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Sen S, Fabozzi L, Fujinami K, Fujinami-Yokokawa YU, Wright GA, Webster A, Mahroo O, Robson AG, Georgiou M, Michaelides M. IQCB1 (NPHP5)-Retinopathy: Clinical and Genetic Characterization and Natural History. Am J Ophthalmol 2024; 264:205-215. [PMID: 38522724 DOI: 10.1016/j.ajo.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
PURPOSE To describe the clinical and genetic features, and explore the natural history of retinopathy associated with IQCB1 variants in children and adults with retinopathy. DESIGN Retrospective cohort study at a single tertiary care referral center. METHODS The study recruited 19 patients with retinopathy, harboring likely disease-causing variants in IQCB1. Demographic data and clinical presentation, best corrected visual acuity (BCVA), fundus appearance, optical coherence tomography (OCT) and autofluorescence features, electroretinography (ERG) and molecular genetics are reported. RESULTS Ten patients had best corrected visual acuity better than 1.0 LogMAR, and BCVA remained stable till the last review. Seven patients had a vision of hand movements or worse in at least one eye at presentation. There was no correlation found between age of onset and severity of vision loss. Nine patients (47.4%) had a diagnosis of end-stage renal failure at presentation. The other 10 patients (52.6%) had a diagnosis of non-syndromic IQCB1-retinopathy and maintained normal renal function until the last follow-up. The mean age at diagnosis of renal failure was 26.3 ±19.8 years. OCT showed ellipsoid zone (EZ) disruption with foveal sparing in 8/13 patients. All patients had stable OCT findings. Full-field ERGs in four adults revealed a severe cone-rod dystrophy and three children had extinguished ERGs. We identified 17 IQCB1 variants, all predicted to cause loss of function. CONCLUSION IQCB1-retinopathy is a severe early-onset cone-rod dystrophy. The dissociation between severely decreased retinal function and relative preservation of retinal structure over a wide age window makes the disease a candidate for gene therapy.
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Affiliation(s)
- Sagnik Sen
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom; UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom
| | - Lorenzo Fabozzi
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom
| | - Kaoru Fujinami
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom; UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom; Laboratory of Visual Physiology, Division of Vision Research (K.F., Y.F.-Y.), National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
| | - Y U Fujinami-Yokokawa
- UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom; Laboratory of Visual Physiology, Division of Vision Research (K.F., Y.F.-Y.), National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan; Department of Health Policy and Management (Y.F.-Y.), Keio University School of Medicine, Tokyo, Japan
| | - Genevieve A Wright
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom
| | - Andrew Webster
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom; UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom
| | - Omar Mahroo
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom; UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom
| | - Anthony G Robson
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom; UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom
| | - Michalis Georgiou
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom; UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom; Jones Eye Institute (M.G.), University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Michel Michaelides
- Moorfields Eye Hospital (S.S, L.F., K.F., G.W., A.W., O.M., A.R., M.G., M.MM), London, United Kingdom; UCL Institute of Ophthalmology (S.S., K.F., Y.F.-K., A.W., O.M., A.R., M.G., M.M.), University College London, London, United Kingdom.
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Aljammal R, Saravanan T, Guan T, Rhodes S, Robichaux MA, Ramamurthy V. Excessive tubulin glutamylation leads to progressive cone-rod dystrophy and loss of outer segment integrity. Hum Mol Genet 2024; 33:802-817. [PMID: 38297980 DOI: 10.1093/hmg/ddae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Mutations in Cytosolic Carboxypeptidase-like Protein 5 (CCP5) are associated with vision loss in humans. To decipher the mechanisms behind CCP5-associated blindness, we generated a novel mouse model lacking CCP5. In this model, we found that increased tubulin glutamylation led to progressive cone-rod dystrophy, with cones showing a more pronounced and earlier functional loss than rod photoreceptors. The observed functional reduction was not due to cell death, levels, or the mislocalization of major phototransduction proteins. Instead, the increased tubulin glutamylation caused shortened photoreceptor axonemes and the formation of numerous abnormal membranous whorls that disrupted the integrity of photoreceptor outer segments (OS). Ultimately, excessive tubulin glutamylation led to the progressive loss of photoreceptors, affecting cones more severely than rods. Our results highlight the importance of maintaining tubulin glutamylation for normal photoreceptor function. Furthermore, we demonstrate that murine cone photoreceptors are more sensitive to disrupted tubulin glutamylation levels than rods, suggesting an essential role for axoneme in the structural integrity of the cone outer segment. This study provides valuable insights into the mechanisms of photoreceptor diseases linked to excessive tubulin glutamylation.
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Affiliation(s)
- Rawaa Aljammal
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Thamaraiselvi Saravanan
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Tongju Guan
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Scott Rhodes
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Michael A Robichaux
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
| | - Visvanathan Ramamurthy
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Dr., Morgantown, WV 26506, United States
- Department of Ophthalmology and Visual Sciences, One Stadium Dr, West Virginia University, Morgantown, WV 26506, United States
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Kolawole OU, Gregory-Evans CY, Bikoo R, Huang AZ, Gregory-Evans K. Novel pathogenic variants in Tubulin Tyrosine Like 5 ( TTLL5) associated with cone-dominant retinal dystrophies and an abnormal optical coherence tomography phenotype. Mol Vis 2023; 29:329-337. [PMID: 38264610 PMCID: PMC10805330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 12/10/2023] [Indexed: 01/25/2024] Open
Abstract
Purpose Autosomal recessive cone and cone-rod dystrophies (CD/CRD) are inherited forms of vison loss. Here, we report on and correlate the clinical phenotypes with the underlying genetic mutations. Methods Clinical information was collected from subjects, including a family history with a chart review. They underwent a full ophthalmic examination, including best-corrected visual acuity, direct and indirect ophthalmoscopy, color vision testing, color fundus photography, contrast sensitivity, autofluorescence, and spectral domain-optical coherence tomography (SD-OCT), and full-field electroretinography. Next-generation panel-based genetic testing was used to identify DNA variants in subject buccal swab samples. Results Genetic testing in two patients revealed three novel variants in the TTLL5 gene associated with CD/CRD: two missense variants (c.1433G>A;p.(Arg478Gln), c.241C>G;p.(Leu81Val), and one loss-of-function variant (c.2384_2387del;p.(Ala795Valfs*9). Based on in-silico analysis, structural modeling, and comparison to previously reported mutations, these novel variants are very likely to be disease-causing mutations. Combining retinal imaging with SD-OCT analysis, we observed an unusual sheen in the CD/CRD phenotypes. Conclusion Based on the protein domain location of novel TTLL5 variants and the localization of TTLL5 to the connecting cilium, we conclude that the CD/CRD disease phenotype is characterized as a ciliopathy caused by protein tracking dysfunction. This initially affects cone photoreceptors, where photoreceptor cilia express a high level of TTLL5, but extends to rod photoreceptors over time. Fundus photography correlated with SD-OCT imaging suggests that the macular sheen characteristically seen with TTLL5 mutations derives from the photoreceptor's outer segments at the posterior pole.
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Affiliation(s)
- Olubayo U Kolawole
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Canada
| | | | - Riyaz Bikoo
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Canada
| | - Albert Z Huang
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Canada
| | - Kevin Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Canada
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Li Z, Cheng W, Zi F, Wang J, Huang X, Sheng X, Rong W. Four different gene-related cone-rod dystrophy: clinical and genetic findings in six Chinese families with diverse modes of inheritance. Front Genet 2023; 14:1157156. [PMID: 38028590 PMCID: PMC10652761 DOI: 10.3389/fgene.2023.1157156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose: To investigate pathogenic variants in six families with cone-rod dystrophy (CORD) presenting various inheritance patterns by using whole-exome sequencing (WES) and analyzing phenotypic features. Methods: A total of six families with CORD were enrolled in Ningxia Eye Hospital for this study. The probands and their family members received comprehensive ophthalmic examinations, and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined via Sanger sequencing. Furthermore, co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using in silico analysis and evaluated according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Of the six families, two families were assigned as X-linked recessive (XL), two families were assigned as autosomal recessive (AR), and two families were assigned as autosomal dominant (AD). Pathogenic variants were detected in CACNA1F in two X-linked recessive probands, among which family 1 had a hemizygous frameshift variant c.2201del (p.Val734Glyfs*17) and family 2 had a hemizygous missense variant c.245G>A (p.Arg82Gln). Both probands had high myopia, with fundus tessellation accompanied by abnormalities in the outer structure of the macular area. The homozygous splice variant c.2373 + 5G>T in PROM1 and the homozygous nonsense variant c.604C>T (p.Arg202Ter) in ADAM9 were detected in two autosomal recessive families of the probands. Both probands showed different degrees of atrophy in the macular area, and the lesions showed hypofluorescence changes in autofluorescence. The heterozygous variation in CRX c.682C>T (p.Gln228Ter) was detected in two autosomal dominant families. The onset age of the two probands was late, with better vision and severe macular atrophy. According to ACMG guidelines and the analysis of online in silico tools, all variations were labeled as potentially harmful or pathogenic. Conclusion: Pathogenic variants in CACNA1F, PROM1, ADAM9, and CRX genes were identified in six families affected by the diverse inheritance patterns of CORD. Furthermore, the potential impact of the nonsense-mediated decay (NMD) mechanism on the manifestation of CORD phenotypes was examined and addressed. Simultaneously, the spectrum of pathogenic variants and clinical phenotypes associated with the CORD gene was extended.
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Affiliation(s)
- Zhen Li
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Wanyu Cheng
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Feiyin Zi
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Juan Wang
- Department of Ophthalmology, Qingdao West Coast New District Central Hospital, Qingdao, China
| | - Xiaoyu Huang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | | | - Weining Rong
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
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Wongchaisuwat N, Amato A, Lamborn AE, Yang P, Everett L, Pennesi ME. Retinitis pigmentosa GTPase regulator-related retinopathy and gene therapy. Saudi J Ophthalmol 2023; 37:276-286. [PMID: 38155670 PMCID: PMC10752277 DOI: 10.4103/sjopt.sjopt_168_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 12/30/2023] Open
Abstract
Retinitis pigmentosa GTPase regulator (RPGR)-related retinopathy is a retinal dystrophy inherited in a X-linked recessive manner that typically causes progressive visual loss starting in childhood with severe visual impairment by the fourth decade of life. It manifests as an early onset and severe form of retinitis pigmentosa. There are currently no effective treatments for RPGR-related retinopathy; however, there are multiple clinical trials in progress exploring gene augmentation therapy aimed at slowing down or halting the progression of disease and possibly restoring visual function. This review focuses on the molecular biology, clinical manifestations, and the recent progress of gene therapy clinical trials.
