %K Young Adult %X

IMPORTANCE: The families evaluated in this study represent the second report of cone-rod dystrophy (CRD) cases caused by mutations in RAB28, a recently discovered gene associated with CRD.

OBJECTIVE: To determine the disease-causing gene in 2 families of Spanish descent presenting with CRD who do not have ABCA4 mutations.

DESIGN, SETTING, AND PARTICIPANTS: Molecular genetics and observational case studies of 2 families, each with 1 affected proband with CRD and 3 or 5 unaffected family members. The affected individual from each family received a complete ophthalmic examination including assessment of refractive errors and best-corrected visual acuity, biomicroscopy, color fundus photography, electroretinography analysis, and visual-evoked potential analysis. After complete sequencing of the ABCA4 gene with negative results, the screening for disease-causing mutations was performed by whole-exome sequencing. Possible disease-associated variants were determined by filtering based on minor allele frequency, predicted pathogenicity, and segregation analysis in all family members.

MAIN OUTCOMES AND MEASURES: The appearance of the macula was evaluated by clinical examination, fundus photography, and fundus autofluorescence imaging, and visual function was assessed by electroretinography. Disease-causing mutations were assessed by sequence analyses.

RESULTS: Ophthalmologic findings included markedly reduced visual acuity, bull's eye maculopathy, foveal hyperpigmentation, peripapillary atrophy, dyschromatopsia, extinguished photopic responses, and reduced scotopic responses observed on electroretinography consistent with the CRD phenotype often associated with ABCA4 mutations. Although no ABCA4 mutations were detected in either patient, whole-exome sequencing analysis identified 2 new homozygous mutations in the recently described RAB28 gene, the c.172 + 1G>C splice site variant in IVS2 and the missense c.T651G:p.C217W substitution. Both variants were determined as deleterious by predictive programs and were segregated with the disease in both families. Sequencing of 107 additional patients of Spanish descent with CRD did not reveal other cases with RAB28 mutations.

CONCLUSIONS AND RELEVANCE: Deleterious mutations in RAB28 result in a classic CRD phenotype and are an infrequent cause of CRD in the Spanish population.

%B JAMA Ophthalmol %V 133 %P 133-9 %8 2015 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/25356532?dopt=Abstract %R 10.1001/jamaophthalmol.2014.4266 %0 Journal Article %J Sci Rep %D 2015 %T NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa. %A Ge, Zhongqi %A Bowles, Kristen %A Goetz, Kerry %A Scholl, Hendrik P N %A Wang, Feng %A Wang, Xinjing %A Xu, Shan %A Wang, Keqing %A Wang, Hui %A Chen, Rui %K Antigens, Neoplasm %K Cell Cycle Proteins %K Child %K Child, Preschool %K Cohort Studies %K Cytoskeletal Proteins %K Female %K Genetic Association Studies %K Genetic Testing %K High-Throughput Nucleotide Sequencing %K Humans %K Inheritance Patterns %K Male %K Molecular Diagnostic Techniques %K Mutation %K Neoplasm Proteins %K Pedigree %K Phenotype %K Receptors, G-Protein-Coupled %K Receptors, Glutamate %K Retinitis Pigmentosa %X

The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE(®)) was established in an effort to facilitate basic and clinical research of human inherited eye disease. In order to provide high quality genetic testing to eyeGENE(®)'s enrolled patients which potentially aids clinical diagnosis and disease treatment, we carried out a pilot study and performed Next-generation sequencing (NGS) based molecular diagnosis for 105 Retinitis Pigmentosa (RP) patients randomly selected from the network. A custom capture panel was designed, which incorporated 195 known retinal disease genes, including 61 known RP genes. As a result, disease-causing mutations were identified in 52 out of 105 probands (solving rate of 49.5%). A total of 82 mutations were identified, and 48 of them were novel. Interestingly, for three probands the molecular diagnosis was inconsistent with the initial clinical diagnosis, while for five probands the molecular information suggested a different inheritance model other than that assigned by the physician. In conclusion, our study demonstrated that NGS target sequencing is efficient and sufficiently precise for molecular diagnosis of a highly heterogeneous patient cohort from eyeGENE(®).

