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Banerjee A, Farci P. Fibrosis and Hepatocarcinogenesis: Role of Gene-Environment Interactions in Liver Disease Progression. Int J Mol Sci 2024; 25:8641. [PMID: 39201329 PMCID: PMC11354981 DOI: 10.3390/ijms25168641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/02/2024] Open
Abstract
The liver is a complex organ that performs vital functions in the body. Despite its extraordinary regenerative capacity compared to other organs, exposure to chemical, infectious, metabolic and immunologic insults and toxins renders the liver vulnerable to inflammation, degeneration and fibrosis. Abnormal wound healing response mediated by aberrant signaling pathways causes chronic activation of hepatic stellate cells (HSCs) and excessive accumulation of extracellular matrix (ECM), leading to hepatic fibrosis and cirrhosis. Fibrosis plays a key role in liver carcinogenesis. Once thought to be irreversible, recent clinical studies show that hepatic fibrosis can be reversed, even in the advanced stage. Experimental evidence shows that removal of the insult or injury can inactivate HSCs and reduce the inflammatory response, eventually leading to activation of fibrolysis and degradation of ECM. Thus, it is critical to understand the role of gene-environment interactions in the context of liver fibrosis progression and regression in order to identify specific therapeutic targets for optimized treatment to induce fibrosis regression, prevent HCC development and, ultimately, improve the clinical outcome.
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Affiliation(s)
- Anindita Banerjee
- Department of Transfusion Transmitted Diseases, ICMR-National Institute of Immunohaematology, Mumbai 400012, Maharashtra, India;
| | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Song C, Li L, Liu C, Hu L, Bai J, Liang W, Zhao L, Song W, Li S. Whole-exome sequencing screening for candidate genes and variants associated with primary sporadic keratoconus in Chinese patients. Exp Eye Res 2024; 245:109978. [PMID: 38908538 DOI: 10.1016/j.exer.2024.109978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/29/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
The pathogenesis of keratoconus (KC) is complex, and genetic factors play an important role. The purpose of this study was to screen and analyse candidate genes and variants in Chinese patients with primary sporadic KC. Whole-exome sequencing (WES) was performed to identify candidate genes and variants in 105 unrelated Chinese patients with primary sporadic KC. Through a series of screening processes, 54 candidate variants in 26 KC candidate genes were identified in 53 KC patients (53/105, 50.5%). These 54 candidate variants included 10 previously identified variants in 9 KC candidate genes and 44 novel variants in 20 KC candidate genes. The previously identified variants occurred in 25.7% (27/105) of patients. Of these, 4 variants (COL6A5, c.5014T > G; CAST, c.1814G > A; ZNF469, c.946G > A; and MPDZ, c.3836A > G) were identified for the first time in Chinese KC patients. The novel variants occurred in 33.3% (35/105) of patients. Of the 26 screened KC candidate genes, 11 KC candidate genes (CAT, COL12A1, FLG, HKDC1, HSPG2, PLOD1, ITGA2, TFAP2B, USH2A, WNT10A, and COL6A5) were found to be potentially pathogenic in Chinese KC patients for the first time. Gene Ontology (GO) biological process (BP) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on the 26 KC candidate genes using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The results showed that the KC candidate genes were significantly enriched in biological processes such as collagen fibril organization and extracellular matrix (ECM) organization and in ECM-receptor interaction and protein digestion and absorption pathways. The results further expand the spectrum of KC candidate variants and provide a basis for further KC gene studies.
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Affiliation(s)
- Chunyuan Song
- Aier Eye Hospital, Jinan University, Guangzhou, 510071, China
| | - Ling Li
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Chang Liu
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Luping Hu
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China
| | - Jie Bai
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Weiyan Liang
- Aier Eye Hospital of Anhui Medical University, Anhui, 230031, China; Tianjin Aier Eye Hospital, Tianjin, 300000, China
| | - Lin Zhao
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Wenxiu Song
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Shaowei Li
- Aier Eye Hospital, Jinan University, Guangzhou, 510071, China; Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China; Aier Eye Hospital of Anhui Medical University, Anhui, 230031, China; Tianjin University, Tianjin, 300072, China.
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Ariyachet C, Nokkeaw A, Boonkaew B, Tangkijvanich P. ZNF469 is a profibrotic regulator of extracellular matrix in hepatic stellate cells. J Cell Biochem 2024; 125:e30578. [PMID: 38704698 DOI: 10.1002/jcb.30578] [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: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/07/2024]
Abstract
Activation of quiescent hepatic stellate cells (HSCs) into proliferative myofibroblasts drives extracellular cellular matrix (ECM) accumulation and liver fibrosis; nevertheless, the transcriptional network that promotes such a process is not completely understood. ZNF469 is a putative C2H2 zinc finger protein that may bind to specific genome sequences. It is found to be upregulated upon HSC activation; however, the molecular function of ZNF469 is completely unknown. Here, we show that knockdown of ZNF469 in primary human HSCs impaired proliferation, migration, and collagen production. Conversely, overexpression of ZNF469 in HSCs yielded the opposite results. Transforming growth factor-β 1 promoted expression of ZNF469 in a Smad3-dependent manner, where the binding of Smad3 was confirmed at the ZNF469 promoter. RNA sequencing data of ZNF469-knockdown HSCs revealed the ECM-receptor interaction, which provides structural and signaling support to cells, was the most affected pathway, and significant downregulation of various collagen and proteoglycan genes was observed. To investigate the function of ZNF469, we cloned a full-length open reading frame of ZNF469 with an epitope tag and identified a nuclear localization of the protein. Luciferase reporter and chromatin immunoprecipitation assays revealed the presence of ZNF469 at the promoter of ECM genes, supporting its function as a transcription factor. Analysis of human fibrotic and cirrhotic tissues showed increased expression of ZNF469 and a positive correlation between expression levels of ZNF469 and ECM genes. Moreover, this observation was similar in other fibrotic organs, including the heart, lung, and skin, suggesting that myofibroblasts from various origins generally require ZNF469 to promote ECM production. Together, this study is the first to reveal the role of ZNF469 as a profibrotic factor in HSCs and suggests ZNF469 as a novel target for antifibrotic therapy.
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Affiliation(s)
- Chaiyaboot Ariyachet
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Archittapon Nokkeaw
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Medical Biochemistry Program, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Bootsakorn Boonkaew
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Medical Biochemistry Program, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pisit Tangkijvanich
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Geng X, Zhu L, Li J, Li Z. Brittle cornea syndrome: A novel mutation. Heliyon 2024; 10:e32506. [PMID: 38961930 PMCID: PMC11219502 DOI: 10.1016/j.heliyon.2024.e32506] [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: 01/25/2024] [Revised: 06/01/2024] [Accepted: 06/05/2024] [Indexed: 07/05/2024] Open
Abstract
Purpose To report the clinical, tomographic, histopathological and genetic findings of a patient with brittle cornea syndrome and a novel mutation in the ZNF469 gene likely implicated in the development of this disorder. Methods A 64-year-old man presented with a two-year history of worsening vision in both eyes. The patient and his son were examined by imaging and genetic analysis. Results The patient exhibited persistent ocular irritation, decreased vision, corneal epithelial defects and corneal stromal opacity. Confocal microscopy revealed that the anterior corneal stroma had a large amount of highly reflective and striated tissue. However, his son had no symptoms. Genetic analysis identified a heterozygous c.1781C > T:p.P594L variation in the ZNF469 gene. Conclusions We reported a novel mutation in the ZNF469 gene (c.1781C > T:p.P594L) in a patient with brittle cornea syndrome from China, which enriched the spectrum of ZNF469 variants implicated in brittle cornea syndrome.
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Affiliation(s)
- Xingchen Geng
- Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Lei Zhu
- Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Jingguo Li
- Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Zhanrong Li
- Henan Eye Hospital, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
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Moore P, Wolf A, Sathyamoorthy M. An Eye into the Aorta: The Role of Extracellular Matrix Regulatory Genes ZNF469 and PRDM5, from Their Previous Association with Brittle Cornea Syndrome to Their Novel Association with Aortic and Arterial Aneurysmal Diseases. Int J Mol Sci 2024; 25:5848. [PMID: 38892036 PMCID: PMC11172047 DOI: 10.3390/ijms25115848] [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: 04/29/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024] Open
Abstract
The extracellular matrix is a complex network of proteins and other molecules that are essential for the support, integrity, and structure of cells and tissues within the human body. The genes ZNF469 and PRDM5 each produce extracellular-matrix-related proteins that, when mutated, have been shown to result in the development of brittle cornea syndrome. This dysfunction results from aberrant protein function resulting in extracellular matrix disruption. Our group recently identified and published the first known associations between variants in these genes and aortic/arterial aneurysms and dissection diseases. This paper delineates the proposed effects of mutated ZNF469 and PRDM5 on various essential extracellular matrix components, including various collagens, TGF-B, clusterin, thrombospondin, and HAPLN-1, and reviews our recent reports associating single-nucleotide variants to these genes' development of aneurysmal and dissection diseases.
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Affiliation(s)
- Peyton Moore
- Sathyamoorthy Laboratory, Department of Medicine, Burnett School of Medicine at TCU, Fort Worth, TX 76104, USA
| | - Adam Wolf
- Sathyamoorthy Laboratory, Department of Medicine, Burnett School of Medicine at TCU, Fort Worth, TX 76104, USA
| | - Mohanakrishnan Sathyamoorthy
- Sathyamoorthy Laboratory, Department of Medicine, Burnett School of Medicine at TCU, Fort Worth, TX 76104, USA
- Consultants in Cardiovascular Medicine and Science, Fort Worth, TX 76104, USA
- Fort Worth Institute for Molecular Medicine and Genomics Research, Fort Worth, TX 76104, USA
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Steinhauser S, Estoppey D, Buehler DP, Xiong Y, Pizzato N, Rietsch A, Wu F, Leroy N, Wunderlin T, Claerr I, Tropberger P, Müller M, Davison LM, Sheng Q, Bergling S, Wild S, Moulin P, Liang J, English WJ, Williams B, Knehr J, Altorfer M, Reyes A, Mickanin C, Hoepfner D, Nigsch F, Frederiksen M, Flynn CR, Fodor BD, Brown JD, Kolter C. The transcription factor ZNF469 regulates collagen production in liver fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591188. [PMID: 38712281 PMCID: PMC11071482 DOI: 10.1101/2024.04.25.591188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world's population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.
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Lin Q, Wang X, Han T, Peng X, Zhou X. Variants in the ZNF469 gene in families with Brittle cornea syndrome and keratoconus. Heliyon 2024; 10:e27052. [PMID: 38439828 PMCID: PMC10909740 DOI: 10.1016/j.heliyon.2024.e27052] [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: 06/11/2023] [Revised: 12/11/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Background Brittle cornea syndrome 1 (BCS1) is a rare autosomal recessive disorder characterized by corneal and sclera thinning and fragility that is caused by zinc finger protein 469 (ZNF469) gene mutation. Keratoconus is another disease related to corneal thinning. Several reports have linked ZNF469 variants and keratoconus. We recruited a four-generation BCS1 family and two keratoconus families to explore pathogenic ZNF469 variants. Methods This study included 11 members from a family with BCS1, 2 families with keratoconus, 368 sporadic keratoconus patients and 325 unrelated healthy controls. Whole exome sequencing of DNA from peripheral blood and cross species conservation analysis was used to investigate and verify ZNF469 variants. Results A new homozygous frameshift mutation c. 6727del (p.Asp2243Thr fs*8) in ZNF469 was detected in the BSC1 family. Two ZNF469 heterozygous variants g.88494671G > A (c.793G > A, p.G265S, rs754776767) were detected in keratoconus family 1 and a heterozygous missense variant g.88498262G > A (c.4384G > A, p.D1462 N, rs577890057) was found in keratoconus family 2. Based on the American College of Medical Genetics and Genomics guidelines, rs577890057 and rs754776767 were predicted to be variants of uncertain significance. c. 6727del (p. Asp2243Thr fs*8) in ZNF469 was identified to be pathogenic. Conclusions We identified a new homozygous frameshift mutation and two heterozygous missense variations in ZNF469 in the three families. Our findings extend the spectrum of ZNF469 variants associated with keratoconus.