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Affiliation(s)
- Nida Wongchaisuwat
- Department of Ophthalmology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Alessia Amato
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Andrew E. Lamborn
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Lesley Everett
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Mark E. Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
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Benson MD, Mukherjee S, Agather AR, Blain D, Cunningham D, Mays R, Sun X, Li T, Hufnagel RB, Brooks BP, Huryn LA, Zein WM, Cukras CA. RPGR: Deep Phenotyping and Genetic Characterization With Findings Specific to the 3'-end of ORF15. Invest Ophthalmol Vis Sci 2023; 64:19. [PMID: 37695603 PMCID: PMC10501488 DOI: 10.1167/iovs.64.12.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/27/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose To describe a group of patients with retinitis pigmentosa GTPase regulator (RPGR)-related retinopathy with a tapetal-like retinal sheen and corresponding changes in the reflectivity of the ellipsoid zone on optical coherence tomography (OCT) imaging. Methods A retrospective case series of 66 patients with a disease-causing variant in RPGR was performed. An expert examiner, masked to patient demographics, clinical evaluations, and specific RPGR variant, analyzed color fundus photographs for the presence of a tapetal-like retinal sheen and assessed OCT images for the presence of an abnormally broad hyper-reflective band in the outer retina. Longitudinal reflectivity profiles were generated and compared with healthy controls. Results Twelve patients (18.2%) had a retinal sheen on color images that cosegregated with an abnormally broad hyper-reflective ellipsoid zone band on OCT imaging. Three-fourths of these patients were male, had a cone-rod dystrophy, and had pathogenic RPGR variants located toward the 3'-end of ORF15. This group had a different longitudinal reflectivity profile signature compared with controls. After a period of prolonged dark adaptation, the abnormal hyper-reflective band on OCT became less apparent, and the outer retinal layers adopted a more normal appearance. Conclusions RPGR-related retinopathy should be considered for males presenting with retinal sheen, abnormal ellipsoid zone hyper-reflectivity, and cone or cone-rod dysfunction on ERG, and pursued with molecular testing. Our results have implications for understanding the role of the C-terminal domain encoded by RPGR ORF15 in the phototransduction cascade. Further, the findings may be important to incorporate into both inclusion criteria and outcome measure developments in future RPGR-related cone or cone-rod dystrophy clinical trials.
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Affiliation(s)
- Matthew D. Benson
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Souvick Mukherjee
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Aime R. Agather
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Delphine Blain
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Denise Cunningham
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert Mays
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Xun Sun
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Tiansen Li
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert B. Hufnagel
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Brian P. Brooks
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Laryssa A. Huryn
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Wadih M. Zein
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Catherine A. Cukras
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
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Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. Hum Mol Genet 2023; 32:2005-2015. [PMID: 36811936 PMCID: PMC10244226 DOI: 10.1093/hmg/ddad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined were subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads and discordant read pairs. Polymerase Chain Reaction (PCR) followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. A total of 16 candidate pathogenic SVs were identified in 16 families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS and PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
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Affiliation(s)
- Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinye Qian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Keqing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jongsu Choi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Anna Matynia
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Michael Gorin
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Fengxia Yao
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Kerry Goetz
- Office of the Director, National Eye Institute/National Institutes of Health, Bethesda, MD 20892, USA
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Belo Horizonte, Minas Gerais, 30150270, Brazil
- Department of Ophthalmology, Santa Casa de Misericórdia de Belo Horizonte, Belo Horizonte, Minas Gerais, 30150221, Brazil
- Centro Oftalmológico de Minas Gerais, Belo Horizonte, Minas Gerais, 30180070, Brazil
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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Chen J, Roll-Mecak A. Glutamylation is a negative regulator of microtubule growth. Mol Biol Cell 2023; 34:ar70. [PMID: 37074962 PMCID: PMC10295482 DOI: 10.1091/mbc.e23-01-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/20/2023] Open
Abstract
Microtubules are noncovalent polymers built from αβ-tubulin dimers. The disordered C-terminal tubulin tails are functionalized with multiple glutamate chains of variable lengths added and removed by tubulin tyrosine ligases (TTLLs) and carboxypeptidases (CCPs). Glutamylation is abundant on stable microtubule arrays such as in axonemes and axons, and its dysregulation leads to human pathologies. Despite this, the effects of glutamylation on intrinsic microtubule dynamics are unclear. Here we generate tubulin with short and long glutamate chains and show that glutamylation slows the rate of microtubule growth and increases catastrophes as a function of glutamylation levels. This implies that the higher stability of glutamylated microtubules in cells is due to effectors. Interestingly, EB1 is minimally affected by glutamylation and thus can report on the growth rates of both unmodified and glutamylated microtubules. Finally, we show that glutamate removal by CCP1 and 5 is synergistic and occurs preferentially on soluble tubulin, unlike TTLL enzymes that prefer microtubules. This substrate preference establishes an asymmetry whereby once the microtubule depolymerizes, the released tubulin is reset to a less-modified state, while polymerized tubulin accumulates the glutamylation mark. Our work shows that a modification on the disordered tubulin tails can directly affect microtubule dynamics and furthers our understanding of the mechanistic underpinnings of the tubulin code.
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Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, and
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, and
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
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9
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Odabasi E, Conkar D, Deretic J, Batman U, Frikstad KAM, Patzke S, Firat-Karalar EN. CCDC66 regulates primary cilium length and signaling via interactions with transition zone and axonemal proteins. J Cell Sci 2023; 136:286879. [PMID: 36606424 DOI: 10.1242/jcs.260327] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
The primary cilium is a microtubule-based organelle that serves as a hub for many signaling pathways. It functions as part of the centrosome or cilium complex, which also contains the basal body and the centriolar satellites. Little is known about the mechanisms by which the microtubule-based ciliary axoneme is assembled with a proper length and structure, particularly in terms of the activity of microtubule-associated proteins (MAPs) and the crosstalk between the different compartments of the centrosome or cilium complex. Here, we analyzed CCDC66, a MAP implicated in cilium biogenesis and ciliopathies. Live-cell imaging revealed that CCDC66 compartmentalizes between centrosomes, centriolar satellites, and the ciliary axoneme and tip during cilium biogenesis. CCDC66 depletion in human cells causes defects in cilium assembly, length and morphology. Notably, CCDC66 interacts with the ciliopathy-linked MAPs CEP104 and CSPP1, and regulates axonemal length and Hedgehog pathway activation. Moreover, CCDC66 is required for the basal body recruitment of transition zone proteins and intraflagellar transport B (IFT-B) machinery. Overall, our results establish CCDC66 as a multifaceted regulator of the primary cilium and provide insight into how ciliary MAPs and subcompartments cooperate to ensure assembly of functional cilia.
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Affiliation(s)
- Ezgi Odabasi
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Deniz Conkar
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Jovana Deretic
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Umut Batman
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Kari-Anne M Frikstad
- Department of Radiation Biology, Institute of Cancer Research, OUH-Norwegian Radium Hospital, Oslo N-0379, Norway
| | - Sebastian Patzke
- Department of Radiation Biology, Institute of Cancer Research, OUH-Norwegian Radium Hospital, Oslo N-0379, Norway
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey.,School of Medicine, Koç University, Istanbul 34450, Turkey
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10
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Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.522522. [PMID: 36789417 PMCID: PMC9928032 DOI: 10.1101/2023.01.02.522522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined was subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY, and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads, and discordant read pairs. PCR followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. In total, sixteen candidate pathogenic SVs were identified in sixteen families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive, and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS, PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
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11
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Cehajic-Kapetanovic J, Martinez-Fernandez de la Camara C, Birtel J, Rehman S, McClements ME, Charbel Issa P, Lotery AJ, MacLaren RE. Impaired glutamylation of RPGR ORF15 underlies the cone-dominated phenotype associated with truncating distal ORF15 variants. Proc Natl Acad Sci U S A 2022; 119:e2208707119. [PMID: 36445968 PMCID: PMC9897430 DOI: 10.1073/pnas.2208707119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pathogenic variants in the Retinitis pigmentosa GTPase regulator (RPGR) gene lead to a clinically severe form of X-linked retinal dystrophy. However, it remains unclear why some variants cause a predominant rod, while others result in a cone-dominated phenotype. Post-translational glutamylation of the photoreceptor-specific RPGRORF15 isoform by the TTLL5 enzyme is essential for its optimal function in photoreceptors, and loss of TTLL5 leads to retinal dystrophy with a cone phenotype. Here we show that RPGR retinal disease, studied in a single cohort of 116 male patients, leads to a clear progressive shift from rod- to cone-dominating phenotype as the RPGRORF15 variant location approaches the distal part of the Open Reading Frame 15 (ORF15) region. The rod photoreceptor involvement on the contrary diminishes along the RGPR sequence, and the variants associated with the cone only phenotype are located predominantly in the very distal part, including the C-terminal basic domain. Moreover, these distal truncating RPGRORF15 variants disrupt the interaction with TTLL5 and lead to a significant impairment of RPGR glutamylation. Thus, consistent with the phenotype of TTLL5 pathogenic variants, our study shows that RPGRORF15 variants, which disrupt its basic domain and the interaction with TTLL5, also impair RPGR glutamylation and lead to the cone phenotype. This has implications for ongoing gene therapy clinical trials where the application of RPGR with impaired glutamylation may be less effective in treating RGPR dystrophies and may even convert a rod-cone dystrophy into a cone dystrophy phenotype.
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Affiliation(s)
- Jasmina Cehajic-Kapetanovic
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- 2To whom correspondence may be addressed.
| | - Cristina Martinez-Fernandez de la Camara
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- 2To whom correspondence may be addressed.
| | - Johannes Birtel
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- cDepartment of Ophthalmology, University of Bonn, 53127Bonn, Germany
| | - Salwah Rehman
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
| | - Michelle E. McClements
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
| | - Peter Charbel Issa
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
| | - Andrew J Lotery
- dClinical Neurosciences Research Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, SO16 6YDSouthampton, United Kingdom
- eUniversity Hospital Southampton NHS Foundation Trust, SO16 6YDSouthampton, United Kingdom
| | - Robert E. MacLaren
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- 2To whom correspondence may be addressed.
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12
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Martinez-Fernandez de la Camara C, Cehajic-Kapetanovic J, MacLaren RE. Emerging gene therapy products for RPGR-associated X-linked retinitis pigmentosa. Expert Opin Emerg Drugs 2022; 27:431-443. [PMID: 36562395 DOI: 10.1080/14728214.2022.2152003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Mutations in the RPGR gene are responsible for one of the most prevalent and severe types of retinitis pigmentosa. Gene therapy has shown great promise to treat inherited retinal diseases, and currently, four RPGR gene therapy vectors are being evaluated in clinical trials. AREAS COVERED This manuscript reviews the gene therapy products that are in development for X-linked retinitis pigmentosa caused by mutations in RPGR, and the challenges that scientists and clinicians have faced. EXPERT OPINION The development of a gene therapy product for RPGR-associated retinal degeneration has been a great challenge due to the incomplete understanding of the underlying genetics and mechanism of action of RPGR, and on the other hand, due to the instability of the RPGR gene. Three of the four gene therapy vectors currently in clinical trials include a codon-optimized version of the human RPGR sequence, and the other vector contains a shortened version of the human RPGR. To date, the only Phase I/II results published in a peer-reviewed journal demonstrate a good safety profile and an improvement in the visual field using a codon optimized version of RPGRORF15.
