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Buckley M, Terwagne C, Ganner A, Cubitt L, Brewer R, Kim DK, Kajba CM, Forrester N, Dace P, De Jonghe J, Shepherd STC, Sawyer C, McEwen M, Diederichs S, Neumann-Haefelin E, Turajlic S, Ivakine EA, Findlay GM. Saturation genome editing maps the functional spectrum of pathogenic VHL alleles. Nat Genet 2024; 56:1446-1455. [PMID: 38969834 PMCID: PMC11250436 DOI: 10.1038/s41588-024-01800-z] [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: 05/11/2023] [Accepted: 05/13/2024] [Indexed: 07/07/2024]
Abstract
To maximize the impact of precision medicine approaches, it is critical to identify genetic variants underlying disease and to accurately quantify their functional effects. A gene exemplifying the challenge of variant interpretation is the von Hippel-Lindautumor suppressor (VHL). VHL encodes an E3 ubiquitin ligase that regulates the cellular response to hypoxia. Germline pathogenic variants in VHL predispose patients to tumors including clear cell renal cell carcinoma (ccRCC) and pheochromocytoma, and somatic VHL mutations are frequently observed in sporadic renal cancer. Here we optimize and apply saturation genome editing to assay nearly all possible single-nucleotide variants (SNVs) across VHL's coding sequence. To delineate mechanisms, we quantify mRNA dosage effects and compare functional effects in isogenic cell lines. Function scores for 2,268 VHL SNVs identify a core set of pathogenic alleles driving ccRCC with perfect accuracy, inform differential risk across tumor types and reveal new mechanisms by which variants impact function. These results have immediate utility for classifying VHL variants encountered clinically and illustrate how precise functional measurements can resolve pleiotropic and dosage-dependent genotype-phenotype relationships across complete genes.
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Affiliation(s)
- Megan Buckley
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Chloé Terwagne
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Athina Ganner
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laura Cubitt
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Reid Brewer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dong-Kyu Kim
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christina M Kajba
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Nicole Forrester
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Phoebe Dace
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Joachim De Jonghe
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Scott T C Shepherd
- The Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Chelsea Sawyer
- Scientific Computing, The Francis Crick Institute, London, UK
| | - Mairead McEwen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, A Partnership Between DKFZ and University Medical Center Freiburg, Freiburg, Germany
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Samra Turajlic
- The Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Gregory M Findlay
- The Genome Function Laboratory, The Francis Crick Institute, London, UK.
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Li Y, Xin X, Song W, Zhang X, Chen S, Wang Q, Li A, Li Y. VHL syndrome without clear family history: A rare case report and literature review of Chinese patients. Front Neurol 2022; 13:951054. [PMID: 36324386 PMCID: PMC9618664 DOI: 10.3389/fneur.2022.951054] [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: 05/23/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022] Open
Abstract
Objective To analyze the clinical manifestations and imaging features of a hospitalized patient with intermittent headache who was finally diagnosed with von Hippel–Lindau (VHL) syndrome and to perform whole-exon gene detection to improve the understanding of the diagnosis and treatment strategies of the disease. Methods A case of suspected VHL syndrome in Shanxi Provincial People's Hospital was analyzed. Proband DNA was also extracted for whole exome sequencing and screened for causative mutation sites, which were validated by Sanger sequencing. The literature about VHL gene mutations in Chinese patients in the past 10 years were also reviewed. Results There is a heterozygous mutation site c.499C > G on the VHL gene on the short arm of chromosome 3 of the patient, which is a missense mutation. The mutation results in the substitution of arginine with glycine at amino acid 167 of the encoded protein, which may be primarily responsible for the disease in the patient with VHL syndrome. However, the mutation did not occur in other family members. Conclusion Early recognition and treatment of VHL syndrome can be available with genetic testing technology. Strengthening the understanding of this complex genetic disease and improving the diagnostic rate of VHL syndrome are helpful for the precise treatment of patients with this disease, which may help prolong the survival time of patients to a certain extent and improve their quality of life.