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Affiliation(s)
- Qinghong Lin
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, 200000, China
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200031, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200000, China
- Shanghai Engineering Research Center of Laser and Autostereoscopic 3D for Vision Care (20DZ2255000), Shanghai, 200000, China
- Refractive Surgery Department, Bright Eye Hospital, Shanghai, 200000, China
| | - Xuejun Wang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, 200000, China
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200031, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200000, China
- Shanghai Engineering Research Center of Laser and Autostereoscopic 3D for Vision Care (20DZ2255000), Shanghai, 200000, China
| | - Tian Han
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, 200000, China
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200031, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200000, China
- Shanghai Engineering Research Center of Laser and Autostereoscopic 3D for Vision Care (20DZ2255000), Shanghai, 200000, China
| | - Xiaoliao Peng
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, 200000, China
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200031, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200000, China
- Shanghai Engineering Research Center of Laser and Autostereoscopic 3D for Vision Care (20DZ2255000), Shanghai, 200000, China
| | - Xingtao Zhou
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, 200000, China
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200031, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200000, China
- Shanghai Engineering Research Center of Laser and Autostereoscopic 3D for Vision Care (20DZ2255000), Shanghai, 200000, China
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Yu Y, Miyamoto T, Kimura Y, Itamoto K, Michishita M, Hatakeyama H, Nagashima T, Asada R, Yamaguchi T, Hasegawa D, Nomura Y, Lyons LA, Kosho T. Suspected malnutrition-induced reversible feline skin fragility syndrome in a cat with congenital axial deformities. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2024; 65:227-233. [PMID: 38434166 PMCID: PMC10880391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
A stray cat, an intact female Japanese domestic shorthair cat of unknown age (suspected to be a young adult), was rescued. The cat was lethargic and thin and had marked skin fragility, delayed wound healing without skin hyperextensibility, and hind limb proprioceptive ataxia and paresis. Survey radiography, computed tomography, and magnetic resonance imaging revealed congenital vertebral anomalies, including thoracolumbar transitional vertebrae, scoliosis resulting from a thoracic lateral wedge-shaped vertebra, and a kinked tail, and a dilated spinal cord central canal. Through nutritional support, the cat's general condition normalized, followed by a gradual and complete improvement of skin features. Whole-genome sequencing was completed; however, no pathogenic genetic variant was identified that could have caused this phenotype, including congenital scoliosis. A skin biopsy obtained 7 y after the rescue revealed no remarkable findings on histopathology or transmission electron microscopy. Based on clinical course and microscopic findings, malnutrition-induced reversible feline skin fragility syndrome (FSFS) was suspected, and nutritional support was considered to have improved the skin condition. Key clinical message: This is the second reported case of presumed malnutrition-induced reversible FSFS and was accompanied by long-term follow-up.
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Affiliation(s)
- Yoshihiko Yu
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Tadashi Miyamoto
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Yui Kimura
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Kazuhito Itamoto
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Masaki Michishita
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Hitoshi Hatakeyama
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Tomokazu Nagashima
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Rikako Asada
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Tomomi Yamaguchi
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Daisuke Hasegawa
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Yoshihiro Nomura
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Leslie A Lyons
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
| | - Tomoki Kosho
- Laboratory of Veterinary Radiology (Yu, Asada, Hasegawa), Department of Veterinary Pathology (Michishita, Nagashima), and Laboratory of Comparative Cellular Biology (Hatakeyama), Nippon Veterinary and Life Science University, Musashino, Japan; Miyamoto Animal Hospital, Yamaguchi, Japan (Miyamoto, Kimura); Department of Veterinary Small Animal Clinical Science, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan (Itamoto); Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan (Yamaguchi, Kosho); Department of Medical Genetics and Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan (Yamaguchi, Kosho); Scleroprotein and Leather Research Institute, Tokyo University of Agriculture and Technology, Fuchu, Japan (Nomura); Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA (Lyons); Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan (Kosho)
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9
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Incandela C, D'Oria F, Lapenna L, Acquaviva A. Penetrating keratoplasty in brittle Cornea syndrome: Case series and review of the literature. Eur J Ophthalmol 2024; 34:11-17. [PMID: 37073081 DOI: 10.1177/11206721231171426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
It concerns three siblings (two 28 year old twin boys and a 25 year old woman) who presented a previous history of rupture of eyeball in one eye and very poor vision in the other. At the first ophthalmoscopic and instrumental evaluation, three patients presented with bluish sclera and keratoglobus in the intact eye. A genetic analysis with whole exome sequencing was then performed on the three siblings, identifying a biallelic variant of the PRDM5 gene that led to the diagnosis of Brittle Cornea Syndrome (BCS), a rare autosomal recessive disorder characterized by corneal thinning and blue sclera. To preserve the only intact eye from possible breakage, the three siblings were trained in using protective measures (polycarbonate goggles etc.) to carry out close monitoring of symptoms and were asked to continue with follow-up visits for ocular and systemic diseases associated with BCS. Given the poor best corrected visual acuity achievable with glasses and contact lenses, penetrating keratoplasty was performed, achieving good visual acuity maintained in the 2-year follow-up in two of the three patients. Knowledge of this pathology and its clinical manifestations is essential for early diagnosis and correct management of this rare but very debilitating pathology. To our knowledge, this is the first case series of BCS reported in an Albanian population.
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Affiliation(s)
- Cosimo Incandela
- Department of Ophthalmology, Di Venere's Hospital of Bari, Bari City, Italy
| | - Francesco D'Oria
- Section of Ophthalmology, Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari, Bari, Italy
| | - Lucia Lapenna
- Department of Ophthalmology, Di Venere's Hospital of Bari, Bari City, Italy
| | - Antonio Acquaviva
- Department of Ophthalmology, Di Venere's Hospital of Bari, Bari City, Italy
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10
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Sklar BA, Pisuchpen P, Bareket M, Milman T, Eagle RC, Minor J, Procopio R, Capasso J, Levin AV, Hammersmith K. Identification and Management of a Novel PRDM5 Gene Pathologic Variant in a Family With Brittle Cornea Syndrome. Cornea 2023; 42:1572-1577. [PMID: 37713669 DOI: 10.1097/ico.0000000000003372] [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: 08/16/2022] [Accepted: 07/21/2023] [Indexed: 09/17/2023]
Abstract
PURPOSE The aim of this study was to report a novel PRDM5 pathologic variant and ophthalmic findings in a family with 3 children diagnosed with brittle cornea syndrome (BCS). Histopathologic findings and surgical outcome of a child with BCS who underwent full-thickness corneal transplant are described. METHODS This is an observational case report of a nonconsanguineous Laotian family with 3 siblings diagnosed with BCS. Data collected included visual acuity, cycloplegic refraction, slit-lamp biomicroscopy, dilated fundus examination, corneal pachymetry, corneal topography, and general medical findings. Targeted testing through PRDM5 gene sequencing with copy number variation detection was conducted. RESULTS The 3 siblings included a 12-year-old boy and 8- and 6-year-old sisters, all of whom presented with myopia, blue-tinted sclerae, thin corneas, and variable corneal scarring. All 3 affected children were found to be homozygous for the PRDM5 gene variant c.1117_1123delinsTTTAATGCTTACAAATGTTTG p.Asp373Phefs*57. Coding sequences of PRDM5 and ZNF469 genes were sequenced in their entirety, and this was the only pathologic variant present in this family. The youngest affected sister developed persistent hydrops with severely decreased vision and underwent penetrating keratoplasty. Histopathology revealed severe corneal thinning, diffuse absence of Bowman layer, and ruptured Descemet membrane scrolls. CONCLUSIONS Three siblings with clinical signs of BCS, including corneal thinning, myopia, and blue sclerae, were found to have a novel PRDM5 gene pathologic variant. This pathologic variant has not been previously reported, although 1 downstream nonsense pathologic variant has been reported as pathogenic. The similar phenotypes in all affected patients support the pathogenicity of this variant. Surgical management of BCS presents unique challenges due to severe tissue fragility.
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Affiliation(s)
- Bonnie A Sklar
- Department of Ophthalmology, Wills Eye Hospital, Philadelphia PA
| | - Phattrawan Pisuchpen
- Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Mor Bareket
- Department of Ophthalmology, Kaplan Medical Center, Rehovot, Israel
| | - Tatyana Milman
- Eye Pathology Department, Wills Eye Hospital, Philadelphia PA
| | - Ralph C Eagle
- Eye Pathology Department, Wills Eye Hospital, Philadelphia PA
| | - Jade Minor
- Pediatric and Adult Strabismus Service, Wills Eye Hospital, Philadelphia PA
| | | | - Jenina Capasso
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Clinical Genetics, Golisano Children's Hospital, University of Rochester, Rochester, NY; and
| | - Alex V Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Clinical Genetics, Golisano Children's Hospital, University of Rochester, Rochester, NY; and
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11
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García de Oteyza G, Fernández Engroba J, Charoenrook V. New ZNF469 Mutations in Spanish Siblings With Brittle Cornea Syndrome. Cornea 2023:00003226-990000000-00280. [PMID: 37098112 DOI: 10.1097/ico.0000000000003280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/05/2023] [Indexed: 04/27/2023]
Abstract
PURPOSE The aim of this study was to describe the clinical, tomographic, and genetic findings of 2 Spanish siblings with brittle cornea syndrome and report a new mutation of gene ZNF469 implicated in the development of this disorder. METHODS In this study, 2 male siblings who had been diagnosed with brittle cornea syndrome underwent ophthalmologic and genetic assessment. RESULTS A novel homozygous deletion c.2972del, p.(Pro991Hisfs62) in the ZNF469 gene was identified in a Spanish family. CONCLUSIONS This is the first report of a ZNF469 mutation in a Spanish family causing brittle cornea syndrome. The discovery of this new mutation amplifies the spectrum of ZNF469 variants implicated in this syndrome.
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Affiliation(s)
- Gonzalo García de Oteyza
- Centro de Oftalmología Barraquer, Barcelona, Spain; and
- Institut Universitari Barraquer. Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jorge Fernández Engroba
- Centro de Oftalmología Barraquer, Barcelona, Spain; and
- Institut Universitari Barraquer. Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Victor Charoenrook
- Centro de Oftalmología Barraquer, Barcelona, Spain; and
- Institut Universitari Barraquer. Universitat Autònoma de Barcelona, Barcelona, Spain
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12
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Salamito M, Gillet B, Syx D, Vaganay E, Malbouyres M, Cerutti C, Tissot N, Exbrayat-Héritier C, Perez P, Jones C, Hughes S, Malfait F, Haydont V, Jäger S, Ruggiero F. NRF2 Shortage in Human Skin Fibroblasts Dysregulates Matrisome Gene Expression and Affects Collagen Fibrillogenesis. J Invest Dermatol 2023; 143:386-397.e12. [PMID: 38487918 DOI: 10.1016/j.jid.2022.07.034] [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: 12/04/2021] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 10/14/2022]
Abstract
NRF2 is a master regulator of the antioxidative response that was recently proposed as a potential regulator of extracellular matrix (ECM) gene expression. Fibroblasts are major ECM producers in all connective tissues, including the dermis. A better understanding of NRF2-mediated ECM regulation in skin fibroblasts is thus of great interest for skin homeostasis maintenance and aging protection. In this study, we investigate the impact of NRF2 downregulation on matrisome gene expression and ECM deposits in human primary dermal fibroblasts. RNA-sequencing‒based transcriptome analysis of NRF2 silenced dermal fibroblasts shows that ECM genes are the most regulated gene sets, highlighting the relevance of the NRF2-mediated matrisome program in these cells. Using complementary light and electron microscopy methods, we show that NRF2 deprivation in dermal fibroblasts results in reduced collagen I biosynthesis and impacts collagen fibril deposition. Moreover, we identify ZNF469, a putative transcriptional regulator of collagen biosynthesis, as a target of NRF2. Both ZNF469 silenced fibroblasts and fibroblasts derived from Brittle Corneal Syndrome patients carrying variants in ZNF469 gene show reduced collagen I gene expression. Our study shows that NRF2 orchestrates matrisome expression in human skin fibroblasts through direct or indirect transcriptional mechanisms that could be prioritized to target dermal ECM homeostasis in health and disease.
