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Kavitha B, Ranganathan S, Gopi S, Vetrivel U, Hemavathy N, Mohan V, Radha V. Molecular characterization and re-interpretation of HNF1A variants identified in Indian MODY subjects towards precision medicine. Front Endocrinol (Lausanne) 2023; 14:1177268. [PMID: 37396188 PMCID: PMC10313120 DOI: 10.3389/fendo.2023.1177268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Background HNF1A is an essential component of the transcription factor network that controls pancreatic β-cell differentiation, maintenance, and glucose stimulated insulin secretion (GSIS). A continuum of protein malfunction is caused by variations in the HNF1A gene, from severe loss-of-function (LOF) variants that cause the highly penetrant Maturity Onset Diabetes of the Young (MODY) to milder LOF variants that are far less penetrant but impart a population-wide risk of type 2 diabetes that is up to five times higher. Before classifying and reporting the discovered variations as relevant in clinical diagnosis, a critical review is required. Functional investigations offer substantial support for classifying a variant as pathogenic, or otherwise as advised by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) ACMG/AMP criteria for variant interpretation. Objective To determine the molecular basis for the variations in the HNF1A gene found in patients with monogenic diabetes in India. Methods We performed functional protein analyses such as transactivation, protein expression, DNA binding, nuclear localization, and glucose stimulated insulin secretion (GSIS) assay, along with structural prediction analysis for 14 HNF1A variants found in 20 patients with monogenic diabetes. Results Of the 14 variants, 4 (28.6%) were interpreted as pathogenic, 6 (42.8%) as likely pathogenic, 3 (21.4%) as variants of uncertain significance, and 1 (7.14%) as benign. Patients harboring the pathogenic/likely pathogenic variants were able to successfully switch from insulin to sulfonylureas (SU) making these variants clinically actionable. Conclusion Our findings are the first to show the need of using additive scores during molecular characterization for accurate pathogenicity evaluations of HNF1A variants in precision medicine.
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Affiliation(s)
- Babu Kavitha
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Indian Council of Medical Research (ICMR) Centre for Advanced Research on Diabetes, Affiliated to University of Madras, Chennai, India
| | | | - Sundaramoorthy Gopi
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Indian Council of Medical Research (ICMR) Centre for Advanced Research on Diabetes, Affiliated to University of Madras, Chennai, India
| | - Umashankar Vetrivel
- Department of Bioinformatics, Vision Research Foundation, Chennai, India
- Department of Virology Biotechnology, Indian Council of Medical Research (ICMR)-National Institute of Traditional Medicine, Belagavi, India
| | | | - Viswanathan Mohan
- Department of Diabetology, Madras Diabetes Research Foundation, Chennai and Dr. Mohan’s Diabetes Specialties Centre, International Diabetes Federation (IDF) Centre of Education, Chennai, India
| | - Venkatesan Radha
- Department of Molecular Genetics, Madras Diabetes Research Foundation, Indian Council of Medical Research (ICMR) Centre for Advanced Research on Diabetes, Affiliated to University of Madras, Chennai, India
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Lopez-Perolio I, Leman R, Behar R, Lattimore V, Pearson JF, Castéra L, Martins A, Vaur D, Goardon N, Davy G, Garre P, García-Barberán V, Llovet P, Pérez-Segura P, Díaz-Rubio E, Caldés T, Hruska KS, Hsuan V, Wu S, Pesaran T, Karam R, Vallon-Christersson J, Borg A, Valenzuela-Palomo A, Velasco EA, Southey M, Vreeswijk MPG, Devilee P, Kvist A, Spurdle AB, Walker LC, Krieger S, de la Hoya M. Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA report. J Med Genet 2019; 56:453-460. [PMID: 30890586 PMCID: PMC6591742 DOI: 10.1136/jmedgenet-2018-105834] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/10/2019] [Accepted: 02/06/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2-without incurring overprediction-is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. METHODS Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212-1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant. RESULTS We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies. CONCLUSIONS PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.
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Affiliation(s)
- Irene Lopez-Perolio
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Raphaël Leman
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Raquel Behar
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Vanessa Lattimore
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Laurent Castéra
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, UNIROUEN, Normandie Université, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Dominique Vaur
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Nicolas Goardon
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Grégoire Davy
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Pilar Garre
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Vanesa García-Barberán
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eduardo Díaz-Rubio
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | | | | | - Sitao Wu
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ake Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Alberto Valenzuela-Palomo
- Splicing and genetic susceptibility to cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Eladio A Velasco
- Splicing and genetic susceptibility to cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Sophie Krieger
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
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