%B Sci Rep %V 5 %P 18287 %8 2015 Dec 15 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26667666?dopt=Abstract %R 10.1038/srep18287 %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2014 %T A homozygous missense mutation in NEUROD1 is associated with nonsyndromic autosomal recessive retinitis pigmentosa. %A Wang, Feng %A Li, Huajin %A Xu, Mingchu %A Li, Hui %A Zhao, Li %A Yang, Lizhu %A Zaneveld, Jacques E %A Wang, Keqing %A Li, Yumei %A Sui, Ruifang %A Chen, Rui %K Adult %K Basic Helix-Loop-Helix Transcription Factors %K DNA %K DNA Mutational Analysis %K Female %K Genes, Recessive %K Homozygote %K Humans %K Male %K Mutation, Missense %K Pedigree %K Phenotype %K Retinitis Pigmentosa %X

PURPOSE: Mutations in the same gene can lead to different clinical phenotypes. In this study, we aim to identify novel genotype-phenotype correlations and novel disease genes by analyzing an unsolved autosomal recessive retinitis pigmentosa (ARRP) Han Chinese family.

METHODS: Whole exome sequencing was performed for one proband from the consanguineous ARRP family. Stringent variants filtering and prioritizations were applied to identify the causative mutation.

RESULTS: A homozygous missense variant, c.724G>A; p.V242I, in NEUROD1 was identified as the most likely cause of disease. This allele perfectly segregates in the family and affects an amino acid, which is highly conserved among mammals. A previous study showed that a homozygous null allele in NEUROD1 causes severe syndromic disease with neonatal diabetes, systematic neurological abnormalities, and early-onset retinal dystrophy. Consistent with these results, our patients who are homozygous for a less severe missense allele presented only late-onset retinal degeneration without any syndromic symptoms.

CONCLUSIONS: We identified a potential novel genotype-phenotype correlation between NEUROD1 and nonsyndromic ARRP. Our study supports the idea that NEUROD1 is important for maintenance of the retina function and partial loss-of-function mutation in NEUROD1 is likely a rare cause of nonsyndromic ARRP.

%B Invest Ophthalmol Vis Sci %V 56 %P 150-5 %8 2014 Dec 04 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/25477324?dopt=Abstract %R 10.1167/iovs.14-15382 %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2014 %T A missense mutation in HK1 leads to autosomal dominant retinitis pigmentosa. %A Wang, Feng %A Wang, Yandong %A Zhang, Bin %A Zhao, Li %A Lyubasyuk, Vera %A Wang, Keqing %A Xu, Mingchu %A Li, Yumei %A Wu, Frances %A Wen, Cindy %A Bernstein, Paul S %A Lin, Danni %A Zhu, Susanna %A Wang, Hui %A Zhang, Kang %A Chen, Rui %K Adolescent %K Child %K Child, Preschool %K DNA %K DNA Mutational Analysis %K Female %K Genes, Dominant %K Genetic Linkage %K Genetic Predisposition to Disease %K Heterozygote %K Hexokinase %K Humans %K Male %K Mutation, Missense %K Pedigree %K Phenotype %K Retinitis Pigmentosa %K Young Adult %X

PURPOSE: Retinitis pigmentosa (RP) is a genetically heterogeneous disease with over 60 causative genes known to date. Nevertheless, approximately 40% of RP cases remain genetically unsolved, suggesting that many novel disease-causing genes are yet to be identified. In this study, we aimed to identify the causative mutation for a large autosomal dominant RP (adRP) family with negative results from known retinal disease gene screening.

METHODS: Linkage analysis followed by whole-exome sequencing was performed. Stringent variant filtering and prioritization was carried out to identify the causative mutation.

RESULTS: Linkage analysis identified a minimal disease region of 8 Mb on chromosome 10 with a peak parametric logarithm (base 10) of odds (LOD) score of 3.500. Further whole-exome sequencing identified a heterozygous missense mutation (NM_000188.2:c.2539G>A, p.E847K) in hexokinase 1 (HK1) that segregated with the disease phenotype in the family. Biochemical assays showed that the E847K mutation does not affect hexokinase enzymatic activity or the protein stability, suggesting that the mutation may impact other uncharacterized function or result in a gain of function of HK1.

CONCLUSIONS: Here, we identified HK1 as a novel causative gene for adRP. This is the first report that associates the glucose metabolic pathway with human retinal degenerative disease, suggesting a potential new disease mechanism.