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Affiliation(s)
- Mélanie Salamito
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France; L'Oréal Research & Innovation, Aulnay-sous-Bois, France
| | - Benjamin Gillet
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France
| | - Delfien Syx
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium; Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Elisabeth Vaganay
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France
| | - Marilyne Malbouyres
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine Cerutti
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France
| | | | - Chloé Exbrayat-Héritier
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France
| | | | | | - Sandrine Hughes
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France
| | - Fransiska Malfait
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium; Ghent University Hospital, Ghent University, Ghent, Belgium
| | | | - Sibylle Jäger
- L'Oréal Research & Innovation, Aulnay-sous-Bois, France
| | - Florence Ruggiero
- Université de Lyon, École Normal Supérieure de Lyon (ENSL), Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1, Lyon, France.
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13
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Lin P, Zhang G, Peng R, Zhao M, Li H. Increased expression of bone/cartilage-associated genes and core transcription factors in keloids by RNA sequencing. Exp Dermatol 2022; 31:1586-1596. [PMID: 35730251 DOI: 10.1111/exd.14630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/01/2022] [Accepted: 06/19/2022] [Indexed: 02/05/2023]
Abstract
Fibroblasts in keloids undergo cell identity transition with altered transcriptional characteristics. However, the core transcription factors driving this cellular reprogramming remain largely unknown. Here, we report the results of transcriptional profiling from 48 keloid and 24 control dermal tissues. We identified 1187 upregulated differentially expressed genes (foldchange > 2, false discovery rate < 0.05) in keloids, which were mainly enriched in extracellular matrix organization and bone/cartilage development, with significantly increased expression of bone/cartilage-associated collagens (COL5A1, COL10A1, and COL11A1) and glycoproteins (ACAN, COMP, and SPARC). Deconvolution analysis also revealed significantly increased composition of osteoblasts in keloid dermis. A total of 92 upregulated transcription factors were screened out from differentially expressed genes and mainly enriched in transcription process and skeleton development. Additional sequencing of six keloid individuals with multiple regions and intersection further narrow the list with 10 transcription factors. Finally, AEBP1, CREB3L1, RUNX2, and ZNF469 have been identified as candidate core regulators in promoting the gaining of bone/cartilage-like characteristics in keloids. RNA-sequencing of full-skin keloids consolidated the existence of these four transcription factors. Immunohistochemistry was employed to verify the expression of AEBP1, CREB3L1, RUNX2, and ZNF469 in keloid fibroblasts. In conclusion, we bioinformatically discovered the increased expression of bone/cartilage-associated genes and candidate core transcription factors in keloids. Our findings promise to provide molecular clues to develop novel therapeutic modalities against skin fibrosis.
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Affiliation(s)
- Pingping Lin
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Guohong Zhang
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Rui Peng
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Mingming Zhao
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Hang Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
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14
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Asanad S, Bayomi M, Brown D, Buzzard J, Lai E, Ling C, Miglani T, Mohammed T, Tsai J, Uddin O, Singman E. Ehlers-Danlos syndromes and their manifestations in the visual system. Front Med (Lausanne) 2022; 9:996458. [PMID: 36237549 PMCID: PMC9552959 DOI: 10.3389/fmed.2022.996458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Ehlers-Danlos syndrome (EDS) is a rare, genetically variable, heterogenous group of (currently recognized) thirteen connective tissue disorders characterized by skin hyperextensibility, tissue fragility, and generalized joint hypermobility. In addition to these commonly recognized phenotypes, recent studies have notably highlighted variable ophthalmic features in EDS. In this review, we comprehensively gather and discuss the ocular manifestations of EDS and its thirteen subtypes in the clinical setting.
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Affiliation(s)
- Samuel Asanad
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - May Bayomi
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Douglas Brown
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Joshua Buzzard
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Eric Lai
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Carlthan Ling
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Trisha Miglani
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Taariq Mohammed
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Joby Tsai
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Olivia Uddin
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
| | - Eric Singman
- University of Maryland School of Medicine, Department of Ophthalmology & Visual Sciences, Baltimore, MD, United States
- *Correspondence: Eric Singman
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15
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A novel homozygous ZNF469 variant causing brittle cornea syndrome is associated with corneal ectasias in heterozygous carriers. Int Ophthalmol 2022; 43:807-815. [PMID: 36048286 DOI: 10.1007/s10792-022-02481-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 08/20/2022] [Indexed: 10/14/2022]
Abstract
AIM To describe a family segregating a novel truncating ZNF469 homozygous mutation causing brittle cornea syndrome type 1 in a male patient and associated with corneal ectasia in his two heterozygous young children. METHODS A 49-year-old affected male and his 12- and 8-year-old, apparently healthy, siblings underwent phenotypic and genetic assessment. An Oculus Pentacam Scheimpflug topographer system was employed for keratometries and central corneal thickness measurements. Exome sequencing was performed in DNA from the index case with subsequent Sanger sequencing confirmation of the ZNF469 gene causal variant in his relatives. RESULTS The index case had a history of bilateral keratoglobus, corneal perforations, bilateral hypoacusia, and skeletal anomalies. His two children exhibited topographic anomalies compatible with keratoconus suspects as well as mild skeletal anomalies. Genetic analysis identified a novel homozygous c.2340delC variant in the ZNF469 gene, which predicts a p.(Arg781Glufs*19) truncated protein. Sanger sequencing identified heterozygosity for the c.2340delC variant in DNA from both siblings. CONCLUSION Our results expand the mutational spectrum associated with brittle cornea syndrome and provide the first demonstration of early corneal anomalies in subjects carrying monoallelic ZNF469 variants.
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16
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Identification of Single-Nucleotide Polymorphisms in ZNF469 in a Patient with Aortoiliac Aneurysmal Disease. CARDIOGENETICS 2022. [DOI: 10.3390/cardiogenetics12030020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Thoracic aortic aneurysms and dissections often have inter-related pathologies that are increasingly recognized to have a genetic basis. A patient with a vascular history consisting of a spontaneous aorto-iliac dissection and thoracic aortic aneurysm belonged to a family with a significant self-reported history of aneurysmal disease. Suspecting a genetic component, genetic investigation was undertaken. Three variants of unknown significance were found in the ZNF469 gene, which is responsible for the production of a collagen-related zinc finger protein involved in multiple aspects of the development and regulation of major extracellular matrix components. This is the first report to associate this gene with vasculopathy, and further investigation by our group is underway to understand the role it plays in the development of aneurysmal diseases.
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17
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Cusumano A, Roshanravan H, Chao-Shern C, Sebastiani J, Levialdi Ghiron JH, DeDionisio L, Moore T. Genetic prescreening of a candidate for laser refractive surgery identifies risk for inadequate tissue response: a case report. J Med Case Rep 2022; 16:207. [PMID: 35578349 PMCID: PMC9109339 DOI: 10.1186/s13256-022-03395-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Background Inadequate response to corneal laser refractive surgery, e.g., ectatic corneal diseases, may not be identified by conventional examinations, hence creating therapeutic uncertainty. Herein we demonstrate the application of genetic prescreening to augment preassessment for corneal laser refractive surgery and highlight the ability to prevent the possibility of enrolling a subject at risk for developing ectatic corneal diseases. Case presentation Preoperative tests were performed alongside deoxyribonucleic acid (DNA) sequencing of 75 genes specific to the structure and health of the eye of a 44-year-old Caucasian male candidate for corneal laser refractive surgery. The patient had no medical, family, or psychosocial history, nor symptoms that could lead to suspect any corneal abnormalities, and conventional preoperative tests confirmed that no corneal abnormalities were present. The sequencing results uncovered rare DNA variants within the ADGRV1, PTK2, ZNF469, and KRT15 genes. These variants were considered potential risk factors for inadequate response in the patient post corneal laser refractive surgery. Subsequent reevaluation with three different last-generation corneal tomographers identified in the left eye a “warning” for a deformity of the posterior profile of the cornea. Conclusions Genetic prescreening identifies potential risk of inadequate response to corneal laser refractive surgery where current technologies in use may lead to a hazardous predictive diagnostic uncertainty.
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18
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The Ehlers–Danlos Syndromes against the Backdrop of Inborn Errors of Metabolism. Genes (Basel) 2022; 13:genes13020265. [PMID: 35205310 PMCID: PMC8872221 DOI: 10.3390/genes13020265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
The Ehlers–Danlos syndromes are a group of multisystemic heritable connective tissue disorders with clinical presentations that range from multiple congenital malformations, over adolescent-onset debilitating or even life-threatening complications of connective tissue fragility, to mild conditions that remain undiagnosed in adulthood. To date, thirteen different EDS types have been recognized, stemming from genetic defects in 20 different genes. While initial biochemical and molecular analyses mainly discovered defects in genes coding for the fibrillar collagens type I, III and V or their modifying enzymes, recent discoveries have linked EDS to defects in non-collagenous matrix glycoproteins, in proteoglycan biosynthesis and in the complement pathway. This genetic heterogeneity explains the important clinical heterogeneity among and within the different EDS types. Generalized joint hypermobility and skin hyperextensibility with cutaneous fragility, atrophic scarring and easy bruising are defining manifestations of EDS; however, other signs and symptoms of connective tissue fragility, such as complications of vascular and internal organ fragility, orocraniofacial abnormalities, neuromuscular involvement and ophthalmological complications are variably present in the different types of EDS. These features may help to differentiate between the different EDS types but also evoke a wide differential diagnosis, including different inborn errors of metabolism. In this narrative review, we will discuss the clinical presentation of EDS within the context of inborn errors of metabolism, give a brief overview of their underlying genetic defects and pathophysiological mechanisms and provide a guide for the diagnostic approach.
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Stanton CM, Findlay AS, Drake C, Mustafa MZ, Gautier P, McKie L, Jackson IJ, Vitart V. A Mouse Model of Brittle Cornea Syndrome caused by mutation in Zfp469. Dis Model Mech 2021; 14:272230. [PMID: 34368841 PMCID: PMC8476817 DOI: 10.1242/dmm.049175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/28/2021] [Indexed: 11/20/2022] Open
Abstract
Brittle cornea syndrome (BCS) is a rare recessive condition characterised by extreme thinning of the cornea and sclera. BCS results from loss-of-function mutations in the poorly understood genes ZNF469 or PRDM5. In order to determine the function of ZNF469 and to elucidate pathogenic mechanisms, we used genome editing to recapitulate a human ZNF469 BCS mutation in the orthologous mouse gene Zfp469. Ophthalmic phenotyping showed that homozygous Zfp469 mutation causes significant central and peripheral corneal thinning arising from reduced stromal thickness. Expression of key components of the corneal stroma in primary keratocytes from Zfp469BCS/BCS mice is affected, including decreased Col1a1 and Col1a2 expression. This alters the collagen type I/collagen type V ratio and results in collagen fibrils with smaller diameter and increased fibril density in homozygous mutant corneas, correlating with decreased biomechanical strength in the cornea. Cell-derived matrices generated by primary keratocytes show reduced deposition of collagen type I, offering an in vitro model for stromal dysfunction. Work remains to determine whether modulating ZNF469 activity will have therapeutic benefit in BCS or in conditions such as keratoconus in which the cornea thins progressively. This article has an associated First Person interview with the first author of the paper. Summary: A mouse model of brittle cornea syndrome was created to elucidate molecular mechanisms underlying the pathology of this rare connective tissue disorder in which extremely thin corneas rupture, causing irreversible blindness.
