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González-Iglesias E, López-Vázquez A, Noval S, Nieves-Moreno M, Granados-Fernández M, Arruti N, Rosa-Pérez I, Pacio-Míguez M, Montaño VEF, Rodríguez-Solana P, del Pozo A, Santos-Simarro F, Vallespín E. Next-Generation Sequencing Screening of 43 Families with Non-Syndromic Early-Onset High Myopia: A Clinical and Genetic Study. Int J Mol Sci 2022; 23:ijms23084233. [PMID: 35457050 PMCID: PMC9031962 DOI: 10.3390/ijms23084233] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/04/2022] [Indexed: 02/01/2023] Open
Abstract
Early-onset high myopia (EoHM) is a disease that causes a spherical refraction error of ≥-6 diopters before 10 years of age, with potential multiple ocular complications. In this article, we report a clinical and genetic study of 43 families with EoHM recruited in our center. A complete ophthalmological evaluation was performed, and a sample of peripheral blood was obtained from proband and family members. DNA was analyzed using a customized next-generation sequencing panel that included 419 genes related to ophthalmological disorders with a suspected genetic cause, and genes related to EoHM pathogenesis. We detected pathogenic and likely pathogenic variants in 23.9% of the families and detected variants of unknown significance in 76.1%. Of these, 5.7% were found in genes related to non-syndromic EoHM, 48.6% in genes associated with inherited retinal dystrophies that can include a syndromic phenotype, and 45.7% in genes that are not directly related to EoHM or retinal dystrophy. We found no candidate genes in 23% of the patients, which suggests that further studies are needed. We propose a systematic genetic analysis for patients with EoHM because it helps with follow-up, prognosis and genetic counseling.
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Affiliation(s)
- Eva González-Iglesias
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
| | - Ana López-Vázquez
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Susana Noval
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - María Nieves-Moreno
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - María Granados-Fernández
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Natalia Arruti
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Irene Rosa-Pérez
- Department of Ophthalmology, La Paz University Hospital, 28046 Madrid, Spain; (A.L.-V.); (S.N.); (M.N.-M.); (M.G.-F.); (N.A.); (I.R.-P.)
| | - Marta Pacio-Míguez
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Neurodevelopmental Disorders, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Victoria E. F. Montaño
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
| | - Patricia Rodríguez-Solana
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
| | - Angela del Pozo
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Clinical Bioinformatics, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Fernando Santos-Simarro
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Section of Clinical Genetics, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain
| | - Elena Vallespín
- Section of Molecular Ophthalmology, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, La Paz University Hospital, 28046 Madrid, Spain; (E.G.-I.); (V.E.F.M.); (P.R.-S.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (M.P.-M.); (A.d.P.); (F.S.-S.)
- Correspondence:
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Nieves-Moreno M, Noval S, Peralta J, Palomares-Bralo M, del Pozo A, Garcia-Miñaur S, Santos-Simarro F, Vallespin E. Expanding the Phenotypic Spectrum of PAX6 Mutations: From Congenital Cataracts to Nystagmus. Genes (Basel) 2021; 12:genes12050707. [PMID: 34065151 PMCID: PMC8151272 DOI: 10.3390/genes12050707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Congenital aniridia is a complex ocular disorder, usually associated with severe visual impairment, generally caused by mutations on the PAX6 gene. The clinical phenotype of PAX6 mutations is highly variable, making the genotype–phenotype correlations difficult to establish. Methods: we describe the phenotype of eight patients from seven unrelated families with confirmed mutations in PAX6, and very different clinical manifestations. Results: Only two patients had the classical aniridia phenotype while the other two presented with aniridia-related manifestations, such as aniridia-related keratopathy or partial aniridia. Congenital cataracts were the main manifestation in three of the patients in this series. All the patients had nystagmus and low visual acuity. Conclusions: The diagnosis of mild forms of aniridia is challenging, but these patients have a potentially blinding hereditary disease that might present with a more severe phenotype in future generations. Clinicians should be aware of the mild aniridia phenotype and request genetic testing to perform an accurate diagnosis.
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Affiliation(s)
- Maria Nieves-Moreno
- Department of Ophthalmology, Hospital Universitario La Paz, 28046 Madrid, Spain; (S.N.); (J.P.)