%B Invest Ophthalmol Vis Sci %V 55 %P 7159-64 %8 2014 Oct 14 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/25316723?dopt=Abstract %R 10.1167/iovs.14-15520 %0 Journal Article %J Hum Mol Genet %D 2014 %T New syndrome with retinitis pigmentosa is caused by nonsense mutations in retinol dehydrogenase RDH11. %A Xie, Yajing Angela %A Lee, Winston %A Cai, Carolyn %A Gambin, Tomasz %A Nõupuu, Kalev %A Sujirakul, Tharikarn %A Ayuso, Carmen %A Jhangiani, Shalini %A Muzny, Donna %A Boerwinkle, Eric %A Gibbs, Richard %A Greenstein, Vivienne C %A Lupski, James R %A Tsang, Stephen H %A Allikmets, Rando %K Adolescent %K Child %K Codon, Nonsense %K Female %K Humans %K Male %K Oxidoreductases %K Pedigree %K Phenotype %K Retinitis Pigmentosa %K Syndrome %K Vision Tests %K Visual Acuity %K Young Adult %X

Retinitis pigmentosa (RP), a genetically heterogeneous group of retinopathies that occur in both non-syndromic and syndromic forms, is caused by mutations in ∼100 genes. Although recent advances in next-generation sequencing have aided in the discovery of novel RP genes, a number of the underlying contributing genes and loci remain to be identified. We investigated three siblings, born to asymptomatic parents of Italian-American descent, who each presented with atypical RP with systemic features, including facial dysmorphologies, psychomotor developmental delays recognized since early childhood, learning disabilities and short stature. RP-associated ophthalmological findings included salt-and-pepper retinopathy, attenuation of the arterioles and generalized rod-cone dysfunction as determined by almost extinguished electroretinogram in 2 of 3 siblings. Atypical for RP features included mottled macula at an early age and peripapillary sparing of the retinal pigment epithelium. Whole-exome sequencing data, queried under a recessive model of inheritance, identified compound heterozygous stop mutations, c.C199T:p.R67* and c.C322T:p.R108*, in the retinol dehydrogenase 11 (RDH11) gene, resulting in a non-functional protein, in all affected children. In summary, deleterious mutations in RDH11, an important enzyme for vision-related and systemic retinoic acid metabolism, cause a new syndrome with RP.

%B Hum Mol Genet %V 23 %P 5774-80 %8 2014 Nov 01 %G eng %N 21 %1 https://www.ncbi.nlm.nih.gov/pubmed/24916380?dopt=Abstract %R 10.1093/hmg/ddu291 %0 Journal Article %J Hum Genet %D 2014 %T Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. %A Wang, Feng %A Wang, Hui %A Tuan, Han-Fang %A Nguyen, Duy H %A Sun, Vincent %A Keser, Vafa %A Bowne, Sara J %A Sullivan, Lori S %A Luo, Hongrong %A Zhao, Ling %A Wang, Xia %A Zaneveld, Jacques E %A Salvo, Jason S %A Siddiqui, Sorath %A Mao, Louise %A Wheaton, Dianna K %A Birch, David G %A Branham, Kari E %A Heckenlively, John R %A Wen, Cindy %A Flagg, Ken %A Ferreyra, Henry %A Pei, Jacqueline %A Khan, Ayesha %A Ren, Huanan %A Wang, Keqing %A Lopez, Irma %A Qamar, Raheel %A Zenteno, Juan C %A Ayala-Ramirez, Raul %A Buentello-Volante, Beatriz %A Fu, Qing %A Simpson, David A %A Li, Yumei %A Sui, Ruifang %A Silvestri, Giuliana %A Daiger, Stephen P %A Koenekoop, Robert K %A Zhang, Kang %A Chen, Rui %K Alleles %K Computational Biology %K Exons %K Genes, Recessive %K Genetic Association Studies %K Genetic Testing %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Membrane Glycoproteins %K Molecular Chaperones %K Mutation %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Retinitis Pigmentosa %K Sequence Analysis, DNA %X