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Affiliation(s)
- Chloe M Stanton
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Amy S Findlay
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Camilla Drake
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Mohammad Z Mustafa
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Lisa McKie
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ian J Jackson
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
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20
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Bouhouche A, Albaroudi N, El Alaoui MA, Askander O, Habbadi Z, El Hassani A, Iraqi H, El Fahime E, Belmekki M. Identification of the novel SDR42E1 gene that affects steroid biosynthesis associated with the oculocutaneous genital syndrome. Exp Eye Res 2021; 209:108671. [PMID: 34133966 DOI: 10.1016/j.exer.2021.108671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/31/2021] [Accepted: 06/10/2021] [Indexed: 11/28/2022]
Abstract
Hereditary connective tissue diseases form a heterogeneous group of disorders that affect collagen and extracellular matrix components. The cornea and the skin are among the major forms of connective tissues, and syndromes affecting both organs are often due to mutations in single genes. Brittle cornea syndrome is one of the pathologies that illustrates this association well. Furthermore, sex hormones are known to play a role in the maintenance of the structure and the integrity of the connective tissue including the skin and cornea, and may be involved in pathogenesis of oculocutaneous diseases. Herein, a double consanguineous family of Moroccan origin with two affected siblings, with suspected brittle cornea syndrome, was recruited. Ophthalmic examinations and genetic testing were performed in all the nuclear family individuals. Clinical examinations showed that the two affected boys presented with thinning of the cornea, blue sclera, keratoconus, hyperelasticity of the skin, joint hypermobility, muscle weakness, hearing loss and dental abnormalities that are compatible with the diagnosis of BCS disease. They showed however additional clinical signs including micropenis, hypospadias and cryptorchidism, suggesting abnormalities in endocrine pathways. Using a duo exome sequencing analysis performed in the mother and the propositus, we identified the novel homozygous missense mutation c.461G > A (p.Arg154Gln) in the short-chain dehydrogenase/reductase family 42E member 1 (SDR42E1) gene. This novel mutation, which co-segregated with the disease in the family, was predicted to be pathogenic by bioinformatics tools. SDR42E1 stability analysis using DynaMut web-server showed that the p.Arg154Gln mutations has a destabilizing effect with a ΔΔG value of -1.039 kcal/mol. As this novel gene belongs to the large family of short-chain dehydrogenases/reductases (SDR) thought to be involved in steroid biosynthesis, endocrinological investigations subsequently revealed that the two patients also had low levels of cholesterol. Karyotyping revealed a normal 46,XY karyotype for the two boys, excluding other causes of disorders of sex development due to chromosomal rearrangements. In conclusion, our study reveals that mutation in the novel SDR42E1 gene alters the steroid hormone synthesis and associated with a new syndrome we named oculocutaneous genital syndrome. In addition, this study highlights the role of SDR42E1 in the regulation of cholesterol metabolism in the maintenance of connective tissue and sexual maturation in humans.
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Affiliation(s)
- Ahmed Bouhouche
- Research Team in Neurology and Neurogenetics, Genomics Center of Human Pathologies, Medical School and Pharmacy, Mohammed V University in Rabat, Morocco; Research Genetics Center of the Cheikh Zaid Foundation, Abulcasis International University of Health Sciences, Rabat, Morocco.
| | - Nada Albaroudi
- Department of Ophthalmology, Cheikh Zaid Hospital, Rabat, Morocco
| | - My Abdelaziz El Alaoui
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research, Rabat, Morocco
| | - Omar Askander
- Research Genetics Center of the Cheikh Zaid Foundation, Abulcasis International University of Health Sciences, Rabat, Morocco
| | - Zineb Habbadi
- Department of Endocrinology, Ibn Sina Hospital, Rabat, Morocco
| | | | - Hinde Iraqi
- Department of Endocrinology, Ibn Sina Hospital, Rabat, Morocco
| | - Elmostafa El Fahime
- Research Team in Neurology and Neurogenetics, Genomics Center of Human Pathologies, Medical School and Pharmacy, Mohammed V University in Rabat, Morocco; Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research, Rabat, Morocco
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Dhooge T, Van Damme T, Syx D, Mosquera LM, Nampoothiri S, Radhakrishnan A, Simsek-Kiper PO, Utine GE, Bonduelle M, Migeotte I, Essawi O, Ceylaner S, Al Kindy A, Tinkle B, Symoens S, Malfait F. More than meets the eye: Expanding and reviewing the clinical and mutational spectrum of brittle cornea syndrome. Hum Mutat 2021; 42:711-730. [PMID: 33739556 DOI: 10.1002/humu.24199] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 03/15/2021] [Indexed: 11/10/2022]
Abstract
Brittle cornea syndrome (BCS) is a rare autosomal recessive disorder characterized by corneal thinning and fragility, leading to corneal rupture, the main hallmark of this disorder. Non-ocular symptoms include not only hearing loss but also signs of connective tissue fragility, placing it in the Ehlers-Danlos syndrome (EDS) spectrum. It is caused by biallelic pathogenic variants in ZNF469 or PRDM5, which presumably encode transcription factors for extracellular matrix components. We report the clinical and molecular features of nine novel BCS families, four of which harbor variants in ZNF469 and five in PRDM5. We also performed a genotype- and phenotype-oriented literature overview of all (n = 85) reported patients with ZNF469 (n = 53) and PRDM5 (n = 32) variants. Musculoskeletal findings may be the main reason for referral and often raise suspicion of another heritable connective tissue disorder, such as kyphoscoliotic EDS, osteogenesis imperfecta, or Marfan syndrome, especially when a corneal rupture has not yet occurred. Our findings highlight the multisystemic nature of BCS and validate its inclusion in the EDS classification. Importantly, gene panels for heritable connective tissue disorders should include ZNF469 and PRDM5 to allow for timely diagnosis and appropriate preventive measures for this rare condition.
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Affiliation(s)
- Tibbe Dhooge
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Tim Van Damme
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Delfien Syx
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Laura M Mosquera
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium.,Divison of Pediatric Cardiology, Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, Cochin, Kerala, India
| | - Anil Radhakrishnan
- Department of Ophthalmology, Amrita Institute of Medical Sciences & Research Centre, Cochin, Kerala, India
| | | | - Gülen E Utine
- Department of Pediatric Genetics, Hacettepe University, Ankara, Turkey
| | - Maryse Bonduelle
- Centre for Medical Genetics, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Isabelle Migeotte
- Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Osama Essawi
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | | | - Adila Al Kindy
- Department of Genetics, College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Brad Tinkle
- Division of Medical Genetics, Peyton Manning Children's Hospital, Indianapolis, Indiana, USA
| | - Sofie Symoens
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Fransiska Malfait
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
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22
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Resequencing of candidate genes for Keratoconus reveals a role for Ehlers-Danlos Syndrome genes. Eur J Hum Genet 2021; 29:1745-1755. [PMID: 33737726 DOI: 10.1038/s41431-021-00849-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/22/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023] Open
Abstract
The involvement of genetic factors in the pathogenesis of KC has long been recognized but the identification of variants affecting the underlying protein functions has been challenging. In this study, we selected 34 candidate genes for KC based on previous whole-exome sequencing (WES) and the literature, and resequenced them in 745 KC patients and 810 ethnically matched controls from Belgium, France and Italy. Data analysis was performed using the single variant association test as well as gene-based mutation burden and variance components tests. In our study, we detected enrichment of genetic variation across multiple gene-based tests for the genes COL2A1, COL5A1, TNXB, and ZNF469. The top hit in the single variant association test was obtained for a common variant in the COL12A1 gene. These associations were consistently found across independent subpopulations. Interestingly, COL5A1, TNXB, ZNF469 and COL12A1 are all known Ehlers-Danlos Syndrome (EDS) genes. Though the co-occurrence of KC and EDS has been reported previously, this study is the first to demonstrate a consistent role of genetic variants in EDS genes in the etiology of KC. In conclusion, our data show a shared genetic etiology between KC and EDS, and clearly confirm the currently disputed role of ZNF469 in disease susceptibility for KC.
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23
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Gensemer C, Burks R, Kautz S, Judge DP, Lavallee M, Norris RA. Hypermobile Ehlers-Danlos syndromes: Complex phenotypes, challenging diagnoses, and poorly understood causes. Dev Dyn 2021; 250:318-344. [PMID: 32629534 PMCID: PMC7785693 DOI: 10.1002/dvdy.220] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/24/2020] [Accepted: 06/28/2020] [Indexed: 12/14/2022] Open
Abstract
The Ehlers-Danlos syndromes (EDS) are a group of heritable, connective tissue disorders characterized by joint hypermobility, skin hyperextensibility, and tissue fragility. There is phenotypic and genetic variation among the 13 subtypes. The initial genetic findings on EDS were related to alterations in fibrillar collagen, but the elucidation of the molecular basis of many of the subtypes revealed several genes not involved in collagen biosynthesis or structure. However, the genetic basis of the hypermobile type of EDS (hEDS) is still unknown. hEDS is the most common type of EDS and involves generalized joint hypermobility, musculoskeletal manifestations, and mild skin involvement along with the presence of several comorbid conditions. Variability in the spectrum and severity of symptoms and progression of patient phenotype likely depend on age, gender, lifestyle, and expression domains of the EDS genes during development and postnatal life. In this review, we summarize the current molecular, genetic, epidemiologic, and pathogenetic findings related to EDS with a focus on the hypermobile type.
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Affiliation(s)
- Cortney Gensemer
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina
| | - Randall Burks
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina
| | - Steven Kautz
- Department of Health Sciences and Research, Medical University of South Carolina, Charleston, South Carolina
| | - Daniel P. Judge
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, South Carolina
| | - Mark Lavallee
- Department of Family Medicine, Wellspan Health, York, Pennsylvania
| | - Russell A. Norris
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina
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24
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Veerappa AM. Cascade of interactions between candidate genes reveals convergent mechanisms in keratoconus disease pathogenesis. Ophthalmic Genet 2021; 42:114-131. [PMID: 33554698 DOI: 10.1080/13816810.2020.1868013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Keratoconus is a progressive thinning, steepening and distortion of the cornea which can lead to loss of vision if left untreated. Keratoconus has a complex multifactorial etiology, with genetic and environmental components contributing to the disease pathophysiology. Studies have observed high concordance between monozygotic twins, discordance between dizygotic twins, and high familial segregation indicating the presence of a very strong genetic component in the pathogenesis of keratoconus. The use of genome-wide linkage studies on families and twins, genome-wide association studies (GWAS) on case-controls, next-generation sequencing (NGS)-based genomic screens on both familial and non-familial cohorts have led to the identification of keratoconus candidate genes with much greater success and increased resproducibility of genetic findings. This review focuses on candidate genes identified till date and attempts to understand their role in biological processes underlying keratoconus pathogenesis. In addition, using these genes I propose molecular pathways that could contribute to keratoconus pathogenesis. The pathways identified the presence of direct cross-talk between known candidate genes of keratoconus and remarkably, 28 known candidate genes have a direct relationship among themselves that involves direct protein-protein binding, regulatory activities such as activation and inhibition, chaperone, transcriptional activation/co-activation, and enzyme catalysis. This review attempts to describe these relationships and cross-talks in the context of keratoconus pathogenesis.