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Affiliation(s)
- Cristina Martinez-Fernandez de la Camara
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West Wing, Headley Way, OX3 9DU, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, West Wing, Headley Way, OX3 9DU, Oxford, UK
| | - Jasmina Cehajic-Kapetanovic
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West Wing, Headley Way, OX3 9DU, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, West Wing, Headley Way, OX3 9DU, Oxford, UK
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West Wing, Headley Way, OX3 9DU, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, West Wing, Headley Way, OX3 9DU, Oxford, UK
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13
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Martinez-Fernandez de la Camara C, Cehajic-Kapetanovic J, MacLaren RE. Response: 'letter to the editor: emerging gene therapy products for RPGR-associated X-linked retinitis pigmentosa'. Expert Opin Emerg Drugs 2022; 27:449-450. [PMID: 36562394 DOI: 10.1080/14728214.2022.2152212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Cristina Martinez-Fernandez de la Camara
- Department of Clinical Neurosciences, Nuffield Laboratory of Ophthalmology, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Jasmina Cehajic-Kapetanovic
- Department of Clinical Neurosciences, Nuffield Laboratory of Ophthalmology, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Robert E MacLaren
- Department of Clinical Neurosciences, Nuffield Laboratory of Ophthalmology, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
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14
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Nazlamova L, Villa Vasquez SS, Lord J, Karthik V, Cheung MK, Lakowski J, Wheway G. Microtubule modification defects underlie cilium degeneration in cell models of retinitis pigmentosa associated with pre-mRNA splicing factor mutations. Front Genet 2022; 13:1009430. [PMID: 36176300 PMCID: PMC9513239 DOI: 10.3389/fgene.2022.1009430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common cause of hereditary blindness, and may occur in isolation as a non-syndromic condition or alongside other features in a syndromic presentation. Biallelic or monoallelic mutations in one of eight genes encoding pre-mRNA splicing factors are associated with non-syndromic RP. The molecular mechanism of disease remains incompletely understood, limiting opportunities for targeted treatment. Here we use CRISPR and base edited PRPF6 and PRPF31 mutant cell lines, and publicly-available data from human PRPF31+/− patient derived retinal organoids and PRPF31 siRNA-treated organotypic retinal cultures to confirm an enrichment of differential splicing of microtubule, centrosomal, cilium and DNA damage response pathway genes in these cells. We show that genes with microtubule/centrosome/centriole/cilium gene ontology terms are enriched for weak 3′ and 5′ splice sites, and that subtle defects in spliceosome activity predominantly affect efficiency of splicing of these exons. We suggest that the primary defect in PRPF6 or PRPF31 mutant cells is microtubule and centrosomal defects, leading to defects in cilium and mitotic spindle stability, with the latter leading to DNA damage, triggering differential splicing of DNA damage response genes to activate this pathway. Finally, we expand understanding of “splicing factor RP” by investigating the function of TTLL3, one of the most statistically differentially expressed genes in PRPF6 and PRPF31 mutant cells. We identify that TTLL3 is the only tubulin glycylase expressed in the human retina, essential for monoglycylation of microtubules of the cilium, including the retinal photoreceptor cilium, to prevent cilium degeneration and retinal degeneration. Our preliminary data suggest that rescue of tubulin glycylation through overexpression of TTLL3 is sufficient to rescue cilium number in PRPF6 and PRPF31 mutant cells, suggesting that this defect underlies the cellular defect and may represent a potential target for therapeutic intervention in this group of disorders.
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Affiliation(s)
- Liliya Nazlamova
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Suly Saray Villa Vasquez
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jenny Lord
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Varshini Karthik
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Man-Kim Cheung
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Jörn Lakowski
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- *Correspondence: Gabrielle Wheway,
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15
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Kazmierczak de Camargo JP, Prezia GNDB, Shiokawa N, Sato MT, Rosati R, Beate Winter Boldt A. New Insights on the Regulatory Gene Network Disturbed in Central Areolar Choroidal Dystrophy-Beyond Classical Gene Candidates. Front Genet 2022; 13:886461. [PMID: 35656327 PMCID: PMC9152281 DOI: 10.3389/fgene.2022.886461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Central areolar choroidal dystrophy (CACD) is a rare hereditary disease that mainly affects the macula, resulting in progressive and usually profound visual loss. Being part of congenital retinal dystrophies, it may have an autosomal dominant or recessive inheritance and, until now, has no effective treatment. Given the shortage of genotypic information about the disease, this work systematically reviews the literature for CACD-causing genes. Three independent researchers selected 33 articles after carefully searching and filtering the Scielo, Pubmed, Lilacs, Web of Science, Scopus, and Embase databases. Mutations of six genes (PRPH2, GUCA1A, GUCY2D, CDHR1, ABCA4, and TTLL5) are implicated in the monogenic dominant inheritance of CACD. They are functionally related to photoreceptors (either in the phototransduction process, as in the case of GUCY2D, or the recovery of retinal photodegradation in photoreceptors for GUCA1A, or the formation and maintenance of specific structures within photoreceptors for PRPH2). The identified genetic variants do not explain all observed clinical features, calling for further whole-genome and functional studies for this disease. A network analysis with the CACD-related genes identified in the systematic review resulted in the identification of another 20 genes that may influence CACD onset and symptoms. Furthermore, an enrichment analysis allowed the identification of 13 transcription factors and 4 long noncoding RNAs interacting with the products of the previously mentioned genes. If mutated or dysregulated, they may be directly involved in CACD development and related disorders. More than half of the genes identified by bioinformatic tools do not appear in commercial gene panels, calling for more studies about their role in the maintenance of the retina and phototransduction process, as well as for a timely update of these gene panels.
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Affiliation(s)
| | - Giovanna Nazaré de Barros Prezia
- Post-Graduation Program in Biotechnology Applied to Child and Adolescent Health, Faculdades Pequeno Príncipe and Pelé Pequeno Príncipe Research Institute, Curitiba, Brazil
| | - Naoye Shiokawa
- Retina and Vitreo Consulting Eye Clinic, Curitiba, Brazil
| | - Mario Teruo Sato
- Retina and Vitreo Consulting Eye Clinic, Curitiba, Brazil.,Department of Ophthalmol/Otorhinolaryngology, Federal University of Paraná, Curitiba, Brazil
| | - Roberto Rosati
- Post-Graduation Program in Biotechnology Applied to Child and Adolescent Health, Faculdades Pequeno Príncipe and Pelé Pequeno Príncipe Research Institute, Curitiba, Brazil
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16
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Wu HY, Rong Y, Bansal PK, Wei P, Guo H, Morgan JI. TTLL1 and TTLL4 polyglutamylases are required for the neurodegenerative phenotypes in pcd mice. PLoS Genet 2022; 18:e1010144. [PMID: 35404950 PMCID: PMC9022812 DOI: 10.1371/journal.pgen.1010144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/21/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Polyglutamylation is a dynamic posttranslational modification where glutamate residues are added to substrate proteins by 8 tubulin tyrosine ligase-like (TTLL) family members (writers) and removed by the 6 member Nna1/CCP family of carboxypeptidases (erasers). Genetic disruption of polyglutamylation leading to hyperglutamylation causes neurodegenerative phenotypes in humans and animal models; the best characterized being the Purkinje cell degeneration (pcd) mouse, a mutant of the gene encoding Nna1/CCP1, the prototypic eraser. Emphasizing the functional importance of the balance between glutamate addition and elimination, loss of TTLL1 prevents Purkinje cell degeneration in pcd. However, whether Ttll1 loss protects other vulnerable neurons in pcd, or if elimination of other TTLLs provides protection is largely unknown. Here using a mouse genetic rescue strategy, we characterized the contribution of Ttll1, 4, 5, 7, or 11 to the degenerative phenotypes in cerebellum, olfactory bulb and retinae of pcd mutants. Ttll1 deficiency attenuates Purkinje cell loss and function and reduces olfactory bulb mitral cell death and retinal photoreceptor degeneration. Moreover, degeneration of photoreceptors in pcd is preceded by impaired rhodopsin trafficking to the rod outer segment and likely represents the causal defect leading to degeneration as this too is rescued by elimination of TTLL1. Although TTLLs have similar catalytic properties on model substrates and several are highly expressed in Purkinje cells (e.g. TTLL5 and 7), besides TTLL1 only TTLL4 deficiency attenuated degeneration of Purkinje and mitral cells in pcd. Additionally, TTLL4 loss partially rescued photoreceptor degeneration and impaired rhodopsin trafficking. Despite their common properties, the polyglutamylation profile changes promoted by TTLL1 and TTLL4 deficiencies in pcd mice are very different. We also report that loss of anabolic TTLL5 synergizes with loss of catabolic Nna1/CCP1 to promote photoreceptor degeneration. Finally, male infertility in pcd is not rescued by loss of any Ttll. These data provide insight into the complexity of polyglutamate homeostasis and function in vivo and potential routes to ameliorate disorders caused by disrupted polyglutamylation.
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Affiliation(s)
- Hui-Yuan Wu
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yongqi Rong
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Parmil K. Bansal
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Peng Wei
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Hong Guo
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - James I. Morgan
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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17
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Oh JK, Vargas Del Valle JG, Lima de Carvalho JR, Sun YJ, Levi SR, Ryu J, Yang J, Nagasaki T, Emanuelli A, Rasool N, Allikmets R, Sparrow JR, Izquierdo NJ, Duncan JL, Mahajan VB, Tsang SH. Expanding the phenotype of TTLL5-associated retinal dystrophy: a case series. Orphanet J Rare Dis 2022; 17:146. [PMID: 35365235 PMCID: PMC8973795 DOI: 10.1186/s13023-022-02295-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inherited retinal dystrophies describe a heterogeneous group of retinal diseases that lead to the irreversible degeneration of rod and cone photoreceptors and eventual blindness. Recessive loss-of-function mutations in Tubulin Tyrosine Ligase Like 5 (TTLL5) represent a recently described cause of inherited cone-rod and cone dystrophy. This study describes the unusual phenotypes of three patients with autosomal recessive mutations in TTLL5. Examination of these patients included funduscopic evaluation, spectral-domain optical coherence tomography, short-wavelength autofluorescence, and full-field electroretinography (ffERG). Genetic diagnoses were confirmed using whole exome capture. Protein modeling of the identified variants was performed to explore potential genotype-phenotype correlations. RESULTS Genetic testing revealed five novel variants in TTLL5 in three unrelated patients with retinal dystrophy. Clinical imaging demonstrated features of sectoral cone-rod dystrophy and cone dystrophy, with phenotypic variability seen across all three patients. One patient also developed high-frequency hearing loss during a similar time period as the onset of retinal disease, potentially suggestive of a syndromic disorder. Retinal structure findings were corroborated with functional measures including ffERG findings that supported these diagnoses. Modeling of the five variants suggest that they cause different effects on protein function, providing a potential reason for genotype-phenotype correlation in these patients. CONCLUSIONS The authors report retinal phenotypic findings in three unrelated patients with novel mutations causing autosomal recessive TTLL5-mediated retinal dystrophy. These findings broaden the understanding of the phenotypes associated with TTLL5-mediated retinal disease and suggest that mutations in TTLL5 should be considered as a potential cause of sectoral retinal dystrophy in addition to cone-rod and cone dystrophies.
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Affiliation(s)
- Jin Kyun Oh
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- State University of New York at Downstate Medical Center, Brooklyn, NY, USA
| | | | - Jose Ronaldo Lima de Carvalho
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Ophthalmology, Hospital das Clinicas de Pernambuco (HCPE) - Empresa Brasileira de Servicos Hospitalares (EBSERH), Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
- Department of Ophthalmology, Federal University of São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Young Joo Sun
- Omics Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Sarah R Levi
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Joseph Ryu
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jing Yang
- Omics Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Takayuki Nagasaki
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Andres Emanuelli
- Department of Ophthalmology, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
| | - Nailyn Rasool
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Natalio J Izquierdo
- Department of Surgery, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Vinit B Mahajan
- Omics Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Harkness Eye Institute, Columbia University Medical Center, 635 West 165th Street, Box 212, New York, NY, 10032, USA.