- Correspondence:
| | - Susana Noval
- Department of Ophthalmology, Hospital Universitario La Paz, 28046 Madrid, Spain; (S.N.); (J.P.)
| | - Jesus Peralta
- Department of Ophthalmology, Hospital Universitario La Paz, 28046 Madrid, Spain; (S.N.); (J.P.)
| | - María Palomares-Bralo
- Department of Molecular Developmental Disorders, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - Angela del Pozo
- Department of Bioinformatics, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - Sixto Garcia-Miñaur
- Department of Clinical Genetics, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain; (S.G.-M.); (F.S.-S.)
| | - Fernando Santos-Simarro
- Department of Clinical Genetics, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain; (S.G.-M.); (F.S.-S.)
| | - Elena Vallespin
- Department of Molecular Ophthalmology, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain;
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Romero-Laorden N, Castro E, Medina A, Lorente D, González-Billalabeitia E, Méndez-Vidal MJ, Gonzalez del Alba A, Lozano R, Borrega P, Fernandez Parra E, Sáez MI, Garcia Carbonero I, Rodriguez Vida A, Morales Barrera R, del Pozo A, Pritchard C, Lapunzina P, Piulats Rodriguez JM, Puente J, Olmos D. Impact of treatment sequence on the outcomes of metastatic castration resistant prostate cancer patients (mCRPC) with germline BRCA2 mutations: A subanalysis of the PROREPAIR-B study. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.5071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Elena Castro
- Spanish National Cancer Research Centre, Madrid, Spain
| | - Ana Medina
- Medical Oncology Department, Centro Oncologico de Galicia, A Coruña, Spain
| | - David Lorente
- Servicio Oncologia Medica Hospital Universitario La Fe, Valencia, Spain
| | | | | | | | - Rebeca Lozano
- Spanish National Research Cancer Centre, Madrid, Spain
| | | | | | - M Isabel Sáez
- CRIS Cancer Foundation Prostate Cancer Research Group, Institute of Biomedical Research in Malaga/ CNIO-IBIMA Genitourinary Cancer Research Unit, H Universitarios Virgen de la Victoria y Regional de Málaga, Malaga, Spain
| | | | | | | | - Angela del Pozo
- Medical Genetics and Molecular Institute, La Paz, Madrid, Spain
| | | | - Pablo Lapunzina
- Medical Genetics and Molecular Institute, La Paz, Madrid, Spain
| | | | - Javier Puente
- Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - David Olmos
- Spanish National Cancer Research Centre, Madrid, Spain
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Lozano R, Romero-Laorden N, del Pozo A, Medina A, Mendez MJ, Morales Barrera R, Gonzalez del Alba AA, Rodriguez-Vida A, Hernandez A, Silla-Castro JC, Vazquez S, Gonzalez B, Pinto A, Perez Gracia JL, Querol R, Cañadilla V, Domenech M, Pritchard C, Castro E, Olmos D. Comparative assessment of abiraterone or enzalutamide activity in the PROREPAIR-B study. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.6_suppl.164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
164 Background: Germline mutations in DNA repair genes have been associated with poor prostate cancer outcomes in retrospectives studies. Such defects have been identified in 12% of mCRPC patients. Several studies are ongoing to assess the benefit of these patients from platinum-based chemotherapy and PARP inhibitors, but no conclusive data are available with regards to currently approved therapies for mCRPC, as Abiraterone or Enzalutamide. Methods: PROREPAIR-B (NCT03075735) is a prospective multicentre observational cohort study. Patients diagnosed with mCRPC, with unknown mutational status at study entry and who were going to start a first-line treatment for mCRPC were eligible. For this sub-analysis patients who received Abiraterone or Enzalutamide as first androgen receptor targeted therapy (ART) were selected. The endpoints of this sub-analysis included to assess the impact of BRCA1, BRCA2, ATM, PALB2 and other germline mutations in DNA repair genes on cause-specific survival (CSS), progression-free survival (PFS), time to PSA progression (bPFS) and response to the first ART received as 1st or 2nd line therapy. Results: 337 patients were eligible for this analysis. CSS from mCRPC was not significantly different between gDDR carriers and non-carriers. However, CSS from mCRPC in BRCA2 carriers was significantly shorter than in non-carriers (23.3 Vs 34.6 months, p = 0.02). CSS from first ART, PFS and response-rates were not significantly different between both groups. However, the bPFS was significantly shorter in patients harbouring gDDR mutations (7.3 Vs 3.8 months, p = 0.04), especially in BRCA2 carriers (7.3 Vs 3.0 months, p = 0.03). Conclusions: This is the first study to prospectively follow-up DNA repair germline mutations to determine the outcome on standard treatment for mCRPC. The results suggest that different gDDR defects may have different impact on mCRPC outcomes. Clinical trial information: NCT03075735.
