1
|
Polubothu S, Zecchin D, Al-Olabi L, Lionarons DA, Harland M, Horswell S, Thomas AC, Hunt L, Wlodarchak N, Aguilera P, Brand S, Bryant D, Carrera C, Chen H, Elgar G, Harwood CA, Howell M, Larue L, Loughlin S, MacDonald J, Malvehy J, Barberan SM, da Silva VM, Molina M, Morrogh D, Moulding D, Nsengimana J, Pittman A, Puig-Butillé JA, Parmar K, Sebire NJ, Scherer S, Stadnik P, Stanier P, Tell G, Waelchli R, Zarrei M, Puig S, Bataille V, Xing Y, Healy E, Moore GE, Di WL, Newton-Bishop J, Downward J, Kinsler VA. Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype. Genet Med 2021; 23:1636-1647. [PMID: 34145395 PMCID: PMC8460442 DOI: 10.1038/s41436-021-01204-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Much of the heredity of melanoma remains unexplained. We sought predisposing germline copy-number variants using a rare disease approach. METHODS Whole-genome copy-number findings in patients with melanoma predisposition syndrome congenital melanocytic nevus were extrapolated to a sporadic melanoma cohort. Functional effects of duplications in PPP2R3B were investigated using immunohistochemistry, transcriptomics, and stable inducible cellular models, themselves characterized using RNAseq, quantitative real-time polymerase chain reaction (qRT-PCR), reverse phase protein arrays, immunoblotting, RNA interference, immunocytochemistry, proliferation, and migration assays. RESULTS We identify here a previously unreported genetic susceptibility to melanoma and melanocytic nevi, familial duplications of gene PPP2R3B. This encodes PR70, a regulatory unit of critical phosphatase PP2A. Duplications increase expression of PR70 in human nevus, and increased expression in melanoma tissue correlates with survival via a nonimmunological mechanism. PPP2R3B overexpression induces pigment cell switching toward proliferation and away from migration. Importantly, this is independent of the known microphthalmia-associated transcription factor (MITF)-controlled switch, instead driven by C21orf91. Finally, C21orf91 is demonstrated to be downstream of MITF as well as PR70. CONCLUSION This work confirms the power of a rare disease approach, identifying a previously unreported copy-number change predisposing to melanocytic neoplasia, and discovers C21orf91 as a potentially targetable hub in the control of phenotype switching.
Collapse
Affiliation(s)
- Satyamaanasa Polubothu
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, UK
| | - Davide Zecchin
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Lara Al-Olabi
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | | | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Cancer Research UK Clinical Centre at Leeds, St James's University Hospital, Leeds, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics, Francis Crick Institute, London, UK
| | - Anna C Thomas
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Lilian Hunt
- Advanced Sequencing Facility, Francis Crick Institute, London, UK
| | - Nathan Wlodarchak
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Paula Aguilera
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Sarah Brand
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Dale Bryant
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Cristina Carrera
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Hui Chen
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Greg Elgar
- Advanced Sequencing Facility, Francis Crick Institute, London, UK
| | - Catherine A Harwood
- Centre for Cell Biology and Cutaneous Research, Blizzard Institute, Barts, London, UK
| | - Michael Howell
- High Throughput Screening Facility, Francis Crick Institute, London, UK
| | - Lionel Larue
- Centre de Recherche, Developmental Genetics of Melanocytes, Institut Curie, Orsay, France
| | - Sam Loughlin
- North East Thames Regional Genetics Laboratory Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jeff MacDonald
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Josep Malvehy
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Sara Martin Barberan
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Vanessa Martins da Silva
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Miriam Molina
- Oncogene Biology Laboratory, Francis Crick Institute, London, UK
| | - Deborah Morrogh
- North East Thames Regional Genetics Laboratory Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Dale Moulding
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Cancer Research UK Clinical Centre at Leeds, St James's University Hospital, Leeds, UK
| | - Alan Pittman
- Bioinformatics, St George's University of London, London, UK
| | - Joan-Anton Puig-Butillé
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Kiran Parmar
- Department of Twin Research and Genetic Epidemiology, King's College London, South Wing Block D, London, UK
| | - Neil J Sebire
- Department of Histopathology, Great Ormond Street Hospital for Children, London, UK
| | - Stephen Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Paulina Stadnik
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Gemma Tell
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Regula Waelchli
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, UK
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Susana Puig
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | | | - Yongna Xing
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Eugene Healy
- Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Gudrun E Moore
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Wei-Li Di
- Infection, Immunity and Inflammation Programme, Immunobiology Section, UCL GOS Institute of Child Health, London, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Cancer Research UK Clinical Centre at Leeds, St James's University Hospital, Leeds, UK
| | - Julian Downward
- Oncogene Biology Laboratory, Francis Crick Institute, London, UK
| | - Veronica A Kinsler
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK.
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK.
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, UK.
| |
Collapse
|