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18
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Del Pozo-Valero M, Riveiro-Alvarez R, Martin-Merida I, Blanco-Kelly F, Swafiri S, Lorda-Sanchez I, Trujillo-Tiebas MJ, Carreño E, Jimenez-Rolando B, Garcia-Sandoval B, Corton M, Avila-Fernandez A, Ayuso C. Impact of Next Generation Sequencing in Unraveling the Genetics of 1036 Spanish Families With Inherited Macular Dystrophies. Invest Ophthalmol Vis Sci 2022; 63:11. [PMID: 35119454 PMCID: PMC8819279 DOI: 10.1167/iovs.63.2.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose To assess the potential of next-generation sequencing (NGS) technologies to characterize cases diagnosed with autosomal recessive (ar) or sporadic (s) macular dystrophies (ar/sMD) and describe their mutational spectrum. Methods A cohort of 1036 families was classified according to their suspected clinical diagnosis—Stargardt disease (STGD), cone and cone-rod dystrophy (CCRD) or other maculopathies (otherMD). Molecular studies included genotyping microarrays, Sanger sequencing, NGS, and sequencing of intronic regions of the ABCA4 gene. Clinical reclassification was done after the genetic study. Results At the end of the study, 677 patients (65%) had a confirmed genetic diagnosis, representing 78%, 63%, and 38% of STGD, CCRD, and otherMD groups of patients, respectively. ABCA4 is the most mutated gene in all groups, and a second pathogenic variant was found in 76% of STGD patients with one previously identified mutated ABCA4 allele. Autosomal dominant or X-linked mutations were found in 5% of cases together with not-MD genes (CHM, EYS, RHO, RPGR, RLBP1, OPA1, and USH2A among others) leading to their reclassification. Novel variants in the very rare genes PLA2G5 and TTLL5 revealed additional phenotypic associations. Conclusions This study provides for the first time a genetic landscape of 1036 ar/sMD families according to their suspected diagnosis. The analysis of >200 genes associated with retinal dystrophies and the entire locus of ABCA4 increase the rate of characterization, even regardless of available clinical and familiar data. The use of the suspected a priori diagnosis referred by the clinicians, especially in the past, could lead to clinical reclassifications to other inherited retinal dystrophies.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Saoud Swafiri
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Maria José Trujillo-Tiebas
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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19
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Liang C, Carrel D, Singh NK, Hiester LL, Fanget I, Kim H, Firestein BL. Carboxypeptidase E Independently Changes Microtubule Glutamylation, Dendritic Branching, and Neuronal Migration. ASN Neuro 2022; 14:17590914211062765. [PMID: 35014548 PMCID: PMC8755936 DOI: 10.1177/17590914211062765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Neuronal migration and dendritogenesis are dependent on dynamic changes to the microtubule (MT) network. Among various factors that regulate MT dynamics and stability, post-translational modifications (PTMs) of MTs play a critical role in conferring specificity of regulatory protein binding to MTs. Thus, it is important to understand the regulation of PTMs during brain development as multiple developmental processes are dependent on MTs. In this study, we identified that carboxypeptidase E (CPE) changes tubulin polyglutamylation, a major PTM in the brain, and we examine the impact of CPE-mediated changes to polyglutamylation on cortical neuron migration and dendrite morphology. We show, for the first time, that overexpression of CPE increases the level of polyglutamylated α-tubulin while knockdown decreases the level of polyglutamylation. We also demonstrate that CPE-mediated changes to polyglutamylation are dependent on the CPE zinc-binding motif and that this motif is necessary for CPE action on p150Glued localization. However, overexpression of a CPE mutant that does not increase MT glutamylation mimics the effects of overexpression of wild type CPE on dendrite branching. Furthermore, although overexpression of wild type CPE does not alter cortical neuron migration, overexpression of the mutant may act in a dominant-negative manner as it decreases the number of neurons that reach the cortical plate (CP), as we previously reported for CPE knockdown. Overall, our data suggest that CPE changes MT glutamylation and redistribution of p150Glued and that this function of CPE is independent of its role in shaping dendrite development but plays a partial role in regulating cortical neuron migration.
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Affiliation(s)
- Chen Liang
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA.,Molecular Biosciences Graduate Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Damien Carrel
- SPPIN Laboratory, 555089Université de Paris, Centre National de la Recherche Scientifique UMR 8003, Paris, France
| | - Nisha K Singh
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA.,Molecular Biosciences Graduate Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Liam L Hiester
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA
| | - Isabelle Fanget
- SPPIN Laboratory, 555089Université de Paris, Centre National de la Recherche Scientifique UMR 8003, Paris, France
| | - Hyuck Kim
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA
| | - Bonnie L Firestein
- Department of Cell Biology and Neuroscience, Rutgers, 242612The State University of New Jersey, Piscataway, NJ, USA
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20
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Smirnov V, Grunewald O, Muller J, Zeitz C, Obermaier CD, Devos A, Pelletier V, Bocquet B, Andrieu C, Bacquet JL, Lebredonchel E, Mohand-Saïd S, Defoort-Dhellemmes S, Sahel JA, Dollfus H, Zanlonghi X, Audo I, Meunier I, Boulanger-Scemama E, Dhaenens CM. Novel TTLL5 Variants Associated with Cone-Rod Dystrophy and Early-Onset Severe Retinal Dystrophy. Int J Mol Sci 2021; 22:ijms22126410. [PMID: 34203883 PMCID: PMC8232641 DOI: 10.3390/ijms22126410] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 01/05/2023] Open
Abstract
Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.
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Affiliation(s)
- Vasily Smirnov
- Université de Lille, Faculté de Médecine, 59037 Lille, France;
- CHU Lille, Service d’Exploration Fonctionnelle de la Vision et de Neuro-Ophtalmologie, Hôpital Salengro, 59037 Lille, France;
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
| | - Olivier Grunewald
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, 59045 Lille, France;
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d’Alsace (IGMA), INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, 67000 Strasbourg, France;
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d’Alsace (IGMA), 67000 Strasbourg, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
| | - Carolin D. Obermaier
- Praxis für Humangenetik Tuebingen & Center for Genomics and Transcriptomics, CeGaT GmbH, 72076 Tuebingen, Germany;
| | - Aurore Devos
- Univ. Lille, CHU Lille, Service de Toxicologie et Génopathies, 59037 Lille, France; (A.D.); (E.L.)
| | - Valérie Pelletier
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, 34295 Montpellier, France; (B.B.); (I.M.)
- Institute for Neurosciences of Montpellier (INM), INSERM, University of Montpellier, INSERM, 34295 Montpellier, France
| | - Camille Andrieu
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
| | - Jean-Louis Bacquet
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | - Elodie Lebredonchel
- Univ. Lille, CHU Lille, Service de Toxicologie et Génopathies, 59037 Lille, France; (A.D.); (E.L.)
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
| | - Sabine Defoort-Dhellemmes
- CHU Lille, Service d’Exploration Fonctionnelle de la Vision et de Neuro-Ophtalmologie, Hôpital Salengro, 59037 Lille, France;
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
- Fondation Ophtalmologique Adolphe de Rothschild, 75019 Paris, France;
- Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hélène Dollfus
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | | | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, 34295 Montpellier, France; (B.B.); (I.M.)
- Institute for Neurosciences of Montpellier (INM), INSERM, University of Montpellier, INSERM, 34295 Montpellier, France
| | | | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, 59045 Lille, France;
- Correspondence: ; Tel.: +33-320-444-953
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21
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Hadalin V, Šuštar M, Volk M, Maver A, Sajovic J, Jarc-Vidmar M, Peterlin B, Hawlina M, Fakin A. Cone Dystrophy Associated with a Novel Variant in the Terminal Codon of the RPGR- ORF15. Genes (Basel) 2021; 12:genes12040499. [PMID: 33805381 PMCID: PMC8066792 DOI: 10.3390/genes12040499] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022] Open
Abstract
Mutations in RPGRORF15 are associated with rod-cone or cone/cone-rod dystrophy, the latter associated with mutations at the distal end. We describe the phenotype associated with a novel variant in the terminal codon of the RPGRORF15 c.3457T>A (Ter1153Lysext*38), which results in a C-terminal extension. Three male patients from two families were recruited, aged 31, 35, and 38 years. Genetic testing was performed by whole exome sequencing. Filtered variants were analysed according to the population frequency, ClinVar database, the variant’s putative impact, and predicted pathogenicity; and were classified according to the ACMG guidelines. Examination included visual acuity (Snellen), colour vision (Ishihara), visual field, fundus autofluorescence (FAF), optical coherence tomography (OCT), and electrophysiology. All patients were myopic, and had central scotoma and reduced colour vision. Visual acuities on better eyes were counting fingers, 0.3 and 0.05. Electrophysiology showed severely reduced cone-specific responses and macular dysfunction, while the rod-specific response was normal. FAF showed hyperautofluorescent ring centred at the fovea encompassing an area of photoreceptor loss approximately two optic discs in diameter (3462–6342 μm). Follow up after 2–11 years showed enlargement of the diameter (avg. 100 μm/year). The novel c.3457T>A (Ter1153Lysext*38) mutation in the terminal RPGRORF15 codon is associated with cone dystrophy, which corresponds to the previously described phenotypes associated with mutations in the distal end of the RPGRORF15. Minimal progression during follow-up years suggests a relatively stable disease after the initial loss of the central cones.
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Affiliation(s)
- Vlasta Hadalin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Maja Šuštar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Marija Volk
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (A.M.); (B.P.)
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (A.M.); (B.P.)
| | - Jana Sajovic
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Šlajmerjeva ulica 4, 1000 Ljubljana, Slovenia; (M.V.); (A.M.); (B.P.)
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia; (V.H.); (M.Š.); (J.S.); (M.J.-V.); (M.H.)
- Correspondence:
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22
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Yang WT, Hong SR, He K, Ling K, Shaiv K, Hu J, Lin YC. The Emerging Roles of Axonemal Glutamylation in Regulation of Cilia Architecture and Functions. Front Cell Dev Biol 2021; 9:622302. [PMID: 33748109 PMCID: PMC7970040 DOI: 10.3389/fcell.2021.622302] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
Cilia, which either generate coordinated motion or sense environmental cues and transmit corresponding signals to the cell body, are highly conserved hair-like structures that protrude from the cell surface among diverse species. Disruption of ciliary functions leads to numerous human disorders, collectively referred to as ciliopathies. Cilia are mechanically supported by axonemes, which are composed of microtubule doublets. It has been recognized for several decades that tubulins in axonemes undergo glutamylation, a post-translational polymodification, that conjugates glutamic acid chains onto the C-terminal tail of tubulins. However, the physiological roles of axonemal glutamylation were not uncovered until recently. This review will focus on how cells modulate glutamylation on ciliary axonemes and how axonemal glutamylation regulates cilia architecture and functions, as well as its physiological importance in human health. We will also discuss the conventional and emerging new strategies used to manipulate glutamylation in cilia.
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Affiliation(s)
- Wen-Ting Yang
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
| | - Shi-Rong Hong
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
| | - Kai He
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Kritika Shaiv
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
| | - JingHua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
- Mayo Clinic Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, United States
| | - Yu-Chun Lin
- Institute of Molecular Medicine, National Tsing Hua University, HsinChu City, Taiwan
- Department of Medical Science, National Tsing Hua University, HsinChu City, Taiwan
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23
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Mathkar PP, Chen X, Sulovari A, Li D. Characterization of Hepatitis B Virus Integrations Identified in Hepatocellular Carcinoma Genomes. Viruses 2021; 13:v13020245. [PMID: 33557409 PMCID: PMC7915589 DOI: 10.3390/v13020245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as TERT, MLL4, and CCNE1) as well as non-recurrent cancer-related genes (such as CSMD2, NKD2, and RHOU). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.
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Affiliation(s)
- Pranav P. Mathkar
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
| | - Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (X.C.); (D.L.)
| | - Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Cajal Neuroscience Inc., Seattle, WA 98102, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Correspondence: (X.C.); (D.L.)