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Affiliation(s)
- Rebeca Lozano
- Spanish National Cancer Research Centre, Madrid, Spain
| | | | - Angela del Pozo
- Medical Genetics and Molecular Institute, La Paz, Madrid, Spain
| | - Ana Medina
- Centro Oncologico de Galicia, La Coruna, Spain
| | | | | | | | | | | | | | | | | | | | | | - Rosa Querol
- Hospital de Sabadell, Corporació Sanitària Parc Taulí, Institut Oncològic del Vallès, Sabadell, Spain
| | | | | | | | - Elena Castro
- Spanish National Cancer Research Centre, Madrid, Spain
| | - David Olmos
- Spanish National Cancer Research Centre, Madrid, Spain
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Rodriguez‐Zabala M, Aza‐Carmona M, Rivera‐Pedroza CI, Belinchón A, Guerrero‐Zapata I, Barraza‐García J, Vallespin E, Lu M, del Pozo A, Glucksman MJ, Santos‐Simarro F, Heath KE. FGF9 mutation causes craniosynostosis along with multiple synostoses. Hum Mutat 2017; 38:1471-1476. [DOI: 10.1002/humu.23292] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/05/2017] [Accepted: 07/08/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Maria Rodriguez‐Zabala
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
| | - Miriam Aza‐Carmona
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto Carlos III Madrid Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE) Hospital Universitario La Paz Madrid Spain
| | - Carlos I. Rivera‐Pedroza
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE) Hospital Universitario La Paz Madrid Spain
| | - Alberta Belinchón
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto Carlos III Madrid Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE) Hospital Universitario La Paz Madrid Spain
| | - Isabel Guerrero‐Zapata
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
| | - Jimena Barraza‐García
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto Carlos III Madrid Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE) Hospital Universitario La Paz Madrid Spain
| | - Elena Vallespin
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto Carlos III Madrid Spain
| | - Min Lu
- Department of Biochemistry and Molecular Biology Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago North Chicago Illinois
| | - Angela del Pozo
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto Carlos III Madrid Spain
| | - Marc J. Glucksman
- Department of Biochemistry and Molecular Biology Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago North Chicago Illinois
| | - Fernando Santos‐Simarro
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto Carlos III Madrid Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE) Hospital Universitario La Paz Madrid Spain
| | - Karen E. Heath
- Institute of Medical & Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Instituto Carlos III Madrid Spain
- Multidisciplinary Skeletal dysplasia Unit (UMDE) Hospital Universitario La Paz Madrid Spain
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Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, del Pozo A, Vázquez J, Valencia A, Tress ML. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PLoS Comput Biol 2015; 11:e1004325. [PMID: 26061177 PMCID: PMC4465641 DOI: 10.1371/journal.pcbi.1004325] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [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: 12/16/2014] [Accepted: 05/08/2015] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing of messenger RNA can generate a wide variety of mature RNA transcripts, and these transcripts may produce protein isoforms with diverse cellular functions. While there is much supporting evidence for the expression of alternative transcripts, the same is not true for the alternatively spliced protein products. Large-scale mass spectroscopy experiments have identified evidence of alternative splicing at the protein level, but with conflicting results. Here we carried out a rigorous analysis of the peptide evidence from eight large-scale proteomics experiments to assess the scale of alternative splicing that is detectable by high-resolution mass spectroscopy. We find fewer splice events than would be expected: we identified peptides for almost 64% of human protein coding genes, but detected just 282 splice events. This data suggests that most genes have a single dominant isoform at the protein level. Many of the alternative isoforms that we could identify were only subtly different from the main splice isoform. Very few of the splice events identified at the protein level disrupted functional domains, in stark contrast to the two thirds of splice events annotated in the human genome that would lead to the loss or damage of functional domains. The most striking result was that more than 20% of the splice isoforms we identified were generated by substituting one homologous exon for another. This is significantly more than would be expected from the frequency of these events in the genome. These homologous exon substitution events were remarkably conserved—all the homologous