Retinitis pigmentosa (RP) is a devastating form of retinal degeneration, with significant social and professional consequences. Molecular genetic information is invaluable for an accurate clinical diagnosis of RP due to its high genetic and clinical heterogeneity. Using a gene capture panel that covers 163 of the currently known retinal disease genes, including 48 RP genes, we performed a comprehensive molecular screening in a collection of 123 RP unsettled probands from a wide variety of ethnic backgrounds, including 113 unrelated simplex and 10 autosomal recessive RP (arRP) cases. As a result, 61 mutations were identified in 45 probands, including 38 novel pathogenic alleles. Interestingly, we observed that phenotype and genotype were not in full agreement in 21 probands. Among them, eight probands were clinically reassessed, resulting in refinement of clinical diagnoses for six of these patients. Finally, recessive mutations in CLN3 were identified in five retinal degeneration patients, including four RP probands and one cone-rod dystrophy patient, suggesting that CLN3 is a novel non-syndromic retinal disease gene. Collectively, our results underscore that, due to the high molecular and clinical heterogeneity of RP, comprehensive screening of all retinal disease genes is effective in identifying novel pathogenic mutations and provides an opportunity to discover new genotype-phenotype correlations. Information gained from this genetic screening will directly aid in patient diagnosis, prognosis, and treatment, as well as allowing appropriate family planning and counseling.

%B Hum Genet %V 133 %P 331-45 %8 2014 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/24154662?dopt=Abstract %R 10.1007/s00439-013-1381-5 %0 Journal Article %J J Med Genet %D 2013 %T Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. %A Wang, Xia %A Wang, Hui %A Sun, Vincent %A Tuan, Han-Fang %A Keser, Vafa %A Wang, Keqing %A Ren, Huanan %A Lopez, Irma %A Zaneveld, Jacques E %A Siddiqui, Sorath %A Bowles, Stephanie %A Khan, Ayesha %A Salvo, Jason %A Jacobson, Samuel G %A Iannaccone, Alessandro %A Wang, Feng %A Birch, David %A Heckenlively, John R %A Fishman, Gerald A %A Traboulsi, Elias I %A Li, Yumei %A Wheaton, Dianna %A Koenekoop, Robert K %A Chen, Rui %K Alleles %K Amino Acid Sequence %K Base Sequence %K Exome %K Female %K Genotype %K High-Throughput Nucleotide Sequencing %K Humans %K Leber Congenital Amaurosis %K Mutation %K Pedigree %K Polymorphism, Single Nucleotide %K Reproducibility of Results %K Retinitis Pigmentosa %K Sensitivity and Specificity %X

BACKGROUND: Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are inherited retinal diseases that cause early onset severe visual impairment. An accurate molecular diagnosis can refine the clinical diagnosis and allow gene specific treatments.

METHODS: We developed a capture panel that enriches the exonic DNA of 163 known retinal disease genes. Using this panel, we performed targeted next generation sequencing (NGS) for a large cohort of 179 unrelated and prescreened patients with the clinical diagnosis of LCA or juvenile RP. Systematic NGS data analysis, Sanger sequencing validation, and segregation analysis were utilised to identify the pathogenic mutations. Patients were revisited to examine the potential phenotypic ambiguity at the time of initial diagnosis.

RESULTS: Pathogenic mutations for 72 patients (40%) were identified, including 45 novel mutations. Of these 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. We revisited patients in the latter case and found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. Guided by the molecular diagnosis, we reclassified the clinical diagnosis in two patients.

CONCLUSIONS: We have identified a novel gene and a large number of novel mutations that are associated with LCA/juvenile RP. Our results highlight the importance of molecular diagnosis as an integral part of clinical diagnosis.

%B J Med Genet %V 50 %P 674-88 %8 2013 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/23847139?dopt=Abstract %R 10.1136/jmedgenet-2013-101558 %0 Journal Article %J Sci China Life Sci %D 2013 %T Dawn of ocular gene therapy: implications for molecular diagnosis in retinal disease. %A Zaneveld, Jacques %A Wang, Feng %A Wang, Xia %A Chen, Rui %K Animals %K DNA Mutational Analysis %K Genetic Therapy %K Genetic Vectors %K High-Throughput Nucleotide Sequencing %K Humans %K Leber Congenital Amaurosis %K Macular Degeneration %K Molecular Diagnostic Techniques %K Precision Medicine %K Retinal Diseases %K Retinitis Pigmentosa %X