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24
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Ran J, Zhou J. Targeting the photoreceptor cilium for the treatment of retinal diseases. Acta Pharmacol Sin 2020; 41:1410-1415. [PMID: 32753732 DOI: 10.1038/s41401-020-0486-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/28/2020] [Indexed: 02/08/2023] Open
Abstract
Photoreceptors, as polarised sensory neurons, are essential for light sensation and phototransduction, which are highly dependent on the photoreceptor cilium. Structural defects and/or dysfunction of the photoreceptor cilium caused by mutations in photoreceptor-specific genes or common ciliary genes can lead to retinal diseases, including syndromic and nonsyndromic diseases. In this review, we describe the structure and function of the photoreceptor cilium. We also discuss recent findings that underscore the dysregulation of the photoreceptor cilium in various retinal diseases and the therapeutic potential of targeting ciliary genes in these diseases.
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25
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Power KM, Akella JS, Gu A, Walsh JD, Bellotti S, Morash M, Zhang W, Ramadan YH, Ross N, Golden A, Smith HE, Barr MM, O’Hagan R. Mutation of NEKL-4/NEK10 and TTLL genes suppress neuronal ciliary degeneration caused by loss of CCPP-1 deglutamylase function. PLoS Genet 2020; 16:e1009052. [PMID: 33064774 PMCID: PMC7592914 DOI: 10.1371/journal.pgen.1009052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/28/2020] [Accepted: 08/14/2020] [Indexed: 12/29/2022] Open
Abstract
Ciliary microtubules are subject to post-translational modifications that act as a "Tubulin Code" to regulate motor traffic, binding proteins and stability. In humans, loss of CCP1, a cytosolic carboxypeptidase and tubulin deglutamylating enzyme, causes infantile-onset neurodegeneration. In C. elegans, mutations in ccpp-1, the homolog of CCP1, result in progressive degeneration of neuronal cilia and loss of neuronal function. To identify genes that regulate microtubule glutamylation and ciliary integrity, we performed a forward genetic screen for suppressors of ciliary degeneration in ccpp-1 mutants. We isolated the ttll-5(my38) suppressor, a mutation in a tubulin tyrosine ligase-like glutamylase gene. We show that mutation in the ttll-4, ttll-5, or ttll-11 gene suppressed the hyperglutamylation-induced loss of ciliary dye filling and kinesin-2 mislocalization in ccpp-1 cilia. We also identified the nekl-4(my31) suppressor, an allele affecting the NIMA (Never in Mitosis A)-related kinase NEKL-4/NEK10. In humans, NEK10 mutation causes bronchiectasis, an airway and mucociliary transport disorder caused by defective motile cilia. C. elegans NEKL-4 localizes to the ciliary base but does not localize to cilia, suggesting an indirect role in ciliary processes. This work defines a pathway in which glutamylation, a component of the Tubulin Code, is written by TTLL-4, TTLL-5, and TTLL-11; is erased by CCPP-1; is read by ciliary kinesins; and its downstream effects are modulated by NEKL-4 activity. Identification of regulators of microtubule glutamylation in diverse cellular contexts is important to the development of effective therapies for disorders characterized by changes in microtubule glutamylation. By identifying C. elegans genes important for neuronal and ciliary stability, our work may inform research into the roles of the tubulin code in human ciliopathies and neurodegenerative diseases.
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Affiliation(s)
- Kade M. Power
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Jyothi S. Akella
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Amanda Gu
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Jonathon D. Walsh
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Sebastian Bellotti
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Margaret Morash
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Winnie Zhang
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Yasmin H. Ramadan
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Nicole Ross
- Biology Department, Montclair State University, Montclair, NJ, United States of America
| | - Andy Golden
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Harold E. Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maureen M. Barr
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, United States of America
| | - Robert O’Hagan
- Biology Department, Montclair State University, Montclair, NJ, United States of America
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De Silva SR, Arno G, Robson AG, Fakin A, Pontikos N, Mohamed MD, Bird AC, Moore AT, Michaelides M, Webster AR, Mahroo OA. The X-linked retinopathies: Physiological insights, pathogenic mechanisms, phenotypic features and novel therapies. Prog Retin Eye Res 2020; 82:100898. [PMID: 32860923 DOI: 10.1016/j.preteyeres.2020.100898] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 02/08/2023]
Abstract
X-linked retinopathies represent a significant proportion of monogenic retinal disease. They include progressive and stationary conditions, with and without syndromic features. Many are X-linked recessive, but several exhibit a phenotype in female carriers, which can help establish diagnosis and yield insights into disease mechanisms. The presence of affected carriers can misleadingly suggest autosomal dominant inheritance. Some disorders (such as RPGR-associated retinopathy) show diverse phenotypes from variants in the same gene and also highlight limitations of current genetic sequencing methods. X-linked disease frequently arises from loss of function, implying potential for benefit from gene replacement strategies. We review X-inactivation and X-linked inheritance, and explore burden of disease attributable to X-linked genes in our clinically and genetically characterised retinal disease cohort, finding correlation between gene transcript length and numbers of families. We list relevant genes and discuss key clinical features, disease mechanisms, carrier phenotypes and novel experimental therapies. We consider in detail the following: RPGR (associated with retinitis pigmentosa, cone and cone-rod dystrophy), RP2 (retinitis pigmentosa), CHM (choroideremia), RS1 (X-linked retinoschisis), NYX (complete congenital stationary night blindness (CSNB)), CACNA1F (incomplete CSNB), OPN1LW/OPN1MW (blue cone monochromacy, Bornholm eye disease, cone dystrophy), GPR143 (ocular albinism), COL4A5 (Alport syndrome), and NDP (Norrie disease and X-linked familial exudative vitreoretinopathy (FEVR)). We use a recently published transcriptome analysis to explore expression by cell-type and discuss insights from electrophysiology. In the final section, we present an algorithm for genes to consider in diagnosing males with non-syndromic X-linked retinopathy, summarise current experimental therapeutic approaches, and consider questions for future research.
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Affiliation(s)
- Samantha R De Silva
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony G Robson
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Ana Fakin
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Ljubljana University Medical Centre, Ljubljana, Slovenia
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Moin D Mohamed
- Department of Ophthalmology, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Alan C Bird
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Department of Ophthalmology, UCSF School of Medicine, San Francisco, CA, USA
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, University College London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Department of Ophthalmology, Guy's & St Thomas' NHS Foundation Trust, London, UK; Section of Ophthalmology, King's College London, UK; Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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The emerging role of tubulin posttranslational modifications in cilia and ciliopathies. BIOPHYSICS REPORTS 2020. [DOI: 10.1007/s41048-020-00111-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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Pontikos N, Murphy C, Moghul I, Arno G, Fujinami K, Fujinami Y, Sumodhee D, Downes S, Webster A, Yu J. Phenogenon: Gene to phenotype associations for rare genetic diseases. PLoS One 2020; 15:e0230587. [PMID: 32271766 PMCID: PMC7144978 DOI: 10.1371/journal.pone.0230587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/03/2020] [Indexed: 11/30/2022] Open
Abstract
As high-throughput sequencing is increasingly applied to the molecular diagnosis of rare Mendelian disorders, a large number of patients with diverse phenotypes have their genetic and phenotypic data pooled together to uncover new gene-phenotype relations. We introduce Phenogenon, a statistical tool that combines, Human Phenotype Ontology (HPO) annotated patient phenotypes, gnomAD allele population frequency, and Combined Annotation Dependent Depletion (CADD) score for variant pathogenicity, in order to jointly predict the mode of inheritance and gene-phenotype associations. We ran Phenogenon on our cohort of 3,290 patients who had undergone whole exome sequencing. Among the top associations, we recapitulated previously known, such as "SRD5A3—Abnormal full-field electroretinogram—recessive" and "GRHL2 –Nail dystrophy—recessive", and discovered one potentially novel, “RRAGA–Abnormality of the skin—dominant”. We also developed an interactive web interface available at https://phenogenon.phenopolis.org to visualise and explore the results.
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Affiliation(s)
- Nikolas Pontikos
- UCL Genetics Institute, University College London, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Cian Murphy
- UCL Genetics Institute, University College London, London, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Ismail Moghul
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Gavin Arno
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kaoru Fujinami
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yu Fujinami
- Graduate School of Health Management, Keio University, Tokyo, Japan
- Division of Public Health, Yokokawa Clinic, Osaka, Japan
| | - Dayyanah Sumodhee
- Queen Mary University, Mile End Road, Bethnal Green, London, United Kingdom
| | - Susan Downes
- Oxford Eye Hospital, West Wing, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Andrew Webster
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail:
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The tubulin code and its role in controlling microtubule properties and functions. Nat Rev Mol Cell Biol 2020; 21:307-326. [PMID: 32107477 DOI: 10.1038/s41580-020-0214-3] [Citation(s) in RCA: 393] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Microtubules are core components of the eukaryotic cytoskeleton with essential roles in cell division, shaping, motility and intracellular transport. Despite their functional heterogeneity, microtubules have a highly conserved structure made from almost identical molecular building blocks: the tubulin proteins. Alternative tubulin isotypes and a variety of post-translational modifications control the properties and functions of the microtubule cytoskeleton, a concept known as the 'tubulin code'. Here we review the current understanding of the molecular components of the tubulin code and how they impact microtubule properties and functions. We discuss how tubulin isotypes and post-translational modifications control microtubule behaviour at the molecular level and how this translates into physiological functions at the cellular and organism levels. We then go on to show how fine-tuning of microtubule function by some tubulin modifications can affect homeostasis and how perturbation of this fine-tuning can lead to a range of dysfunctions, many of which are linked to human disease.
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De La Camara CMF, Cehajic-Kapetanovic J, MacLaren RE. RPGR gene therapy presents challenges in cloning the coding sequence. Expert Opin Biol Ther 2020; 20:63-71. [PMID: 31612744 PMCID: PMC7104355 DOI: 10.1080/14712598.2020.1680635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Currently, there are three Phase I/II clinical trials based on gene therapy ongoing to test different AAV.RPGR or deleted RPGR vectors on patients affected by X-linked retinitis pigmentosa. These three vectors differ in the adeno-associated viral (AAV) vector capsid used, and the coding sequences: two contain codon optimized versions of RPGR which give the full-length protein, whilst the third uses a wild-type sequence that contains a large deletion encoding part of the functional domain of the RPGR protein.Areas covered: This review approaches the different studies that have led to the initiation of three different clinical trials for RPGR related X-linked retinitis pigmentosa.Expert opinion: The development of a gene therapy vector to deliver a normal copy of the RPGR gene into the photoreceptors has presented a challenge for the scientific community. The instability of its sequence and the fact that its function is not well understood can lead to the production of a nonfunctional or deleterious protein for the human retina. Since the RPGR protein undergoes post-translational glutamylation in the protein domain that may be particularly affected by gene instability, a functional assay of glutamylation is essential to verify the correct coding sequence.