exons we identified evolved over 460 million years ago—and eight of the fourteen tissue-specific splice isoforms we identified were generated from homologous exons. The combination of proteomics evidence, ancient origin and tissue-specific splicing indicates that isoforms generated from homologous exons may have important cellular roles. Alternative splicing is thought to be one means for generating the protein diversity necessary for the whole range of cellular functions. While the presence of alternatively spliced transcripts in the cell has been amply demonstrated, the same cannot be said for alternatively spliced proteins. The quest for alternative protein isoforms has focused primarily on the analysis of peptides from large-scale mass spectroscopy experiments, but evidence for alternative isoforms has been patchy and contradictory. A careful analysis of the peptide evidence is needed to fully understand the scale of alternative splicing detectable at the protein level. Here we analysed peptides from eight large-scale data sets, identifying just 282 splice events among 12,716 genes. This suggests that most genes have a single dominant isoform. Many of the alternative isoforms that we identified were only subtly different from the main splice variant, and one in five was generated by substitution of homologous exons by swapping one related exon for another. Remarkably, the alternative isoforms generated from homologous exons were highly conserved, first appearing 460 million years ago, and several appear to have tissue-specific roles in the brain and heart. Our results suggest that these particular isoforms are likely to have important cellular roles.
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Affiliation(s)
- Federico Abascal
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Iakes Ezkurdia
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Juan Rodriguez-Rivas
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jose Manuel Rodriguez
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Angela del Pozo
- Instituto de Genetica Medica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | - Jesús Vázquez
- Laboratorio de Proteómica Cardiovascular, Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- * E-mail: (AV); (MLT)
| | - Michael L. Tress
- Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- * E-mail: (AV); (MLT)
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Izarzugaza JMG, Vazquez M, del Pozo A, Valencia A. wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases. BMC Bioinformatics 2013; 14:345. [PMID: 24289158 PMCID: PMC3879071 DOI: 10.1186/1471-2105-14-345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 05/30/2013] [Indexed: 11/13/2022] Open
Abstract
Background Protein kinases are involved in relevant physiological functions and a broad number of mutations in this superfamily have been reported in the literature to affect protein function and stability. Unfortunately, the exploration of the consequences on the phenotypes of each individual mutation remains a considerable challenge. Results The wKinMut web-server offers direct prediction of the potential pathogenicity of the mutations from a number of methods, including our recently developed prediction method based on the combination of information from a range of diverse sources, including physicochemical properties and functional annotations from FireDB and Swissprot and kinase-specific characteristics such as the membership to specific kinase groups, the annotation with disease-associated GO terms or the occurrence of the mutation in PFAM domains, and the relevance of the residues in determining kinase subfamily specificity from S3Det. This predictor yields interesting results that compare favourably with other methods in the field when applied to protein kinases. Together with the predictions, wKinMut offers a number of integrated services for the analysis of mutations. These include: the classification of the kinase, information about associations of the kinase with other proteins extracted from iHop, the mapping of the mutations onto PDB structures, pathogenicity records from a number of databases and the classification of mutations in large-scale cancer studies. Importantly, wKinMut is connected with the SNP2L system that extracts mentions of mutations directly from the literature, and therefore increases the possibilities of finding interesting functional information associated to the studied mutations. Conclusions wKinMut facilitates the exploration of the information available about individual mutations by integrating prediction approaches with the automatic extraction of information from the literature (text mining) and several state-of-the-art databases. wKinMut has been used during the last year for the analysis of the consequences of mutations in the context of a number of cancer genome projects, including the recent analysis of Chronic Lymphocytic Leukemia cases and is publicly available at
http://wkinmut.bioinfo.cnio.es.