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Affiliation(s)
- Avinash M Veerappa
- Department of Ophthalmology, NYU Langone Medical Center, New York, New York, USA
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25
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Lee TL, Lin PH, Chen PL, Hong JB, Wu CC. Hereditary Hearing Impairment with Cutaneous Abnormalities. Genes (Basel) 2020; 12:43. [PMID: 33396879 PMCID: PMC7823799 DOI: 10.3390/genes12010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 12/15/2022] Open
Abstract
Syndromic hereditary hearing impairment (HHI) is a clinically and etiologically diverse condition that has a profound influence on affected individuals and their families. As cutaneous findings are more apparent than hearing-related symptoms to clinicians and, more importantly, to caregivers of affected infants and young individuals, establishing a correlation map of skin manifestations and their underlying genetic causes is key to early identification and diagnosis of syndromic HHI. In this article, we performed a comprehensive PubMed database search on syndromic HHI with cutaneous abnormalities, and reviewed a total of 260 relevant publications. Our in-depth analyses revealed that the cutaneous manifestations associated with HHI could be classified into three categories: pigment, hyperkeratosis/nail, and connective tissue disorders, with each category involving distinct molecular pathogenesis mechanisms. This outline could help clinicians and researchers build a clear atlas regarding the phenotypic features and pathogenetic mechanisms of syndromic HHI with cutaneous abnormalities, and facilitate clinical and molecular diagnoses of these conditions.
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Affiliation(s)
- Tung-Lin Lee
- Department of Medical Education, National Taiwan University Hospital, Taipei City 100, Taiwan;
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 11556, Taiwan;
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei City 100, Taiwan;
| | - Pei-Lung Chen
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei City 100, Taiwan;
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei City 100, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10041, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10041, Taiwan
| | - Jin-Bon Hong
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei City 100, Taiwan
- Department of Dermatology, National Taiwan University Hospital, Taipei City 100, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 11556, Taiwan;
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei City 100, Taiwan;
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10041, Taiwan
- Department of Medical Research, National Taiwan University Biomedical Park Hospital, Hsinchu City 300, Taiwan
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26
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Genetics vs chronic corneal mechanical trauma in the etiology of keratoconus. Exp Eye Res 2020; 202:108328. [PMID: 33172608 DOI: 10.1016/j.exer.2020.108328] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/17/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022]
Abstract
Both genetic and environmental factors have been considered to play a role in the etiology keratoconus. Eye rubbing, and more recently eye compression due to sleeping position, have been identified to be highly related to the condition, and are present in a high percentage of patients. Today, the predominant model is that these factors can provide the "second hit" necessary to generate the condition in a genetically susceptible individual. In addition, the extremely high prevalence in Arab populations, where endogamy could play a role, the high concordance rate in monozygotic twins, and the presence of family history of the condition between 5 and 23% of cases, support a genetic influence. Segregation analysis studies suggest that keratoconus is a complex non-Mendelian disease. Results from linkage analysis, next generation sequencing studies and genome-wide association studies also have suggested that genetic factors are involved in the condition. Recently, it has been proposed that mechanical trauma (i.e. eye rubbing or eye compression at night), is a sine quanon condition for the onset of keratoconus, and quite possibly its only cause. There are various arguments for and against this hypothesis. Indeed, it is possible, as initially suggested around 55 years ago, that the term "keratoconus" include diverse phenotypically similar conditions, which are actually of different etiology.
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27
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Rolvien T, Kornak U, Linke SJ, Amling M, Oheim R. Whole-Exome Sequencing Identifies Novel Compound Heterozygous ZNF469 Mutations in Two Siblings with Mild Brittle Cornea Syndrome. Calcif Tissue Int 2020; 107:294-299. [PMID: 32671420 PMCID: PMC7415034 DOI: 10.1007/s00223-020-00721-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 02/07/2023]
Abstract
Connective tissue diseases, including osteogenesis imperfecta (OI) and Ehlers-Danlos syndrome (EDS), exhibit a high degree of clinical and genetic heterogeneity. We report two sisters with blue sclerae, joint hypermobility and hearing loss. Whole-exome sequencing identified two compound heterozygous ZNF469 loss-of-function mutations due to a frameshift. Since these findings indicate the presence of brittle cornea syndrome (BCS), we performed ocular optical coherence tomography (OCT) and pachymetry, which revealed a moderate decrease in corneal thickness. While only one traumatic fracture was observed in each of the patients, a detailed skeletal assessment indicated no specific patterns of bone mass and microstructure reduction as well as normal bone turnover markers. Taken together, our findings point to a mild form of brittle cornea syndrome with a phenotype compatible with the extraskeletal features of OI but also with EDS.
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Affiliation(s)
- Tim Rolvien
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany
- Department of Orthopedics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- National Bone Board, Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Kornak
- National Bone Board, Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
- FG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stephan J Linke
- Department of Ophthalmology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Amling
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany
- National Bone Board, Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Oheim
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529, Hamburg, Germany.
- National Bone Board, Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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28
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Malfait F, Castori M, Francomano CA, Giunta C, Kosho T, Byers PH. The Ehlers-Danlos syndromes. Nat Rev Dis Primers 2020; 6:64. [PMID: 32732924 DOI: 10.1038/s41572-020-0194-9] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
Abstract
The Ehlers-Danlos syndromes (EDS) are a heterogeneous group of hereditary disorders of connective tissue, with common features including joint hypermobility, soft and hyperextensible skin, abnormal wound healing and easy bruising. Fourteen different types of EDS are recognized, of which the molecular cause is known for 13 types. These types are caused by variants in 20 different genes, the majority of which encode the fibrillar collagen types I, III and V, modifying or processing enzymes for those proteins, and enzymes that can modify glycosaminoglycan chains of proteoglycans. For the hypermobile type of EDS, the molecular underpinnings remain unknown. As connective tissue is ubiquitously distributed throughout the body, manifestations of the different types of EDS are present, to varying degrees, in virtually every organ system. This can make these disorders particularly challenging to diagnose and manage. Management consists of a care team responsible for surveillance of major and organ-specific complications (for example, arterial aneurysm and dissection), integrated physical medicine and rehabilitation. No specific medical or genetic therapies are available for any type of EDS.
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Affiliation(s)
- Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
| | - Clair A Francomano
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cecilia Giunta
- Connective Tissue Unit, Division of Metabolism and Children's Research Centre, University Children's Hospital, Zurich, Switzerland
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Peter H Byers
- Department of Pathology and Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
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Brittle cornea syndrome: Disease-causing mutations in ZNF469 and two novel variants identified in a patient followed for 26 years. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2020; 164:183-188. [DOI: 10.5507/bp.2019.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/05/2019] [Indexed: 11/23/2022] Open
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30
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Case Series of Brittle Cornea Syndrome. Case Rep Ophthalmol Med 2020; 2020:4381273. [PMID: 32257481 PMCID: PMC7109549 DOI: 10.1155/2020/4381273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/07/2020] [Indexed: 11/21/2022] Open
Abstract
Purpose This case series demonstrate diagnostic features, treatment options, and challenges for Brittle Cornea Syndrome. Observations. Three cases presented with bluish sclera and extremely thin cornea. Genetic workup was performed and confirmed the diagnosis of Brittle Cornea Syndrome, a rare autosomal recessive disorder characterized by corneal thinning and blue sclera. Case 1 was a 4-year-old boy who developed cataract and glaucoma after undergoing right tectonic penetrating keratoplasty (PK) secondary to a spontaneous corneal rupture. Glaucoma was controlled medically. Later, the kid underwent right transcorneal lensectomy and vitrectomy with synechiolysis. After 6 weeks, he sustained graft dehiscence that was repaired using onlay patch graft. Case 2 was a 7-year-old boy who underwent PK in the right eye, then a pericardial patch graft in the left eye following spontaneous corneal rupture. Glaucoma in both eyes was controlled medically. Case 3 was the 2-year-old sister of the 2nd case. She had a pachymetry of 238 μm OD and 254 μm OD and 254 Conclusions Long-term follow-up of children diagnosed with Brittle Cornea Syndrome is paramount to minimize the morbidity of corneal rupture and late-onset extraocular conditions.
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Vera AM, Peterson LE, Dong D, Haghshenas V, Yetter TR, Delgado DA, McCulloch PC, Varner KE, Harris JD. High Prevalence of Connective Tissue Gene Variants in Professional Ballet. Am J Sports Med 2020; 48:222-228. [PMID: 31765226 DOI: 10.1177/0363546519887955] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND There is a high prevalence of hypermobility spectrum disorder (HSD) in dancers. While there is no known genetic variant for HSD, hypermobile Ehlers-Danlos syndrome is a genetic disorder that exists within HSD. There are many connective tissue disorders (CTDs) with known (and unknown) genes associated with hypermobility. Hypermobility has distinct advantages for participation in flexibility sports, including ballet. PURPOSE To determine the prevalence of gene variants associated with hypermobility in a large professional ballet company. STUDY DESIGN Cross-sectional study; Level of evidence, 3. METHODS In this cross-sectional investigation, 51 professional male and female dancers from a large metropolitan ballet company were eligible and offered participation after an oral and written informed consent process. Whole blood was obtained from peripheral venipuncture, and DNA was isolated. Isolated DNA was subsequently enriched for the coding exons of 60 genes associated with CTD that included hypermobility as a phenotype, including Ehlers-Danlos syndromes, osteogenesis imperfecta, Marfan syndrome, and others. Genes were targeted with hybrid capture technology. Prepared DNA libraries were then sequenced with next-generation sequencing technology. Genetic database search tools (Human Gene Mutation Database and e!Ensembl, http://useast.ensembl.org/ ) were used to query specific variants. Descriptive statistics were calculated. RESULTS Of 51 dancers, 32 (63%) agreed to participate in DNA analysis (mean ± SD age, 24.3 ± 4.4 years; 18 men, 14 women). Twenty-eight dancers had at least 1 variant in the 60 genes tested, for an 88% prevalence. A total of 80 variants were found. A variant in 26 of the 60 genes was found in at least 1 dancer. Among the 28 dancers with variants, 16 were found in the TTN gene; 10 in ZNF469; 5 in RYR1; 4 in COL12A1; 3 in ABCC6 and COL6A2; 2 in ADAMTS2, CBS, COL1A2, COL6A3, SLC2A10, TNC, and TNXB; and 1 in ATP6V0A2, B4GALT7, BMP1, COL11A1, COL5A2, COL6A1, DSE, FBN1, FBN2, NOTCH1, PRDM5, SMAD3, and TGFBR1. Nine variants found in this population have never been reported. No identified variant was identical to any other variant. No identified variant was known to be disease causing. In the general population, the prevalence of each variant ranges from never reported to 0.33%. In the study population, the prevalence of each variant was 3.13%. There was no association between hypermobility scores and genetic variants. CONCLUSION Genetic variants in CTD-associated genes are highly prevalent (88%) in professional ballet dancers. This may significantly account for the high degree of motion in this population.
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Affiliation(s)
- Angelina M Vera
- Houston Methodist Orthopedics and Sports Medicine, Houston, Texas, USA
| | - Leif E Peterson
- Houston Methodist Orthopedics and Sports Medicine, Houston, Texas, USA
| | - David Dong
- Houston Methodist Orthopedics and Sports Medicine, Houston, Texas, USA
| | - Varan Haghshenas
- Houston Methodist Orthopedics and Sports Medicine, Houston, Texas, USA
| | - Thomas R Yetter
- Houston Methodist Orthopedics and Sports Medicine, Houston, Texas, USA
| | | | | | - Kevin E Varner
- Houston Methodist Orthopedics and Sports Medicine, Houston, Texas, USA
| | - Joshua D Harris
- Houston Methodist Orthopedics and Sports Medicine, Houston, Texas, USA
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Zhao H, Wang H, Liu T, Liu S, Jin L, Huang X, Dai W, Sun K, Feng J. Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. Front Zool 2019; 16:37. [PMID: 31528181 PMCID: PMC6743130 DOI: 10.1186/s12983-019-0336-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation. RESULTS A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species. CONCLUSIONS The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.