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Affiliation(s)
- Cristina Martinez-Fernandez De La Camara
- Department of Clinical Neurosciences, Nuffield Laboratory of Ophthalmology, University of Oxford, John Radcliffe Hospital, Headley Way, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headley Way, UK
| | - Jasmina Cehajic-Kapetanovic
- Department of Clinical Neurosciences, Nuffield Laboratory of Ophthalmology, University of Oxford, John Radcliffe Hospital, Headley Way, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headley Way, UK
| | - Robert E. MacLaren
- Department of Clinical Neurosciences, Nuffield Laboratory of Ophthalmology, University of Oxford, John Radcliffe Hospital, Headley Way, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Headley Way, UK
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Bompard G, van Dijk J, Cau J, Lannay Y, Marcellin G, Lawera A, van der Laan S, Rogowski K. CSAP Acts as a Regulator of TTLL-Mediated Microtubule Glutamylation. Cell Rep 2019; 25:2866-2877.e5. [PMID: 30517872 DOI: 10.1016/j.celrep.2018.10.095] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/22/2017] [Accepted: 10/25/2018] [Indexed: 01/22/2023] Open
Abstract
Tubulin glutamylation is a reversible posttranslational modification that accumulates on stable microtubules (MTs). While abnormally high levels of this modification lead to a number of disorders such as male sterility, retinal degeneration, and neurodegeneration, very little is known about the molecular mechanisms underlying the regulation of glutamylase activity. Here, we found that CSAP forms a complex with TTLL5, and we demonstrate that the two proteins regulate their reciprocal abundance. Moreover, we show that CSAP increases TTLL5-mediated glutamylation and identify the TTLL5-interacting domain. Deletion of this domain leads to complete loss of CSAP activating function without impacting its MT binding. Binding of CSAP to TTLL5 promotes relocalization of TTLL5 toward MTs. Finally, we show that CSAP binds and activates all of the remaining autonomously active TTLL glutamylases. As such, we present CSAP as a major regulator of tubulin glutamylation and associated functions.
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Affiliation(s)
- Guillaume Bompard
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Juliette van Dijk
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Julien Cau
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Yoann Lannay
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Guillaume Marcellin
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Aleksandra Lawera
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Siem van der Laan
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France
| | - Krzysztof Rogowski
- Institute of Human Genetics (IGH), UMR9002 CNRS-University of Montpellier, 34094 Cedex 5, 141 Rue de la Cardonille, 34090 Montpellier, France.
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32
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Cehajic Kapetanovic J, McClements ME, Martinez-Fernandez de la Camara C, MacLaren RE. Molecular Strategies for RPGR Gene Therapy. Genes (Basel) 2019; 10:genes10090674. [PMID: 31487940 PMCID: PMC6770968 DOI: 10.3390/genes10090674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/27/2019] [Accepted: 09/01/2019] [Indexed: 11/16/2022] Open
Abstract
Mutations affecting the Retinitis Pigmentosa GTPase Regulator (RPGR) gene are the commonest cause of X-linked and recessive retinitis pigmentosa (RP), accounting for 10%-20% of all cases of RP. The phenotype is one of the most severe amongst all causes of RP, characteristic for its early onset and rapid progression to blindness in young people. At present there is no cure for RPGR-related retinal disease. Recently, however, there have been important advances in RPGR research from bench to bedside that increased our understanding of RPGR function and led to the development of potential therapies, including the progress of adeno-associated viral (AAV)-mediated gene replacement therapy into clinical trials. This manuscript discusses the advances in molecular research, which have connected the RPGR protein with an important post-translational modification, known as glutamylation, that is essential for its optimal function as a key regulator of photoreceptor ciliary transport. In addition, we review key pre-clinical research that addressed challenges encountered during development of therapeutic vectors caused by high infidelity of the RPGR genomic sequence. Finally, we discuss the structure of three current phase I/II clinical trials based on three AAV vectors and RPGR sequences and link the rationale behind the use of the different vectors back to the bench research that led to their development.
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Affiliation(s)
- Jasmina Cehajic Kapetanovic
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK. '
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK. '
| | | | - Cristina Martinez-Fernandez de la Camara
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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Quarantotti V, Chen J, Tischer J, Gonzalez Tejedo C, Papachristou EK, D'Santos CS, Kilmartin JV, Miller ML, Gergely F. Centriolar satellites are acentriolar assemblies of centrosomal proteins. EMBO J 2019; 38:e101082. [PMID: 31304626 PMCID: PMC6627235 DOI: 10.15252/embj.2018101082] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/24/2019] [Accepted: 05/06/2019] [Indexed: 12/02/2022] Open
Abstract
Centrioles are core structural elements of both centrosomes and cilia. Although cytoplasmic granules called centriolar satellites have been observed around these structures, lack of a comprehensive inventory of satellite proteins impedes our understanding of their ancestry. To address this, we performed mass spectrometry (MS)-based proteome profiling of centriolar satellites obtained by affinity purification of their key constituent, PCM1, from sucrose gradient fractions. We defined an interactome consisting of 223 proteins, which showed striking enrichment in centrosome components. The proteome also contained new structural and regulatory factors with roles in ciliogenesis. Quantitative MS on whole-cell and centriolar satellite proteomes of acentriolar cells was performed to reveal dependencies of satellite composition on intact centrosomes. Although most components remained associated with PCM1 in acentriolar cells, reduced cytoplasmic and satellite levels were observed for a subset of centrosomal proteins. These results demonstrate that centriolar satellites and centrosomes form independently but share a substantial fraction of their proteomes. Dynamic exchange of proteins between these organelles could facilitate their adaptation to changing cellular environments during development, stress response and tissue homeostasis.
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Affiliation(s)
- Valentina Quarantotti
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Jia‐Xuan Chen
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Julia Tischer
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Carmen Gonzalez Tejedo
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | | | - Clive S D'Santos
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - John V Kilmartin
- MRC Laboratory of Molecular BiologyCambridge Biomedical CampusCambridgeUK
| | - Martin L Miller
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Fanni Gergely
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
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Gheiratmand L, Coyaud E, Gupta GD, Laurent EMN, Hasegan M, Prosser SL, Gonçalves J, Raught B, Pelletier L. Spatial and proteomic profiling reveals centrosome-independent features of centriolar satellites. EMBO J 2019; 38:e101109. [PMID: 31304627 PMCID: PMC6627244 DOI: 10.15252/embj.2018101109] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/19/2022] Open
Abstract
Centriolar satellites are small electron-dense granules that cluster in the vicinity of centrosomes. Satellites have been implicated in multiple critical cellular functions including centriole duplication, centrosome maturation, and ciliogenesis, but their precise composition and assembly properties have remained poorly explored. Here, we perform in vivo proximity-dependent biotin identification (BioID) on 22 human satellite proteins, to identify 2,113 high-confidence interactions among 660 unique polypeptides. Mining this network, we validate six additional satellite components. Analysis of the satellite interactome, combined with subdiffraction imaging, reveals the existence of multiple unique microscopically resolvable satellite populations that display distinct protein interaction profiles. We further show that loss of satellites in PCM1-depleted cells results in a dramatic change in the satellite interaction landscape. Finally, we demonstrate that satellite composition is largely unaffected by centriole depletion or disruption of microtubules, indicating that satellite assembly is centrosome-independent. Together, our work offers the first systematic spatial and proteomic profiling of human centriolar satellites and paves the way for future studies aimed at better understanding the biogenesis and function(s) of these enigmatic structures.
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Affiliation(s)
- Ladan Gheiratmand
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Etienne Coyaud
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
| | - Gagan D Gupta
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
- Present address:
Department of Chemistry and BiologyRyerson UniversityTorontoONCanada
| | | | - Monica Hasegan
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Suzanna L Prosser
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - João Gonçalves
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
| | - Brian Raught
- Princess Margaret Cancer CentreUniversity Health NetworkTorontoONCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoONCanada
| | - Laurence Pelletier
- Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
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Sergouniotis PI. Inherited Retinal Disorders: Using Evidence as a Driver for Implementation. Ophthalmologica 2019; 242:187-194. [PMID: 31280272 DOI: 10.1159/000500574] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/25/2019] [Indexed: 11/19/2022]
Abstract
Incremental advances in the field of retinal genetics have transformed our understanding of inherited retinal disorders and have led to the development of powerful diagnostic tests and promising gene-based therapies. Despite this, successful integration of these developments into routine healthcare is frequently ineffective. Providing robust evidence of benefit can accelerate the implementation of clinical genetic interventions. For example, the adoption of a genetic test is much more likely when the test's clinical utility (i.e. its ability to influence management and health outcomes) has been clearly demonstrated. However, accruing such evidence for rare conditions like inherited retinal disorders is challenging. Conducting sufficiently powered studies requires both efficient study designs and large-scale, international collaboration. Reaching all populations and as many affected individuals as possible is key. Equally important are efforts to precisely and consistently capture phenotypic information, including natural history data. This article summarizes some of the current obstacles to implemen-tation and discusses approaches to overcome these barriers.
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Affiliation(s)
- Panagiotis I Sergouniotis
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom, .,Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom, .,Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom,
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36
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Khanna H. More Than Meets the Eye: Current Understanding of RPGR Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1074:521-538. [PMID: 29721984 DOI: 10.1007/978-3-319-75402-4_64] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
This article summarizes the recent advances in our understanding of a major retinal disease gene RPGR (retinitis pigmentosa GTPase regulator), mutations in which are associated with majority of X-linked forms of retinal degenerations. A great deal of work has been done to uncover the ciliary localization of RPGR and its interacting proteins in the retina. However, the molecular mechanisms of action of RPGR in the photoreceptors are still unclear. Recent studies have begun to shed light on the intracellular pathways in which RPGR is likely involved. The deregulation of such pathways may underlie the pathogenesis of severe retinal degeneration associated with RPGR. With the recent advances in the gene augmentation therapy for RPGR-associated disease, there is a lot of excitement in the field. Patients with RPGR mutations, however, present with clinically heterogeneous manifestations. It is therefore imperative to examine the function of RPGR in detail, so that we can design patient-oriented therapeutic strategies for this disease.
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Affiliation(s)
- Hemant Khanna
- Department of Ophthalmology and Neurobiology, UMASS Medical School, Worcester, MA, USA.
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37
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Ferreira LT, Figueiredo AC, Orr B, Lopes D, Maiato H. Dissecting the role of the tubulin code in mitosis. Methods Cell Biol 2018; 144:33-74. [PMID: 29804676 DOI: 10.1016/bs.mcb.2018.03.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitosis is an essential process that takes place in all eukaryotes and involves the equal division of genetic material from a parental cell into two identical daughter cells. During mitosis, chromosome movement and segregation are orchestrated by a specialized structure known as the mitotic spindle, composed of a bipolar array of microtubules. The fundamental structure of microtubules comprises of α/β-tubulin heterodimers that associate head-to-tail and laterally to form hollow filaments. In vivo, microtubules are modified by abundant and evolutionarily conserved tubulin posttranslational modifications (PTMs), giving these filaments the potential for a wide chemical diversity. In recent years, the concept of a "tubulin code" has emerged as an extralayer of regulation governing microtubule function. A range of tubulin isoforms, each with a diverse set of PTMs, provides a readable code for microtubule motors and other microtubule-associated proteins. This chapter focuses on the complexity of tubulin PTMs with an emphasis on detyrosination and summarizes the methods currently used in our laboratory to experimentally manipulate these modifications and study their impact in mitosis.
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Affiliation(s)
- Luísa T Ferreira
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ana C Figueiredo
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Bernardo Orr
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Danilo Lopes
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Helder Maiato
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Faculdade de Medicina, Universidade do Porto, Porto, Portugal.