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Affiliation(s)
- Jose M G Izarzugaza
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain.
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Abstract
BACKGROUND Most of the many mutations described in human protein kinases are tolerated without significant disruption of the corresponding structures or molecular functions, while some of them have been associated to a variety of human diseases, including cancer. In the last decade, a plethora of computational methods to predict the effect of missense single-nucleotide variants (SNVs) have been developed. Still, current high-throughput sequencing efforts and the concomitant need for massive interpretation of protein sequence variants will demand for more efficient and/or accurate computational methods in the forthcoming years. RESULTS We present KinMut, a support vector machine (SVM) approach, to identify pathogenic mutations in the protein kinase superfamily. KinMut relays on a combination of sequence-derived features that describe mutations at different levels: (1) Gene level: membership to a specific group in Kinbase and the annotation with GO terms; (2) Domain level: annotated PFAM domains; and (3) Residue level: physicochemical features of amino acids, specificity determining positions, and functional annotations from SwissProt and FireDB. The system has been trained with the set of 3492 human kinase mutations in UniProt for which experimental validation of their pathogenic or neutral character exists. In addition, we discuss the relative importance of these independent properties and their combination for the development of a kinase-specific predictor. Finally, we compare KinMut with other state-of-the-art prediction methods. CONCLUSIONS Family-specific features appear among the most discriminative information sources, which allow us to produce accurate results in a reliable and very simple way with minimal supervision. Our study aims to broaden the knowledge on the mechanisms by which mutations in the human kinome contribute to disease with a particular focus in cancer. The classifier as well as further documentation is available at http://kinmut.bioinfo.cnio.es/.
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Affiliation(s)
- Jose M G Izarzugaza
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Mol Biol Evol 2012; 29:2265-83. [PMID: 22446687 PMCID: PMC3424414 DOI: 10.1093/molbev/mss100] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and strongly suggests that the translation of alternative transcripts may be subject to selective constraints.
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Affiliation(s)
- Iakes Ezkurdia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
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Abstract
BACKGROUND A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-structured ontologies exist regarding the activity of proteins (i.e. 'gene ontology' -GO-). However, functional metrics can overcome the problems in the comparing and evaluating functional assignments and predictions. As a reference of proximity, previous approaches to compare GO terms considered linkage in terms of ontology weighted by a probability distribution that balances the non-uniform 'richness' of different parts of the Direct Acyclic Graph. Here, we have followed a different approach to quantify functional similarities between GO terms. RESULTS We propose a new method to derive 'functional distances' between GO terms that is based on the simultaneous occurrence of terms in the same set of Interpro entries, instead of relying on the structure of the GO. The coincidence of GO terms reveals natural biological links between the GO functions and defines a distance model Df which fulfils the properties of a Metric Space. The distances obtained in this way can be represented as a hierarchical 'Functional Tree'. CONCLUSION The method proposed provides a new definition of distance that enables the similarity between GO terms to be quantified. Additionally, the 'Functional Tree' defines groups with biological meaning enhancing its utility for protein function comparison and prediction. Finally, this approach could be for function-based protein searches in databases, and for analysing the gene clusters produced by DNA array experiments.
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Affiliation(s)
- Angela del Pozo
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, E-28029 Madrid, Spain.
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Abstract
Real-world images are complex objects, difficult to describe but at the same time possessing a high degree of redundancy. A very recent study on the statistical properties of natural images reveals that natural images can be viewed through different partitions which are essentially fractal in nature. One particular fractal component, related to the most singular (sharpest)transitions in the image, seems to be highly informative about the whole scene. In this paper we will show how to decompose the image into their fractal components.We will see that the most singular component is related to (but not coincident with) the edges of the objects present in the scenes. We will propose a new, simple method to reconstruct the image with information contained in that most informative component.We will see that the quality of the reconstruction is strongly dependent on the capability to extract the relevant edges in the determination of the most singular set. We will discuss the results from the perspective of coding, proposing this method as a starting point for future developments.
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Affiliation(s)
- Antonio Turiel
- Lab. de Phys. Statistique, Ecole Normale Superieure, Paris.
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