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Affiliation(s)
- Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Sen Liu
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo, 454000 China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Xiaobin Huang
- Vector Laboratory, Institute of Pathogens and Vectors, Branch of Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, 671003 China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
- College of Life Science, Jilin Agricultural University, Changchun, 130118 China
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Abstract
PURPOSE Brittle cornea syndrome (BCS) is a rare recessive disorder affecting connective tissues, most prominently in the eye. Pathogenic mutations causing BCS have been identified in PRDM5 and ZNF469 genes. This study investigates the genetic cause of BCS in a large, consanguineous Pakistani family with 4 affected and 3 unaffected individuals. METHODS The coding region and exon-intron splice junctions of PRDM5 and ZNF469 genes were amplified by polymerase chain reaction, and bidirectional Sanger sequencing was performed to find the pathogenic change responsible for causing the disease in the family. RESULTS A novel homozygous duplication c.9831dupC (p.Arg3278GlnfsX197) in the ZNF469 gene was identified, which was found to be co-segregating with the disease in the family. CONCLUSIONS This is the first report of a ZNF469 homozygous mutation causing a BCS phenotype in a consanguineous Pakistani family. Our data extend the mutation spectrum of ZNF469 variants implicated in BCS.
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Loukovitis E, Sfakianakis K, Syrmakesi P, Tsotridou E, Orfanidou M, Bakaloudi DR, Stoila M, Kozei A, Koronis S, Zachariadis Z, Tranos P, Kozeis N, Balidis M, Gatzioufas Z, Fiska A, Anogeianakis G. Genetic Aspects of Keratoconus: A Literature Review Exploring Potential Genetic Contributions and Possible Genetic Relationships with Comorbidities. Ophthalmol Ther 2018; 7:263-292. [PMID: 30191404 PMCID: PMC6258591 DOI: 10.1007/s40123-018-0144-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 01/24/2023] Open
Abstract
INTRODUCTION Keratoconus (KC) is a complex, genetically heterogeneous, multifactorial degenerative disorder that is accompanied by corneal ectasia which usually progresses asymmetrically. With an incidence of approximately 1 per 2000 and 2 cases per 100,000 population presenting annually, KC follows an autosomal recessive or dominant pattern of inheritance and is, apparently, associated with genes that interact with environmental, genetic, and/or other factors. This is an important consideration in refractive surgery in the case of familial KC, given the association of KC with other genetic disorders and the imbalance between dizygotic twins. The present review attempts to identify the genetic loci contributing to the different KC clinical presentations and relate them to the common genetically determined comorbidities associated with KC. METHODS The PubMed, MEDLINE, Google Scholar, and GeneCards databases were screened for KC-related articles published in English between January 2006 and November 2017. Keyword combinations of "keratoconus," "risk factor(s)," "genetics," "genes," "genetic association(s)," and "cornea" were used. In total, 217 articles were retrieved and analyzed, with greater weight placed on the more recent literature. Further bibliographic research based on the 217 articles revealed another 124 relevant articles that were included in this review. Using the reviewed literature, an attempt was made to correlate genes and genetic risk factors with KC characteristics and genetically related comorbidities associated with KC based on genome-wide association studies, family-based linkage analysis, and candidate-gene approaches. RESULTS An association matrix between known KC-related genes and KC symptoms and/or clinical signs together with an association matrix between identified KC genes and genetically related KC comorbidities/syndromes were constructed. CONCLUSION Twenty-four genes were identified as potential contributors to KC and 49 KC-related comorbidities/syndromes were found. More than 85% of the known KC-related genes are involved in glaucoma, Down syndrome, connective tissue disorders, endothelial dystrophy, posterior polymorphous corneal dystrophy, and cataract.
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Affiliation(s)
| | - Konstantinos Sfakianakis
- Division of Surgical Anatomy, Laboratory of Anatomy, Medical School, Democritus University of Thrace, University Campus, Alexandroupolis, Greece
| | - Panagiota Syrmakesi
- AHEPA University Hospital, Thessaloníki, Greece
- Ophthalmica Eye Institute, Thessaloníki, Greece
| | - Eleni Tsotridou
- Ophthalmica Eye Institute, Thessaloníki, Greece
- Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Myrsini Orfanidou
- Ophthalmica Eye Institute, Thessaloníki, Greece
- Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Dimitra Rafailia Bakaloudi
- Ophthalmica Eye Institute, Thessaloníki, Greece
- Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Maria Stoila
- Ophthalmica Eye Institute, Thessaloníki, Greece
- Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Athina Kozei
- Ophthalmica Eye Institute, Thessaloníki, Greece
- School of Pharmacology, University of Nicosia, Makedonitissis, Nicosia, Cyprus
| | | | | | | | | | | | - Zisis Gatzioufas
- Department of Ophthalmology, Cornea, Cataract and Refractive Surgery, University Hospital Basel, Basel, Switzerland
| | - Aliki Fiska
- Laboratory of Anatomy, Medical School, Democritus University of Thrace, University Campus, Alexandroupolis, Greece
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Brittle-Cornea-Syndrom Typ 1 durch Compound-Heterozygotie zweier Mutationen im ZNF469-Gen. Ophthalmologe 2018; 116:780-784. [DOI: 10.1007/s00347-018-0796-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Wan Q, Tang J, Han Y, Xiao Q, Deng Y. Brittle cornea syndrome: a case report and review of the literature. BMC Ophthalmol 2018; 18:252. [PMID: 30227830 PMCID: PMC6142315 DOI: 10.1186/s12886-018-0903-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 08/28/2018] [Indexed: 02/09/2023] Open
Abstract
Background To report a patient who presented with bluish scleral discoloration, keratoconus, and progressive high myopia. Case presentation A 6-year-old Chinese female patient presented with a significant bluish discoloration of the sclera in both eyes and extreme corneal thinning with anterior corneal protrusion. General pediatric physical examination was normal for all systems and no genetic disorders known were observed. Conclusions We aim to highlight the importance of diagnosis and treatment of patients suffering from Brittle cornea syndrome. Timely diagnosis and early provision of protective glasses seem to be the most important step in treating BCS. To our knowledge, this is the first case of BCS being reported in the Asia area.
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Affiliation(s)
- Qi Wan
- Department of Ophthalmology, The people's hospital of Leshan, Leshan City, People's Republic of China.
| | - Jing Tang
- Department of Ophthalmology, The people's hospital of Leshan, Leshan City, People's Republic of China
| | - Yu Han
- Department of Ophthalmology, The people's hospital of Leshan, Leshan City, People's Republic of China
| | - Qibin Xiao
- Department of Ophthalmology, The people's hospital of Leshan, Leshan City, People's Republic of China
| | - Yingping Deng
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China
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Valgaeren H, Koppen C, Van Camp G. A new perspective on the genetics of keratoconus: why have we not been more successful? Ophthalmic Genet 2017; 39:158-174. [DOI: 10.1080/13816810.2017.1393831] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hanne Valgaeren
- Department of Biomedical Sciences, Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
| | - Carina Koppen
- Department of Ophthalmology, Antwerp University Hospital, Edegem, Belgium
- Department of Ophthalmology, Visual Optics and Visual Rehabilitation, University of Antwerp, Antwerp, Belgium
| | - Guy Van Camp
- Department of Biomedical Sciences, Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Antwerp, Belgium
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Byers PH, Belmont J, Black J, De Backer J, Frank M, Jeunemaitre X, Johnson D, Pepin M, Robert L, Sanders L, Wheeldon N. Diagnosis, natural history, and management in vascular Ehlers-Danlos syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2017; 175:40-47. [PMID: 28306228 DOI: 10.1002/ajmg.c.31553] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Vascular Ehlers Danlos syndrome (vEDS) is an uncommon genetic disorders characterized by arterial aneurysm, dissection and rupture, bowel rupture, and rupture of the gravid uterus. The frequency is estimated as 1/50,000-1/200,000 and results from pathogenic variants in COL3A1, which encodes the chains of type III procollagen, a major protein in vessel walls and hollow organs. Initial diagnosis depends on the recognitions of clinical features, including family history. Management is complex and requires multiple specialists who can respond to and manage the major complications. A summary of recommendations for management include: Identify causative variants in COL3A1 prior to application of diagnosis, modulate life style to minimize injury, risk of vessel/organ rupture, identify and create care team, provide individual plans for emergency care ("vascular EDS passport") with diagnosis and management plan for use when traveling, centralize management at centers of excellence (experience) when feasible, maintain blood pressure in the normal range and treat hypertension aggressively, surveillance of vascular tree by doppler ultrasound, CTA (low radiation alternatives) or MRA if feasible on an annual basis. These recommendations represent a consensus of an international group of specialists with a broad aggregate experience in the care of individuals with vascular EDS that will need to be assessed on a regular basis as new information develops. © 2017 Wiley Periodicals, Inc.
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Brady AF, Demirdas S, Fournel-Gigleux S, Ghali N, Giunta C, Kapferer-Seebacher I, Kosho T, Mendoza-Londono R, Pope MF, Rohrbach M, Van Damme T, Vandersteen A, van Mourik C, Voermans N, Zschocke J, Malfait F. The Ehlers-Danlos syndromes, rare types. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2017; 175:70-115. [PMID: 28306225 DOI: 10.1002/ajmg.c.31550] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Ehlers-Danlos syndromes comprise a clinically and genetically heterogeneous group of heritable connective tissue disorders, which are characterized by joint hypermobility, skin hyperextensibility, and tissue friability. In the Villefranche Nosology, six subtypes were recognized: The classical, hypermobile, vascular, kyphoscoliotic, arthrochalasis, and dermatosparaxis subtypes of EDS. Except for the hypermobile subtype, defects had been identified in fibrillar collagens or in collagen-modifying enzymes. Since 1997, a whole spectrum of novel, clinically overlapping, rare EDS-variants have been delineated and genetic defects have been identified in an array of other extracellular matrix genes. Advances in molecular testing have made it possible to now identify the causative mutation for many patients presenting these phenotypes. The aim of this literature review is to summarize the current knowledge on the rare EDS subtypes and highlight areas for future research. © 2017 Wiley Periodicals, Inc.
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Malfait F, Francomano C, Byers P, Belmont J, Berglund B, Black J, Bloom L, Bowen JM, Brady AF, Burrows NP, Castori M, Cohen H, Colombi M, Demirdas S, De Backer J, De Paepe A, Fournel-Gigleux S, Frank M, Ghali N, Giunta C, Grahame R, Hakim A, Jeunemaitre X, Johnson D, Juul-Kristensen B, Kapferer-Seebacher I, Kazkaz H, Kosho T, Lavallee ME, Levy H, Mendoza-Londono R, Pepin M, Pope FM, Reinstein E, Robert L, Rohrbach M, Sanders L, Sobey GJ, Van Damme T, Vandersteen A, van Mourik C, Voermans N, Wheeldon N, Zschocke J, Tinkle B. The 2017 international classification of the Ehlers-Danlos syndromes. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2017; 175:8-26. [PMID: 28306229 DOI: 10.1002/ajmg.c.31552] [Citation(s) in RCA: 1001] [Impact Index Per Article: 143.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Ehlers-Danlos syndromes (EDS) are a clinically and genetically heterogeneous group of heritable connective tissue disorders (HCTDs) characterized by joint hypermobility, skin hyperextensibility, and tissue fragility. Over the past two decades, the Villefranche Nosology, which delineated six subtypes, has been widely used as the standard for clinical diagnosis of EDS. For most of these subtypes, mutations had been identified in collagen-encoding genes, or in genes encoding collagen-modifying enzymes. Since its publication in 1998, a whole spectrum of novel EDS subtypes has been described, and mutations have been identified in an array of novel genes. The International EDS Consortium proposes a revised EDS classification, which recognizes 13 subtypes. For each of the subtypes, we propose a set of clinical criteria that are suggestive for the diagnosis. However, in view of the vast genetic heterogeneity and phenotypic variability of the EDS subtypes, and the clinical overlap between EDS subtypes, but also with other HCTDs, the definite diagnosis of all EDS subtypes, except for the hypermobile type, relies on molecular confirmation with identification of (a) causative genetic variant(s). We also revised the clinical criteria for hypermobile EDS in order to allow for a better distinction from other joint hypermobility disorders. To satisfy research needs, we also propose a pathogenetic scheme, that regroups EDS subtypes for which the causative proteins function within the same pathway. We hope that the revised International EDS Classification will serve as a new standard for the diagnosis of EDS and will provide a framework for future research purposes. © 2017 Wiley Periodicals, Inc.