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38
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Pontikos N, Yu J, Moghul I, Withington L, Blanco-Kelly F, Vulliamy T, Wong TLE, Murphy C, Cipriani V, Fiorentino A, Arno G, Greene D, Jacobsen JOB, Clark T, Gregory DS, Nemeth AM, Halford S, Inglehearn CF, Downes S, Black GC, Webster AR, Hardcastle AJ, Plagnol V. Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data. Bioinformatics 2018; 33:2421-2423. [PMID: 28334266 DOI: 10.1093/bioinformatics/btx147] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/14/2017] [Indexed: 11/12/2022] Open
Abstract
Summary Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritization based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare genetic diseases. Availability and Implementation A demo of the website is available at https://phenopolis.github.io . If you wish to install a local copy, source code and installation instruction are available at https://github.com/phenopolis . The software is implemented using Python, MongoDB, HTML/Javascript and various bash shell scripts. Contact n.pontikos@ucl.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nikolas Pontikos
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Institute of Ophthalmology, University College London, London EC1V 9EL, UK.,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ismail Moghul
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | | | - Fiona Blanco-Kelly
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK.,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Tom Vulliamy
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Tsz Lun Ernest Wong
- Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Cian Murphy
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Warwick Medical School, The University of Warwick, Coventry CV4 7AL, UK
| | - Valentina Cipriani
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.,Institute of Ophthalmology, University College London, London EC1V 9EL, UK.,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Alessia Fiorentino
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Gavin Arno
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK.,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Daniel Greene
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Julius O B Jacobsen
- Barts and The London School of Medicine and Dentistry, William Harvey Research Institute, Queen Mary University of London, John Vane Building, Charterhouse Square, London EC1M 6BQ, UK
| | - Tristan Clark
- Computer Science Department, University College London, London WC1E 6BT, UK
| | - David S Gregory
- Computer Science Department, University College London, London WC1E 6BT, UK
| | - Andrea M Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Chris F Inglehearn
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, St James's University Hospital, Leeds LS9 7TF, UK
| | - Susan Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Graeme C Black
- Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Andrew R Webster
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK.,Moorfields Eye Hospital, London EC1V 2PD, UK
| | | | | | - Vincent Plagnol
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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39
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Ye B, Liu B, Hao L, Zhu X, Yang L, Wang S, Xia P, Du Y, Meng S, Huang G, Qin X, Wang Y, Yan X, Li C, Hao J, Zhu P, He L, Tian Y, Fan Z. Klf4 glutamylation is required for cell reprogramming and early embryonic development in mice. Nat Commun 2018; 9:1261. [PMID: 29593216 PMCID: PMC5871780 DOI: 10.1038/s41467-018-03008-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/10/2018] [Indexed: 12/20/2022] Open
Abstract
Temporal and spatial-specific regulation of pluripotency networks is largely dependent on the precise modifications of core transcription factors. Misregulation of glutamylation is implicated in severe physiological abnormalities. However, how glutamylation regulates cell reprogramming and pluripotency networks remains elusive. Here we show that cytosolic carboxypeptidases 1 (CCP1) or CCP6 deficiency substantially promotes induced pluripotent cell (iPSC) induction and pluripotency of embryonic stem cells (ESCs). Klf4 polyglutamylation at Glu381 by tubulin tyrosine ligase-like 4 (TTLL4) and TTLL1 during cell reprogramming impedes its lysine 48-linked ubiquitination and sustains Klf4 stability. Klf4-E381A knockin mice display impaired blastocyst development and embryonic lethality. Deletion of TTLL4 or TTLL1 abrogates cell reprogramming and early embryogenesis. Thus, Klf4 polyglutamylation plays a critical role in the regulation of cell reprogramming and pluripotency maintenance. Embryonic stem cell pluripotency depends upon precise regulation by a core transcription network. Here the authors show that polyglutamylation mediated stabilization of the transcription factor Klf4 by TTLL1 and TTLL4 promotes reprogramming, pluripotency and preimplantation embryonic development.
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Affiliation(s)
- Buqing Ye
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Benyu Liu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lu Hao
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhu
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liuliu Yang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pengyan Xia
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shu Meng
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanling Huang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiwen Qin
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanying Wang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinlong Yan
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chong Li
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junfeng Hao
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luyun He
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Tian
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Martinez-Fernandez De La Camara C, Nanda A, Salvetti AP, Fischer MD, MacLaren RE. Gene therapy for the treatment of X-linked retinitis pigmentosa. Expert Opin Orphan Drugs 2018; 6:167-177. [PMID: 30057863 PMCID: PMC6059358 DOI: 10.1080/21678707.2018.1444476] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION X-linked retinitis pigmentosa caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene is the most common form of recessive RP. The phenotype is characterised by its severity and rapid disease progression. Gene therapy using adeno-associated viral vectors is currently the most promising therapeutic approach. However, the construction of a stable vector encoding the full-length RPGR transcript has previously proven to be a limiting step towards gene therapy clinical trials. Recently however, a codon optimised version of RPGR has been shown to increase the stability and fidelity of the sequence, conferring a therapeutic effect in murine and canine animal models. AREAS COVERED This manuscript reviews the natural history of X-linked retinitis pigmentosa and the research performed from the discovery of the causative gene, RPGR, to the preclinical testing of potential therapies that have led to the initiation of three clinical trials. EXPERT OPINION X-linked retinitis pigmentosa is an amenable disease to be treated by gene therapy. Codon optimisation has overcome the challenge of designing an RPGR vector without mutations, and with a therapeutic effect in different animal models. With the RPGR gene therapy clinical trials still in the early stages, the confirmation of the safety, tolerability and potency of the therapy is still ongoing.
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Affiliation(s)
| | - Anika Nanda
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Anna Paola Salvetti
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Department of Biomedical and Clinical Sciences “Luigi Sacco”, Sacco Hospital, University of Milan, Milano, Italy
| | - M. Dominik Fischer
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Centre for Ophthalmology Tübingen, University Eye Hospital, Tübingen, Germany
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
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41
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Bedoni N, Haer-Wigman L, Vaclavik V, Tran VH, Farinelli P, Balzano S, Royer-Bertrand B, El-Asrag ME, Bonny O, Ikonomidis C, Litzistorf Y, Nikopoulos K, Yioti GG, Stefaniotou MI, McKibbin M, Booth AP, Ellingford JM, Black GC, Toomes C, Inglehearn CF, Hoyng CB, Bax N, Klaver CCW, Thiadens AA, Murisier F, Schorderet DF, Ali M, Cremers FPM, Andréasson S, Munier FL, Rivolta C. Mutations in the polyglutamylase gene TTLL5, expressed in photoreceptor cells and spermatozoa, are associated with cone-rod degeneration and reduced male fertility. Hum Mol Genet 2018; 25:4546-4555. [PMID: 28173158 DOI: 10.1093/hmg/ddw282] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/19/2016] [Accepted: 08/20/2016] [Indexed: 12/30/2022] Open
Abstract
Hereditary retinal degenerations encompass a group of genetic diseases characterized by extreme clinical variability. Following next-generation sequencing and autozygome-based screening of patients presenting with a peculiar, recessive form of cone-dominated retinopathy, we identified five homozygous variants [p.(Asp594fs), p.(Gln117*), p.(Met712fs), p.(Ile756Phe), and p.(Glu543Lys)] in the polyglutamylase-encoding gene TTLL5, in eight patients from six families. The two male patients carrying truncating TTLL5 variants also displayed a substantial reduction in sperm motility and infertility, whereas those carrying missense changes were fertile. Defects in this polyglutamylase in humans have recently been associated with cone photoreceptor dystrophy, while mouse models carrying truncating mutations in the same gene also display reduced fertility in male animals. We examined the expression levels of TTLL5 in various human tissues and determined that this gene has multiple viable isoforms, being highly expressed in testis and retina. In addition, antibodies against TTLL5 stained the basal body of photoreceptor cells in rat and the centrosome of the spermatozoon flagellum in humans, suggesting a common mechanism of action in these two cell types. Taken together, our data indicate that mutations in TTLL5 delineate a novel, allele-specific syndrome causing defects in two as yet pathogenically unrelated functions, reproduction and vision.
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Affiliation(s)
- Nicola Bedoni
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Lonneke Haer-Wigman
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Veronika Vaclavik
- Jules Gonin Eye Hospital, Lausanne, Switzerland.,Fertas Andrology Laboratory, Lausanne, Switzerland
| | - Viet H Tran
- Jules Gonin Eye Hospital, Lausanne, Switzerland
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Sara Balzano
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Beryl Royer-Bertrand
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Institute for Research in Ophtalmology, University of Lausanne and Ecole Polytechnique Federale de Lausanne, Switzerland
| | - Mohammed E El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Olivier Bonny
- Service of Nephrology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Christos Ikonomidis
- Department of Otorhinolaryngology, Head and Neck Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Yan Litzistorf
- Department of Otorhinolaryngology, Head and Neck Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Konstantinos Nikopoulos
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Georgia G Yioti
- Department of Ophthalmology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Maria I Stefaniotou
- Department of Ophthalmology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Martin McKibbin
- The Eye Department, St. James's University Hospital, Leeds, UK
| | - Adam P Booth
- Royal Eye Infirmary, Derriford Hospital, Plymouth, UK
| | - Jamie M Ellingford
- Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Graeme C Black
- Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Carmel Toomes
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Chris F Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nathalie Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Alberta A Thiadens
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Daniel F Schorderet
- Institute for Research in Ophtalmology, University of Lausanne and Ecole Polytechnique Federale de Lausanne, Switzerland
| | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, UK
| | - Frans P M Cremers
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | | | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
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42
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Identification of DmTTLL5 as a Major Tubulin Glutamylase in the Drosophila Nervous System. Sci Rep 2017; 7:16254. [PMID: 29176602 PMCID: PMC5701211 DOI: 10.1038/s41598-017-16586-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/14/2017] [Indexed: 01/09/2023] Open
Abstract
Microtubules (MTs) play crucial roles during neuronal life. They are formed by heterodimers of alpha and beta-tubulins, which are subjected to several post-translational modifications (PTMs). Amongst them, glutamylation consists in the reversible addition of a variable number of glutamate residues to the C-terminal tails of tubulins. Glutamylation is the most abundant MT PTM in the mammalian adult brain, suggesting that it plays an important role in the nervous system (NS). Here, we show that the previously uncharacterized CG31108 gene encodes an alpha-tubulin glutamylase acting in the Drosophila NS. We show that this glutamylase, which we named DmTTLL5, initiates MT glutamylation specifically on alpha-tubulin, which are the only glutamylated tubulin in the Drosophila brain. In DmTTLL5 mutants, MT glutamylation was not detected in the NS, allowing for determining its potential function. DmTTLL5 mutants are viable and we did not find any defect in vesicular axonal transport, synapse morphology and larval locomotion. Moreover, DmTTLL5 mutant flies display normal negative geotaxis behavior and their lifespan is not altered. Thus, our work identifies DmTTLL5 as the major enzyme responsible for initiating neuronal MT glutamylation specifically on alpha-tubulin and we show that the absence of MT glutamylation is not detrimental for Drosophila NS function.
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O'Hagan R, Silva M, Nguyen KCQ, Zhang W, Bellotti S, Ramadan YH, Hall DH, Barr MM. Glutamylation Regulates Transport, Specializes Function, and Sculpts the Structure of Cilia. Curr Biol 2017; 27:3430-3441.e6. [PMID: 29129530 PMCID: PMC5698134 DOI: 10.1016/j.cub.2017.09.066] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/09/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Ciliary microtubules (MTs) are extensively decorated with post-translational modifications (PTMs), such as glutamylation of tubulin tails. PTMs and tubulin isotype diversity act as a "tubulin code" that regulates cytoskeletal stability and the activity of MT-associated proteins such as kinesins. We previously showed that, in C. elegans cilia, the deglutamylase CCPP-1 affects ciliary ultrastructure, localization of the TRP channel PKD-2 and the kinesin-3 KLP-6, and velocity of the kinesin-2 OSM-3/KIF17, whereas a cell-specific α-tubulin isotype regulates ciliary ultrastructure, intraflagellar transport, and ciliary functions of extracellular vesicle (EV)-releasing neurons. Here we examine the role of PTMs and the tubulin code in the ciliary specialization of EV-releasing neurons using genetics, fluorescence microscopy, kymography, electron microscopy, and sensory behavioral assays. Although the C. elegans genome encodes five tubulin tyrosine ligase-like (TTLL) glutamylases, only ttll-11 specifically regulates PKD-2 localization in EV-releasing neurons. In EV-releasing cephalic male (CEM) cilia, TTLL-11 and the deglutamylase CCPP-1 regulate remodeling of 9+0 MT doublets into 18 singlet MTs. Balanced TTLL-11 and CCPP-1 activity fine-tunes glutamylation to control the velocity of the kinesin-2 OSM-3/KIF17 and kinesin-3 KLP-6 without affecting the intraflagellar transport (IFT) kinesin-II. TTLL-11 is transported by ciliary motors. TTLL-11 and CCPP-1 are also required for the ciliary function of releasing bioactive EVs, and TTLL-11 is itself a novel EV cargo. Therefore, MT glutamylation, as part of the tubulin code, controls ciliary specialization, ciliary motor-based transport, and ciliary EV release in a living animal. We suggest that cell-specific control of MT glutamylation may be a conserved mechanism to specialize the form and function of cilia.