Personalized medicine aims to utilize genomic information about patients to tailor treatment. Gene replacement therapy for rare genetic disorders is perhaps the most extreme form of personalized medicine, in that the patients' genome wholly determines their treatment regimen. Gene therapy for retinal disorders is poised to become a clinical reality. The eye is an optimal site for gene therapy due to the relative ease of precise vector delivery, immune system isolation, and availability for monitoring of any potential damage or side effects. Due to these advantages, clinical trials for gene therapy of retinal diseases are currently underway. A necessary precursor to such gene therapies is accurate molecular diagnosis of the mutation(s) underlying disease. In this review, we discuss the application of Next Generation Sequencing (NGS) to obtain such a diagnosis and identify disease causing genes, using retinal disorders as a case study. After reviewing ocular gene therapy, we discuss the application of NGS to the identification of novel Mendelian disease genes. We then compare current, array based mutation detection methods against next NGS-based methods in three retinal diseases: Leber's Congenital Amaurosis, Retinitis Pigmentosa, and Stargardt's disease. We conclude that next-generation sequencing based diagnosis offers several advantages over array based methods, including a higher rate of successful diagnosis and the ability to more deeply and efficiently assay a broad spectrum of mutations. However, the relative difficulty of interpreting sequence results and the development of standardized, reliable bioinformatic tools remain outstanding concerns. In this review, recent advances NGS based molecular diagnoses are discussed, as well as their implications for the development of personalized medicine.

%B Sci China Life Sci %V 56 %P 125-33 %8 2013 Feb %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23393028?dopt=Abstract %R 10.1007/s11427-013-4443-y %0 Journal Article %J Invest Ophthalmol Vis Sci %D 2013 %T Next-generation sequencing-based molecular diagnosis of a Chinese patient cohort with autosomal recessive retinitis pigmentosa. %A Fu, Qing %A Wang, Feng %A Wang, Hui %A Xu, Fei %A Zaneveld, Jacques E %A Ren, Huanan %A Keser, Vafa %A Lopez, Irma %A Tuan, Han-Fang %A Salvo, Jason S %A Wang, Xia %A Zhao, Li %A Wang, Keqing %A Li, Yumei %A Koenekoop, Robert K %A Chen, Rui %A Sui, Ruifang %K Adolescent %K Adult %K Asian People %K Child %K China %K Cohort Studies %K Female %K Genes, Recessive %K Humans %K Male %K Middle Aged %K Molecular Diagnostic Techniques %K Mutation %K Retinitis Pigmentosa %K Sequence Analysis, DNA %K Young Adult %X

PURPOSE: Retinitis pigmentosa (RP) is a highly heterogeneous genetic disease; therefore, an accurate molecular diagnosis is essential for appropriate disease treatment and family planning. The prevalence of RP in China had been reported at 1 in 3800, resulting in an estimated total of 340,000 Chinese RP patients. However, genetic studies of Chinese RP patients have been very limited. To date, no comprehensive molecular diagnosis has been done for Chinese RP patients. With the emergence of next-generation sequencing (NGS), comprehensive molecular diagnosis of RP is now within reach. The purpose of this study was to perform the first NGS-based comprehensive molecular diagnosis for Chinese RP patients.

METHODS: Thirty-one well-characterized autosomal recessive RP (arRP) families were recruited. For each family, the DNA sample from one affected member was sequenced using our custom capture panel, which includes 163 retinal disease genes. Variants were called, filtered, and annotated by our in-house automatic pipeline.

RESULTS: Twelve arRP families were successfully molecular diagnosed, achieving a diagnostic rate of approximately 40%. Interestingly, approximately 63% of the pathogenic mutations we identified are novel, which is higher than that observed in a similar study on European descent (45%). Moreover, the clinical diagnoses of two families were refined based on the pathogenic mutations identified in the patients.

CONCLUSIONS: We conclude that comprehensive molecular diagnosis can be vital for an accurate clinical diagnosis of RP. Applying this tool on patients from different ethnic groups is essential for enhancing our knowledge of the global spectrum of RP disease-causing mutations.