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D'hondt S, Van Damme T, Malfait F. Vascular phenotypes in nonvascular subtypes of the Ehlers-Danlos syndrome: a systematic review. Genet Med 2017; 20:562-573. [PMID: 28981071 PMCID: PMC5993673 DOI: 10.1038/gim.2017.138] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/18/2017] [Indexed: 12/31/2022] Open
Abstract
Purpose Within the spectrum of the Ehlers-Danlos syndromes (EDS), vascular complications are usually associated with the vascular subtype of EDS. Vascular complications are also observed in other EDS subtypes, but the reports are anecdotal and the information is dispersed. To better document the nature of vascular complications among “nonvascular” EDS subtypes, we performed a systematic review. Methods We queried three databases for English-language studies from inception until May 2017, documenting both phenotypes and genotypes of patients with nonvascular EDS subtypes. The outcome included the number and nature of vascular complications. Results A total of 112 papers were included and data were collected from 467 patients, of whom 77 presented with a vascular phenotype. Severe complications included mainly hematomas (53%), frequently reported in musculocontractural and classical-like EDS; intracranial hemorrhages (18%), with a high risk in dermatosparaxis EDS; and arterial dissections (16%), frequently reported in kyphoscoliotic and classical EDS. Other, more minor, vascular complications were reported in cardiac-valvular, arthrochalasia, spondylodysplastic, and periodontal EDS. Conclusion Potentially life-threatening vascular complications are a rare but important finding in several nonvascular EDS subtypes, highlighting a need for more systematic documentation. This review will help familiarize clinicians with the spectrum of vascular complications in EDS and guide follow-up and management.
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Affiliation(s)
- Sanne D'hondt
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Tim Van Damme
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
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Rong SS, Ma STU, Yu XT, Ma L, Chu WK, Chan TCY, Wang YM, Young AL, Pang CP, Jhanji V, Chen LJ. Genetic associations for keratoconus: a systematic review and meta-analysis. Sci Rep 2017; 7:4620. [PMID: 28676647 PMCID: PMC5496893 DOI: 10.1038/s41598-017-04393-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/15/2017] [Indexed: 12/21/2022] Open
Abstract
Genetic associations for keratoconus could be useful for understanding disease pathogenesis and discovering biomarkers for early detection of the disease. We conducted a systematic review and meta-analysis to summarize all reported genetic associations for the disease. We searched in the MEDLINE, Embase, Web of Science, and HuGENET databases for genetic studies of keratoconus published from 1950 to June 2016. The summary odds ratio and 95% confidence intervals of all polymorphisms were estimated using the random-effect model. Among 639 reports that were retrieved, 24 fulfilled required criteria as eligible studies for meta-analysis, involving a total of 53 polymorphisms in 28 genes/loci. Results of our meta-analysis lead to the prioritization of 8 single-nucleotide polymorphisms (SNPs) in 6 genes/loci for keratoconus in Whites. Of them 5 genes/loci were originally detected in genome-wide association studies, including FOXO1 (rs2721051, P = 5.6 × 10-11), RXRA-COL5A1 (rs1536482, P = 2.5 × 10-9), FNDC3B (rs4894535, P = 1.4 × 10-8), IMMP2L (rs757219, P = 6.1 × 10-7; rs214884, P = 2.3 × 10-5), and BANP-ZNF469 (rs9938149, P = 1.3 × 10-5). The gene COL4A4 (rs2229813, P = 1.3 × 10-12; rs2228557, P = 4.5 × 10-7) was identified in previous candidate gene studies. We also found SNPs in 10 genes/loci that had a summary P value < 0.05. Sensitivity analysis indicated that the results were robust. Replication studies and understanding the roles of these genes in keratoconus are warranted.
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Affiliation(s)
- Shi Song Rong
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - Sarah Tsz Ue Ma
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xin Ting Yu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Department of Gastroenterology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Li Ma
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Kit Chu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tommy Chung Yan Chan
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
- Hong Kong Eye Hospital, Kowloon, Hong Kong, China
| | - Yu Meng Wang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Alvin L Young
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Vishal Jhanji
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China.
- UPMC Eye Centre, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China.
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Yildiz E, Bardak H, Gunay M, Bardak Y, Imamoglu S, Ozbas H, Bagci O. Novel Zinc Finger Protein Gene 469 (ZNF469) Variants in Advanced Keratoconus. Curr Eye Res 2017. [PMID: 28622062 DOI: 10.1080/02713683.2017.1325910] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE Common polymorphic variants upstream of Zinc finger protein gene 469 (ZNF469) have been associated with central corneal thickness. Rare ZNF469 variants have been shown in keratoconus patients. The aim of the current study was to investigate the frequency of ZNF 469 gene variants in rapidly progressive advance keratoconus patients who underwent corneal transplant surgery by the age of 30, compared to their frequency in the normal Turkish population. METHODS A search in a patient database was performed to identify patients with a rapidly progressive keratoconus requiring corneal transplant surgery by the age of 30 in at least one eye. Twenty-six advance keratoconus patients (study group) and 109 health subjects (control group) were included in the study. Blood samples were donated, and genomic DNA was extracted. The entire coding sequence of the ZNF469 gene including the 84 bp of the putative intron was amplified using PCR primers and analyzed using next generation sequencing (NGS). RESULTS Fifteen single nucleotide polymorphisms previously reported and registered to the dbSNP database were detected in the study group. The allele frequencies of these polymorphisms were higher in the keratoconus group compared to the control group and to the ExAC genome database. Three new missense heterozygote variants and one new synonym variant were detected in keratoconus group. According to prediction software, the P873T and Q2188H variants were shown to be non-tolerated, whereas G3424S could be tolerated. The synonymous variant R1060R is not predicted to lead to abnormal splicing by Human Splicing Finder in silico analysis. CONCLUSION New detected ZNF 469 P873T and Q2188H heterozygote coding variants in isolated advance keratoconus patients may be associated with the disease pathogenesis.
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Affiliation(s)
- Elvin Yildiz
- a Ministry of Health, Haydarpasa Numune Training and Research Hospital , Department of Ophthalmology , Istanbul , Turkey
| | - Handan Bardak
- a Ministry of Health, Haydarpasa Numune Training and Research Hospital , Department of Ophthalmology , Istanbul , Turkey
| | - Murat Gunay
- b Ministry of Health, Zeynep Kamil Maternity and Children's Training and Research Hospital , Istanbul , Turkey
| | - Yavuz Bardak
- a Ministry of Health, Haydarpasa Numune Training and Research Hospital , Department of Ophthalmology , Istanbul , Turkey
| | - Serhat Imamoglu
- a Ministry of Health, Haydarpasa Numune Training and Research Hospital , Department of Ophthalmology , Istanbul , Turkey
| | - Halil Ozbas
- c Suleyman Demirel University School of Medicine , Department of Medical Genetics , Isparta , Turkey
| | - Ozkan Bagci
- c Suleyman Demirel University School of Medicine , Department of Medical Genetics , Isparta , Turkey
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Yu X, Chen B, Zhang X, Shentu X. Identification of seven novel ZNF469 mutations in keratoconus patients in a Han Chinese population. Mol Vis 2017; 23:296-305. [PMID: 28484309 PMCID: PMC5410165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/26/2017] [Indexed: 12/03/2022] Open
Abstract
PURPOSE To test for the potential presence of novel mutations in the zinc finger protein (ZNF469) gene in patients with sporadic keratoconus (KC) from a Han Chinese population. METHODS Fifty-three patients with primary KC, 30 patients with high myopia (HM), and 100 unrelated population-matched healthy controls without any ocular or systemic disorders, all of Han Chinese ethnicity, were recruited. Blood samples were donated, and genomic DNA was isolated from peripheral blood leukocytes. Sequence variations in ZNF469 were initially identified in patients with KC with next-generation sequencing and subsequently confirmed using Sanger sequencing. Sequence variants identified in patients with KC were subsequently screened in 30 patients with HM and 100 healthy control subjects. Other genes that were reported to be related to KC were also screened in the patients with KC who carried the mutations in ZNF469. The Sorting Intolerant Form Tolerant (SIFT) program was used to predict the effect of amino acid substitution on the ZNF469 protein. RESULTS Sixteen sequence variants in the coding regions of ZNF469 were identified in this Chinese KC cohort. After five known single nucleotide polymorphisms (SNPs), one false-positive result, and three mutations that were also detected in the results of the whole-exome sequencing (WES) data performed in 220 Han Chinese individuals without ocular abnormalities were removed, seven novel mutations in ZNF469 (c.2059G>A, c.2137C>A, c.3466G>A, c.3749C>T, c.4300G>A, c.4684G>A, and c.7262G>A) that were predicted to be potentially damaging were identified. The patient with KC with the c.3466G>A mutation was also shown to carry one dedicator of cytokinesis 9 (DOCK9) mutation (c.1940C>T). None of the mutations were detected in the patients with HM or the healthy controls. All of the seven mutations in the patients with KC were heterozygote. CONCLUSIONS The results suggested for the first time that ZNF469 has a pathogenic role in Chinese patients with KC and have widened the mutation spectrum of KC in the Han Chinese population.
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Swierkowska J, Gajecka M. Genetic factors influencing the reduction of central corneal thickness in disorders affecting the eye. Ophthalmic Genet 2017; 38:501-510. [DOI: 10.1080/13816810.2017.1313993] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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Karolak JA, Gambin T, Rydzanicz M, Szaflik JP, Polakowski P, Frajdenberg A, Mrugacz M, Podfigurna-Musielak M, Stankiewicz P, Gajecka M. Evidence against ZNF469 being causative for keratoconus in Polish patients. Acta Ophthalmol 2016; 94:289-94. [PMID: 26806788 DOI: 10.1111/aos.12968] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/28/2015] [Indexed: 01/26/2023]
Abstract
PURPOSE Keratoconus (KTCN) is a degenerative disorder characterized by stromal thinning and protrusion of the cornea, resulting in severe impairment of visual function. A recent study proposed that rare heterozygous mutations in ZNF469 determine KTCN aetiology. METHODS To investigate the contribution of ZNF469 to KTCN, we Sanger sequenced ZNF469 in 42 unrelated Polish patients with KTCN and 49 Polish individuals with high myopia (HM) and compared the results with whole-exome sequencing (WES) data performed in 268 Polish individuals without ocular abnormalities. RESULTS The average number of ZNF469 non-synonymous variants was 16.31 and 16.0 for individuals with KTCN and HM, respectively (p = 0.3724). All identified variants were previously reported. Alternative allele frequency (AAF) was determined based on the WES results. Among missense variants, only one (rs528085780) has AAF ≤ 0.001 and was identified in one patient with sporadic KTCN. However, the resulting Arg1864Lys substitution was not predicted to be deleterious. CONCLUSION In summary, we have not found a significant enrichment of sequence variants in ZNF469 in Polish patients with KTCN. High prevalence of ZNF469 variants identified in our KTCN group is typical for a common genetic variation observed in general population. Our findings indicate that variation in ZNF469 is not responsible for KTCN and other genetic variants are involved in the development and progression of this disease in Polish patients.