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Affiliation(s)
- Robert O'Hagan
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Malan Silva
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ken C Q Nguyen
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, 1410 Pelham Parkway, Bronx, NY 10461, USA
| | - Winnie Zhang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sebastian Bellotti
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yasmin H Ramadan
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, 1410 Pelham Parkway, Bronx, NY 10461, USA
| | - Maureen M Barr
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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44
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Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
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45
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Disease mechanisms of X-linked retinitis pigmentosa due to RP2 and RPGR mutations. Biochem Soc Trans 2017; 44:1235-1244. [PMID: 27911705 DOI: 10.1042/bst20160148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 01/24/2023]
Abstract
Photoreceptor degeneration is the prominent characteristic of retinitis pigmentosa (RP), a heterogeneous group of inherited retinal dystrophies resulting in blindness. Although abnormalities in many pathways can cause photoreceptor degeneration, one of the most important causes is defective protein transport through the connecting cilium, the structure that connects the biosynthetic inner segment with the photosensitive outer segment of the photoreceptors. The majority of patients with X-linked RP have mutations in the retinitis pigmentosa GTPase regulator (RPGR) or RP2 genes, the protein products of which are both components of the connecting cilium and associated with distinct mechanisms of protein delivery to the outer segment. RP2 and RPGR proteins are associated with severe diseases ranging from classic RP to atypical forms. In this short review, we will summarise current knowledge generated by experimental studies and knockout animal models, compare and discuss the prominent hypotheses about the two proteins' functions in retinal cell biology.
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46
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Liu Y, Lu Y, Liu S, Liao S. Novel compound heterozygous mutations of ALDH1A3 contribute to anophthalmia in a non-consanguineous Chinese family. Genet Mol Biol 2017; 40:430-435. [PMID: 28590501 PMCID: PMC5488456 DOI: 10.1590/1678-4685-gmb-2016-0120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/31/2016] [Indexed: 02/05/2023] Open
Abstract
Anophthalmia is a rare eye development anomaly resulting in absent ocular globes or
tissue in the orbit since birth. Here, we investigated a newborn with bilateral
anophthalmia in a Chinese family. Exome sequencing revealed that compound
heterozygous mutations c.287G > A (p.(Arg96His)) and c.709G > A (p.(Gly237Arg))
of the ALDH1A3 gene were present in the affected newborn. Both
mutations were absent in all of the searched databases, including 10,000 in-house
Chinese exome sequences, and these mutations were confirmed as having been
transmitted from the parents. Comparative amino acid sequence analysis across
distantly related species revealed that the residues at positions 96 and 234 were
evolutionarily highly conserved. In silico analysis predicted these
changes to be damaging, and in vitro expression analysis revealed
that the mutated alleles were associated with decreased protein production and
impaired tetrameric protein formation. This study firstly reported that compound
heterozygous mutations of the ALDH1A3 gene can result in
anophthalmia in humans, thus highlighting those heterozygous mutations in
ALDH1A3 should be considered for molecular screening in
anophthalmia, particularly in cases from families without consanguineous
relationships.
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Affiliation(s)
- Yunqiang Liu
- Department of Medical Genetics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yongjie Lu
- Department of Medical Genetics, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Shasha Liu
- Diabetes Center & Institute of Transplantation, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shunyao Liao
- Diabetes Center & Institute of Transplantation, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Wloga D, Joachimiak E, Louka P, Gaertig J. Posttranslational Modifications of Tubulin and Cilia. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028159. [PMID: 28003186 DOI: 10.1101/cshperspect.a028159] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tubulin undergoes several highly conserved posttranslational modifications (PTMs) including acetylation, detyrosination, glutamylation, and glycylation. These PTMs accumulate on a subset of microtubules that are long-lived, including those in the basal bodies and axonemes. Tubulin PTMs are distributed nonuniformly. In the outer doublet microtubules of the axoneme, the B-tubules are highly enriched in the detyrosinated, polyglutamylated, and polyglycylated tubulin, whereas the A-tubules contain mostly unmodified tubulin. The nonuniform patterns of tubulin PTMs may functionalize microtubules in a position-dependent manner. Recent studies indicate that tubulin PTMs contribute to the assembly, disassembly, maintenance, and motility of cilia. In particular, tubulin glutamylation has emerged as a key PTM that affects ciliary motility through regulation of axonemal dynein arms and controls the stability and length of the axoneme.
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Affiliation(s)
- Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Department of Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Panagiota Louka
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
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48
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May-Simera H, Nagel-Wolfrum K, Wolfrum U. Cilia - The sensory antennae in the eye. Prog Retin Eye Res 2017; 60:144-180. [PMID: 28504201 DOI: 10.1016/j.preteyeres.2017.05.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Abstract
Cilia are hair-like projections found on almost all cells in the human body. Originally believed to function merely in motility, the function of solitary non-motile (primary) cilia was long overlooked. Recent research has demonstrated that primary cilia function as signalling hubs that sense environmental cues and are pivotal for organ development and function, tissue hoemoestasis, and maintenance of human health. Cilia share a common anatomy and their diverse functional features are achieved by evolutionarily conserved functional modules, organized into sub-compartments. Defects in these functional modules are responsible for a rapidly growing list of human diseases collectively termed ciliopathies. Ocular pathogenesis is common in virtually all classes of syndromic ciliopathies, and disruptions in cilia genes have been found to be causative in a growing number of non-syndromic retinal dystrophies. This review will address what is currently known about cilia contribution to visual function. We will focus on the molecular and cellular functions of ciliary proteins and their role in the photoreceptor sensory cilia and their visual phenotypes. We also highlight other ciliated cell types in tissues of the eye (e.g. lens, RPE and Müller glia cells) discussing their possible contribution to disease progression. Progress in basic research on the cilia function in the eye is paving the way for therapeutic options for retinal ciliopathies. In the final section we describe the latest advancements in gene therapy, read-through of non-sense mutations and stem cell therapy, all being adopted to treat cilia dysfunction in the retina.
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Affiliation(s)
- Helen May-Simera
- Institute of Molecular Physiology, Cilia Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany.
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49
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Broadgate S, Yu J, Downes SM, Halford S. Unravelling the genetics of inherited retinal dystrophies: Past, present and future. Prog Retin Eye Res 2017; 59:53-96. [PMID: 28363849 DOI: 10.1016/j.preteyeres.2017.03.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The identification of the genes underlying monogenic diseases has been of interest to clinicians and scientists for many years. Using inherited retinal dystrophies as an example of monogenic disease we describe the history of molecular genetic techniques that have been pivotal in the discovery of disease causing genes. The methods that were developed in the 1970's and 80's are still in use today but have been refined and improved. These techniques enabled the concept of the Human Genome Project to be envisaged and ultimately realised. When the successful conclusion of the project was announced in 2003 many new tools and, as importantly, many collaborations had been developed that facilitated a rapid identification of disease genes. In the post-human genome project era advances in computing power and the clever use of the properties of DNA replication has allowed the development of next-generation sequencing technologies. These methods have revolutionised the identification of disease genes because for the first time there is no need to define the position of the gene in the genome. The use of next generation sequencing in a diagnostic setting has allowed many more patients with an inherited retinal dystrophy to obtain a molecular diagnosis for their disease. The identification of novel genes that have a role in the development or maintenance of retinal function is opening up avenues of research which will lead to the development of new pharmacological and gene therapy approaches. Neither of which can be used unless the defective gene and protein is known. The continued development of sequencing technologies also holds great promise for the advent of truly personalised medicine.
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Affiliation(s)
- Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
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50
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Dias MDS, Hamel CP, Meunier I, Varin J, Blanchard S, Boyard F, Sahel JA, Zeitz C. Novel splice-site mutation in TTLL5 causes cone dystrophy in a consanguineous family. Mol Vis 2017; 23:131-139. [PMID: 28356705 PMCID: PMC5360453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/16/2017] [Indexed: 11/03/2022] Open
Abstract
PURPOSE To report the clinical and genetic findings of one family with autosomal recessive cone dystrophy (CD) and to identify the causative mutation. METHODS An institutional study of three family members from two generations. The clinical examination included best-corrected Snellen visual acuity measurement, fundoscopy, the Farnsworth D-15 color vision test, a full-field electroretinogram (ERG) that incorporated the International Society for Clinical Electrophysiology of Vision standards and methodology, fundus autofluorescence (FAF) and infrared (IR), and spectral-domain optical coherence tomography (SD-OCT). Genetic findings were achieved with DNA analysis using whole exome sequencing (WES) and Sanger sequencing. RESULTS The proband, a 9-year-old boy, presented with a condition that appeared to be congenital and stationary. The clinical presentation initially reflected incomplete congenital stationary night blindness (icCSNB) because of myopia, a decrease in visual acuity, abnormal oscillatory potentials, and reduced amplitudes on the 30 Hz flicker ERG but was atypical because there were no clear electronegative responses. However, no disease-causing mutations in the genes underlying icCSNB were identified. Following WES analysis of family members, a homozygous splice-site mutation in intron 3 of TTLL5 (c.182-3_182-1delinsAA) was found cosegregating within the phenotype in the family. CONCLUSIONS The distinction between icCSNB and CD phenotypes is not always straightforward in young patients. The patient was quite young, which most likely explains why the progression of the CD was not obvious. WES analysis provided prompt diagnosis for this family; thus, the use of this technique to refine the diagnosis is highlighted in this study.
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Affiliation(s)
- Miguel de Sousa Dias
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
| | - Christian P. Hamel
- INSERM U 1051, Institut des Neurosciences de Montpellier, Hôpital Saint-Eloi, Montpellier, France,Affections Sensorielles Génétiques, CHU de Montpellier, 191 Avenue du Doyen Gaston Giraud, Montpellier, France,Université Montpellier, 163 Avenue Auguste Broussonnet, Montpellier, France
| | - Isabelle Meunier
- INSERM U 1051, Institut des Neurosciences de Montpellier, Hôpital Saint-Eloi, Montpellier, France,Affections Sensorielles Génétiques, CHU de Montpellier, 191 Avenue du Doyen Gaston Giraud, Montpellier, France,Université Montpellier, 163 Avenue Auguste Broussonnet, Montpellier, France
| | - Juliette Varin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
| | | | - Fiona Boyard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
| | - José-Alain Sahel
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, 28 rue de Charenton, Paris, France,Institute of Ophthalmology, University College of London, London EC1V 9EL, UK,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France,Academie des Sciences, Institut de France, Paris, France,Department of Ophthalmology, The University of Pittsburghschool of Medicine, Pittsburg, PA
| | - Christina Zeitz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 17 rue Moreau, Paris, France
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