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Affiliation(s)
- Yaheng Li
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
- Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
| | - Xiaohong Xin
- Core Laboratory, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi University, Taiyuan, China
- Academy of Microbial Ecology, Shanxi Medical University, Taiyuan, China
| | - Wenzhu Song
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Xuan Zhang
- Department of Neurosurgery, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Shengli Chen
- Department of Neurosurgery, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
| | - Qian Wang
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
- Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
| | - Aizhong Li
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
- Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
| | - Yafeng Li
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi Medical University, Taiyuan, China
- Shanxi Provincial Key Laboratory of Kidney Disease, Taiyuan, China
- Core Laboratory, Shanxi Provincial People's Hospital (Fifth Hospital) of Shanxi University, Taiyuan, China
- Academy of Microbial Ecology, Shanxi Medical University, Taiyuan, China
- *Correspondence: Yafeng Li
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Glushkova M, Dimova P, Yordanova I, Todorov T, Tourtourikov I, Mitev V, Todorova A. Molecular-genetic diagnostics of von Hippel-Lindau syndrome (VHL) in Bulgaria: first complex mutation event in the VHL gene. Int J Neurosci 2017; 128:117-124. [PMID: 28849724 DOI: 10.1080/00207454.2017.1372436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Von Hippel-Lindau syndrome is an autosomal-dominant disease characterized by the formation of various tumours and cysts in many different parts of the body. Von Hippel-Lindau syndrome is caused by VHL gene mutations leading to production of impaired tumor suppressor Von Hippel-Lindau syndrome protein or its complete absence. PURPOSE To study five patients with clinically suspected Von Hippel-Lindau syndrome, who were referred for molecular genetic testing. METHODS Sanger sequencing of the coding regions of the VHL gene. RESULTS Five clinically relevant germline mutations were detected. One of the pathogenic variants has not been previously reported. This novel mutation is a complex mutation event combining a duplication and an indel, rearranging exon 3 of the VHL gene - c. [516_517dupGTCAAGCCT; 532_542delCTGGACATCGTinsATTA], p. (Glu173Serfs*4). CONCLUSION Overall, our results showed that the diagnosis of Von Hippel-Lindau syndrome in our country is difficult most probably because of its heterogeneous clinical manifestation and insufficient knowledge on the diagnostic criteria for the disease. From genetic point of view our results add some novel data on the mutation profile of the VHL gene. In order to prove or revise the diagnosis, early genetic testing is strongly recommended in affected patients and their family members to ensure appropriate follow-up and treatment of the malignancies.
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Affiliation(s)
- Maria Glushkova
- a Department of Medical Chemistry and Biochemistry , Medical University Sofia , Sofia , Bulgaria.,c Genetic Medico-Diagnostic Laboratory Genica , Sofia , Bulgaria
| | - Petia Dimova
- b Epilepsy Center, Department of Neurosurgery , University Hospital 'St. Ivan Rilski' , Sofia , Bulgaria
| | - Iglika Yordanova
- c Genetic Medico-Diagnostic Laboratory Genica , Sofia , Bulgaria
| | - Tihomir Todorov
- c Genetic Medico-Diagnostic Laboratory Genica , Sofia , Bulgaria
| | | | - Vanyo Mitev
- a Department of Medical Chemistry and Biochemistry , Medical University Sofia , Sofia , Bulgaria
| | - Albena Todorova
- a Department of Medical Chemistry and Biochemistry , Medical University Sofia , Sofia , Bulgaria.,c Genetic Medico-Diagnostic Laboratory Genica , Sofia , Bulgaria
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Mathó C, Sansó G, Diez B, Barontini M, Pennisi PA. VHL Germline Mutations in Argentinian Patients with Clinical Diagnoses or Single Typical Manifestations of Type 1 von Hippel-Lindau Disease. Genet Test Mol Biomarkers 2016; 20:771-776. [PMID: 27617348 DOI: 10.1089/gtmb.2016.0204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS von Hippel-Lindau (VHL) disease is caused by mutations in the VHL tumor suppressor gene. As tumors that develop in the context of VHL also occur in a sporadic context, the frequency of this syndrome may be underestimated. Our aim was to identify VHL gene mutations in Argentinian patients who fulfilled the clinical criteria for type 1 VHL disease and in patients with VHL-associated manifestations that did not meet these criteria. METHODS We performed a retrospective cohort study, including patients who met current diagnostic criteria for type 1 VHL (Group 1, n = 19) and patients with VHL-associated manifestations that did not meet these criteria (Group 2, n = 21). Genomic DNA was extracted from peripheral blood leukocytes. Mutation analysis involved DNA sequencing, while large deletions were determined by universal primer quantitative fluorescent multiplex polymerase chain reaction (UPQFM-PCR) and multiplex ligation-dependent probe amplification (MLPA) analysis. RESULTS VHL mutations were detected in 16/19 (84.2%) patients in Group 1 and included: gross deletions (4/16); nonsense mutations (6/16); frameshift mutations (4/16); missense mutations (1/16); and splicing mutations (1/16). Three of these mutations were novel. No alterations were found in 3 of 19 VHL patients. In Group 2, one nonsense VHL mutation was detected in a young patient with a solitary central nervous system hemangioblastoma without familial history. A study of 30 first-degree relatives revealed four carriers with VHL mutations. CONCLUSIONS We found three novel mutations in the VHL gene in our population. Our results emphasize the importance of a complete genetic study of VHL to confirm type 1 VHL disease, not only in patients with clinical diagnostic criteria but also in those presenting a single typical manifestation.
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Affiliation(s)
- Cecilia Mathó
- 1 Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez , CABA, Argentina
| | - Gabriela Sansó
- 1 Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez , CABA, Argentina
| | - Blanca Diez
- 2 Fundación para la Lucha contra las Enfermedades Neurológicas de la Infancia , CABA, Argentina
| | - Marta Barontini
- 1 Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez , CABA, Argentina
| | - Patricia A Pennisi
- 1 Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez , CABA, Argentina
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