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Affiliation(s)
- Justyna A. Karolak
- Department of Genetics and Pharmaceutical Microbiology; Poznan University of Medical Sciences; Poznan Poland
- Institute of Human Genetics; Polish Academy of Sciences; Poznan Poland
| | - Tomasz Gambin
- Institute of Computer Science; Warsaw University of Technology; Warsaw Poland
- Department of Molecular & Human Genetics; Baylor College of Medicine; Houston Texas USA
| | | | - Jacek P. Szaflik
- Department of Ophthalmology; Medical University of Warsaw; SPKSO University Ophthalmic Hospital; Warsaw Poland
| | - Piotr Polakowski
- Department of Ophthalmology; Medical University of Warsaw; SPKSO University Ophthalmic Hospital; Warsaw Poland
| | | | - Malgorzata Mrugacz
- Department of Ophthalmology and Eye Rehabilitation; Medical University of Bialystok; Bialystok Poland
| | | | - Pawel Stankiewicz
- Department of Molecular & Human Genetics; Baylor College of Medicine; Houston Texas USA
| | - Marzena Gajecka
- Institute of Human Genetics; Polish Academy of Sciences; Poznan Poland
- Department of Genetics and Pharmaceutical Microbiology; Poznan University of Medical Sciences; Poznan Poland
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Wang MS, Zhang RW, Su LY, Li Y, Peng MS, Liu HQ, Zeng L, Irwin DM, Du JL, Yao YG, Wu DD, Zhang YP. Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication. Cell Res 2016; 26:556-73. [PMID: 27033669 PMCID: PMC4856766 DOI: 10.1038/cr.2016.44] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/18/2016] [Accepted: 02/22/2016] [Indexed: 01/05/2023] Open
Abstract
As noted by Darwin, chickens have the greatest phenotypic diversity of all birds, but an interesting evolutionary difference between domestic chickens and their wild ancestor, the Red Junglefowl, is their comparatively weaker vision. Existing theories suggest that diminished visual prowess among domestic chickens reflect changes driven by the relaxation of functional constraints on vision, but the evidence identifying the underlying genetic mechanisms responsible for this change has not been definitively characterized. Here, a genome-wide analysis of the domestic chicken and Red Junglefowl genomes showed significant enrichment for positively selected genes involved in the development of vision. There were significant differences between domestic chickens and their wild ancestors regarding the level of mRNA expression for these genes in the retina. Numerous additional genes involved in the development of vision also showed significant differences in mRNA expression between domestic chickens and their wild ancestors, particularly for genes associated with phototransduction and photoreceptor development, such as RHO (rhodopsin), GUCA1A, PDE6B and NR2E3. Finally, we characterized the potential role of the VIT gene in vision, which experienced positive selection and downregulated expression in the retina of the village chicken. Overall, our results suggest that positive selection, rather than relaxation of purifying selection, contributed to the evolution of vision in domestic chickens. The progenitors of domestic chickens harboring weaker vision may have showed a reduced fear response and vigilance, making them easier to be unconsciously selected and/or domesticated.
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Affiliation(s)
- Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Rong-wei Zhang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Yan Su
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - David M Irwin
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada
| | - Jiu-Lin Du
- Institute of Neuroscience and State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals
- Kunming College of Life Science, Unisversity of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan 650091, China
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Porter LF, Galli GG, Williamson S, Selley J, Knight D, Elcioglu N, Aydin A, Elcioglu M, Venselaar H, Lund AH, Bonshek R, Black GC, Manson FD. A role for repressive complexes and H3K9 di-methylation in PRDM5-associated brittle cornea syndrome. Hum Mol Genet 2015; 24:6565-79. [PMID: 26395458 PMCID: PMC4634368 DOI: 10.1093/hmg/ddv345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/29/2015] [Accepted: 08/18/2015] [Indexed: 12/11/2022] Open
Abstract
Type 2 brittle cornea syndrome (BCS2) is an inherited connective tissue disease with a devastating ocular phenotype caused by mutations in the transcription factor PR domain containing 5 (PRDM5) hypothesized to exert epigenetic effects through histone and DNA methylation. Here we investigate clinical samples, including skin fibroblasts and retinal tissue from BCS2 patients, to elucidate the epigenetic role of PRDM5 and mechanisms of its dysregulation in disease. First we report abnormal retinal vascular morphology in the eyes of two cousins with BCS2 (PRDM5 Δ exons 9-14) using immunohistochemistry, and mine data from skin fibroblast expression microarrays from patients with PRDM5 mutations p.Arg590* and Δ exons 9-14, as well as from a PRDM5 ChIP-sequencing experiment. Gene ontology analysis of dysregulated PRDM5-target genes reveals enrichment for extracellular matrix (ECM) genes supporting vascular integrity and development. Q-PCR and ChIP-qPCR confirm upregulation of critical mediators of ECM stability in vascular structures (COL13A1, COL15A1, NTN1, CDH5) in patient fibroblasts. We identify H3K9 di-methylation (H3K9me2) at these PRDM5-target genes in fibroblasts, and demonstrate that the BCS2 mutation p.Arg83Cys diminishes interaction of PRDM5 with repressive complexes, including NuRD complex protein CHD4, and the repressive chromatin interactor HP1BP3, by co-immunoprecipitation combined with mass spectrometry. We observe reduced heterochromatin protein 1 binding protein 3 (HP1BP3) staining in the retinas of two cousins lacking exons 9-14 by immunohistochemistry, and dysregulated H3K9me2 in skin fibroblasts of three patients (p.Arg590*, p.Glu134* and Δ exons 9-14) by western blotting. These findings suggest that defective interaction of PRDM5 with repressive complexes, and dysregulation of H3K9me2, play a role in PRDM5-associated disease.
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Affiliation(s)
- Louise F Porter
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK, Manchester Royal Eye Hospital, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Giorgio G Galli
- Stem Cell Program, Boston Children's Hospital, Harvard Stem Cell and Regenerative Biology Department and Harvard Stem Cell Institute, Harvard University, Boston, MA, USA, Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Sally Williamson
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Julian Selley
- Faculty of Life Sciences, Michael Smith Building, Manchester, UK
| | - David Knight
- Faculty of Life Sciences, Michael Smith Building, Manchester, UK
| | - Nursel Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul, Turkey
| | - Ali Aydin
- Department of Ophthalmology, University of Medipol Medical Faculty, Istanbul, Turkey
| | - Mustafa Elcioglu
- Department of Ophthalmology, Okmeydani Research and Training Hospital, Istanbul, Turkey
| | - Hanka Venselaar
- Centre of Molecular and Biomolecular Informatics, Radboudumc Institute for Molecular Life Sciences, Nijmegen, The Netherlands and
| | - Anders H Lund
- Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Richard Bonshek
- Manchester Royal Eye Hospital, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, National Ophthalmic Pathology Service Laboratory, Department of Histopathology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Forbes D Manson
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
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Porter LF, Gallego-Pinazo R, Keeling CL, Kamieniorz M, Zoppi N, Colombi M, Giunta C, Bonshek R, Manson FD, Black GC. Bruch's membrane abnormalities in PRDM5-related brittle cornea syndrome. Orphanet J Rare Dis 2015; 10:145. [PMID: 26560304 PMCID: PMC4642625 DOI: 10.1186/s13023-015-0360-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 10/19/2015] [Indexed: 01/03/2023] Open
Abstract
Background Brittle cornea syndrome (BCS) is a rare, generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Recessive mutations in transcription factors ZNF469 and PRDM5 cause BCS. Both transcription factors are suggested to act on a common pathway regulating extracellular matrix genes, particularly fibrillar collagens. We identified bilateral myopic choroidal neovascularization as the presenting feature of BCS in a 26-year-old-woman carrying a novel PRDM5 mutation (p.Glu134*). We performed immunohistochemistry of anterior and posterior segment ocular tissues, as expression of PRDM5 in the eye has not been described, or the effects of PRDM5-associated disease on the retina, particularly the extracellular matrix composition of Bruch’s membrane. Methods Immunohistochemistry using antibodies against PRDM5, collagens type I, III, and IV was performed on the eyes of two unaffected controls and two patients (both with Δ9-14 PRDM5). Expression of collagens, integrins, tenascin and fibronectin in skin fibroblasts of a BCS patient with a novel p.Glu134* PRDM5 mutation was assessed using immunofluorescence. Results PRDM5 is expressed in the corneal epithelium and retina. We observe reduced expression of major components of Bruch’s membrane in the eyes of two BCS patients with a PRDM5 Δ9-14 mutation. Immunofluorescence performed on skin fibroblasts from a patient with p.Glu134* confirms the generalized nature of extracellular matrix abnormalities in BCS. Conclusions PDRM5-related disease is known to affect the cornea, skin and joints. Here we demonstrate, to the best of our knowledge for the first time, that PRDM5 localizes not only in the human cornea, but is also widely expressed in the retina. Our findings suggest that ECM abnormalities in PRDM5-associated disease are more widespread than previously reported. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0360-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louise F Porter
- Institute of Human Development, Centre for Genomic Medicine, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK. .,Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Oxford Road, Manchester, M13 9WL, UK. .,Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
| | - Roberto Gallego-Pinazo
- Department of Ophthalmology, Unit of Macula, University and Polytechnic Hospital La Fe, Valencia, Spain.
| | - Catherine L Keeling
- Histopathology, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL, UK.
| | - Martyna Kamieniorz
- Histopathology, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL, UK.
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy.
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, School of Medicine, University of Brescia, Brescia, Italy.
| | - Cecilia Giunta
- Division of Metabolism, Connective Tissue Unit, University Children's Hospital and Children's Research Centre, (CRC) Zurich, Switzerland.
| | - Richard Bonshek
- Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Oxford Road, Manchester, M13 9WL, UK. .,Department of Histopathology, National Ophthalmic Pathology Service (NSOPS) Laboratory, Central Manchester University Hospitals, NHS Foundation Trust, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL, UK.
| | - Forbes D Manson
- Institute of Human Development, Centre for Genomic Medicine, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK.
| | - Graeme C Black
- Institute of Human Development, Centre for Genomic Medicine, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK. .,Centre for Genomic Medicine, Central Manchester University Hospitals, NHS Foundation Trust, MAHSC, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK.
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Khirade MF, Lal G, Bapat SA. Derivation of a fifteen gene prognostic panel for six cancers. Sci Rep 2015; 5:13248. [PMID: 26272668 PMCID: PMC4536526 DOI: 10.1038/srep13248] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/22/2015] [Indexed: 12/21/2022] Open
Abstract
The hallmarks of cancer deem biological pathways and molecules to be conserved. This approach may be useful for deriving a prognostic gene signature. Weighted Gene Co-expression Network Analysis of gene expression datasets in eleven cancer types identified modules of highly correlated genes and interactive networks conserved across glioblastoma, breast, ovary, colon, rectal and lung cancers, from which a universal classifier for tumor stratification was extracted. Specific conserved gene modules were validated across different microarray platforms and datasets. Strikingly, preserved genes within these modules defined regulatory networks associated with immune regulation, cell differentiation, metastases, cell migration, metastases, oncogenic transformation, and resistance to apoptosis and senescence, with AIF1 and PRRX1 being suggested to be master regulators governing these biological processes. A universal classifier from these conserved networks enabled execution of common set of principles across different cancers that revealed distinct, differential correlation of biological functions with patient survival in a cancer-specific manner. Correlation analysis further identified a panel of 15 risk genes with potential prognostic value, termed as the GBOCRL-IIPr panel [(GBM-Breast-Ovary-Colon-Rectal-Lung)–Immune–Invasion–Prognosis], that surprisingly, were not amongst the master regulators or important network hubs. This panel may now be integrated in predicting patient outcomes in the six cancers.
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Affiliation(s)
- Mamata F Khirade
- National Centre for Cell Science, NCCS Complex, Pune 411007, India
| | - Girdhari Lal
- National Centre for Cell Science, NCCS Complex, Pune 411007, India
| | - Sharmila A Bapat
- National Centre for Cell Science, NCCS Complex, Pune 411007, India
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