%B Invest Ophthalmol Vis Sci %V 54 %P 4158-66 %8 2013 Jun 14 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/23661369?dopt=Abstract %R 10.1167/iovs.13-11672 %0 Journal Article %J Nat Genet %D 2009 %T A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. %A Khanna, Hemant %A Davis, Erica E %A Murga-Zamalloa, Carlos A %A Estrada-Cuzcano, Alejandro %A Lopez, Irma %A den Hollander, Anneke I %A Zonneveld, Marijke N %A Othman, Mohammad I %A Waseem, Naushin %A Chakarova, Christina F %A Maubaret, Cecilia %A Diaz-Font, Anna %A MacDonald, Ian %A Muzny, Donna M %A Wheeler, David A %A Morgan, Margaret %A Lewis, Lora R %A Logan, Clare V %A Tan, Perciliz L %A Beer, Michael A %A Inglehearn, Chris F %A Lewis, Richard A %A Jacobson, Samuel G %A Bergmann, Carsten %A Beales, Philip L %A Attié-Bitach, Tania %A Johnson, Colin A %A Otto, Edgar A %A Bhattacharya, Shomi S %A Hildebrandt, Friedhelm %A Gibbs, Richard A %A Koenekoop, Robert K %A Swaroop, Anand %A Katsanis, Nicholas %K Adaptor Proteins, Signal Transducing %K Alleles %K Animals %K Bardet-Biedl Syndrome %K Ciliary Body %K Europe %K Genetic Variation %K GTP Phosphohydrolases %K Humans %K Mutation %K Polymorphism, Single Nucleotide %K Retinal Degeneration %K Retinitis Pigmentosa %K RNA, Messenger %K Uveitis %K Zebrafish %X

Despite rapid advances in the identification of genes involved in disease, the predictive power of the genotype remains limited, in part owing to poorly understood effects of second-site modifiers. Here we demonstrate that a polymorphic coding variant of RPGRIP1L (retinitis pigmentosa GTPase regulator-interacting protein-1 like), a ciliary gene mutated in Meckel-Gruber (MKS) and Joubert (JBTS) syndromes, is associated with the development of retinal degeneration in individuals with ciliopathies caused by mutations in other genes. As part of our resequencing efforts of the ciliary proteome, we identified several putative loss-of-function RPGRIP1L mutations, including one common variant, A229T. Multiple genetic lines of evidence showed this allele to be associated with photoreceptor loss in ciliopathies. Moreover, we show that RPGRIP1L interacts biochemically with RPGR, loss of which causes retinal degeneration, and that the Thr229-encoded protein significantly compromises this interaction. Our data represent an example of modification of a discrete phenotype of syndromic disease and highlight the importance of a multifaceted approach for the discovery of modifier alleles of intermediate frequency and effect.

%B Nat Genet %V 41 %P 739-45 %8 2009 Jun %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/19430481?dopt=Abstract %R 10.1038/ng.366 %0 Journal Article %J Am J Hum Genet %D 2009 %T Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. %A Wang, Hui %A den Hollander, Anneke I %A Moayedi, Yalda %A Abulimiti, Abuduaini %A Li, Yumei %A Collin, Rob W J %A Hoyng, Carel B %A Lopez, Irma %A Abboud, Emad B %A Al-Rajhi, Ali A %A Bray, Molly %A Lewis, Richard Alan %A Lupski, James R %A Mardon, Graeme %A Koenekoop, Robert K %A Chen, Rui %K Animals %K Child %K Codon, Nonsense %K DNA-Binding Proteins %K Homozygote %K Humans %K Mice %K Middle Aged %K Pedigree %K Retina %K Retinal Diseases %K Retinitis Pigmentosa %X

Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are the most common hereditary causes of visual impairment in infants and children. Using homozygosity mapping, we narrowed down the critical region of the LCA3 locus to 3.8 Mb between markers D14S1022 and D14S1005. By direct Sanger sequencing of all genes within this region, we found a homozygous nonsense mutation in the SPATA7 gene in Saudi Arabian family KKESH-060. Three other loss-of-function mutations were subsequently discovered in patients with LCA or juvenile RP from distinct populations. Furthermore, we determined that Spata7 is expressed in the mature mouse retina. Our findings reveal another human visual-disease gene that causes LCA and juvenile RP.

%B Am J Hum Genet %V 84 %P 380-7 %8 2009 Mar %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/19268277?dopt=Abstract %R 10.1016/j.ajhg.2009.02.005