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Goel S, Deshpande S, Dhaniwala N, Singh R, Suneja A, Jadawala VH. A Comprehensive Review of Genetic Variations in Collagen-Encoding Genes and Their Implications in Intervertebral Disc Degeneration. Cureus 2024; 16:e52708. [PMID: 38384607 PMCID: PMC10880043 DOI: 10.7759/cureus.52708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
This comprehensive review examines the intricate relationship between genetic variations in collagen-encoding genes and their implications in intervertebral disc degeneration (IVDD). Intervertebral disc degeneration is a prevalent spinal condition characterized by structural and functional changes in intervertebral discs (IVDs), and understanding its genetic underpinnings is crucial for advancing diagnostic and therapeutic strategies. The review begins by exploring the background and importance of collagen in IVDs, emphasizing its role in providing structural integrity. It then delves into the significance of genetic variations within collagen-encoding genes, categorizing and discussing their potential impact on disc health. The methods employed in studying these variations, such as genome-wide association studies (GWASs) and next-generation sequencing (NGS), are also reviewed. The subsequent sections analyze existing literature to establish associations between genetic variations and IVDD, unraveling molecular mechanisms linking genetic factors to disc degeneration. The review concludes with a summary of key findings, implications for future research and clinical practice, and a reflection on the importance of understanding genetic variations in collagen-encoding genes to diagnose and treat IVDD. The insights gleaned from this review contribute to our understanding of IVDD and hold promise for the development of personalized interventions based on individual genetic profiles.
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Affiliation(s)
- Sachin Goel
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sanjay Deshpande
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Nareshkumar Dhaniwala
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Rahul Singh
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Anmol Suneja
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Vivek H Jadawala
- Orthopaedics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Moles-Fernández A, Duran-Lozano L, Montalban G, Bonache S, López-Perolio I, Menéndez M, Santamariña M, Behar R, Blanco A, Carrasco E, López-Fernández A, Stjepanovic N, Balmaña J, Capellá G, Pineda M, Vega A, Lázaro C, de la Hoya M, Diez O, Gutiérrez-Enríquez S. Computational Tools for Splicing Defect Prediction in Breast/Ovarian Cancer Genes: How Efficient Are They at Predicting RNA Alterations? Front Genet 2018; 9:366. [PMID: 30233647 PMCID: PMC6134256 DOI: 10.3389/fgene.2018.00366] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/22/2018] [Indexed: 12/31/2022] Open
Abstract
In silico tools for splicing defect prediction have a key role to assess the impact of variants of uncertain significance. Our aim was to evaluate the performance of a set of commonly used splicing in silico tools comparing the predictions against RNA in vitro results. This was done for natural splice sites of clinically relevant genes in hereditary breast/ovarian cancer (HBOC) and Lynch syndrome. A study divided into two stages was used to evaluate SSF-like, MaxEntScan, NNSplice, HSF, SPANR, and dbscSNV tools. A discovery dataset of 99 variants with unequivocal results of RNA in vitro studies, located in the 10 exonic and 20 intronic nucleotides adjacent to exon-intron boundaries of BRCA1, BRCA2, MLH1, MSH2, MSH6, PMS2, ATM, BRIP1, CDH1, PALB2, PTEN, RAD51D, STK11, and TP53, was collected from four Spanish cancer genetic laboratories. The best stand-alone predictors or combinations were validated with a set of 346 variants in the same genes with clear splicing outcomes reported in the literature. Sensitivity, specificity, accuracy, negative predictive value (NPV) and Mathews Coefficient Correlation (MCC) scores were used to measure the performance. The discovery stage showed that HSF and SSF-like were the most accurate for variants at the donor and acceptor region, respectively. The further combination analysis revealed that HSF, HSF+SSF-like or HSF+SSF-like+MES achieved a high performance for predicting the disruption of donor sites, and SSF-like or a sequential combination of MES and SSF-like for predicting disruption of acceptor sites. The performance confirmation of these last results with the validation dataset, indicated that the highest sensitivity, accuracy, and NPV (99.44%, 99.44%, and 96.88, respectively) were attained with HSF+SSF-like or HSF+SSF-like+MES for donor sites and SSF-like (92.63%, 92.65%, and 84.44, respectively) for acceptor sites. We provide recommendations for combining algorithms to conduct in silico splicing analysis that achieved a high performance. The high NPV obtained allows to select the variants in which the study by in vitro RNA analysis is mandatory against those with a negligible probability of being spliceogenic. Our study also shows that the performance of each specific predictor varies depending on whether the natural splicing sites are donors or acceptors.
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Affiliation(s)
| | - Laura Duran-Lozano
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Irene López-Perolio
- Laboratorio de Oncología Molecular - Centro de Investigación Biomédica en Red de Cancer, Instituto de Investigación Sanitaria San Carlos, Hospital Clínico San Carlos, Madrid, Spain
| | - Mireia Menéndez
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Marta Santamariña
- Grupo de Medicina Xenómica-USC, Fundación Pública Galega de Medicina Xenómica-SERGAS, CIBER de Enfermedades Raras, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Raquel Behar
- Laboratorio de Oncología Molecular - Centro de Investigación Biomédica en Red de Cancer, Instituto de Investigación Sanitaria San Carlos, Hospital Clínico San Carlos, Madrid, Spain
| | - Ana Blanco
- Grupo de Medicina Xenómica-USC, Fundación Pública Galega de Medicina Xenómica-SERGAS, CIBER de Enfermedades Raras, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Estela Carrasco
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Adrià López-Fernández
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Neda Stjepanovic
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Medical Oncology Department, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Medical Oncology Department, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Ana Vega
- Grupo de Medicina Xenómica-USC, Fundación Pública Galega de Medicina Xenómica-SERGAS, CIBER de Enfermedades Raras, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Institut d'Investigació Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Miguel de la Hoya
- Laboratorio de Oncología Molecular - Centro de Investigación Biomédica en Red de Cancer, Instituto de Investigación Sanitaria San Carlos, Hospital Clínico San Carlos, Madrid, Spain
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Area of Clinical and Molecular Genetics, University Hospital Vall d'Hebron, Barcelona, Spain
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