Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks
BackgroundSplicing is the molecular mechanism to produce mature messenger RNA (mRNA) before its translation into protein. It is estimated that 50% of disease-causing mutations disrupt splicing, mostly of them affecting canonical positions. However, variants occurring in coding regions or deep-intron...
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2025-01-01
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| author | Laura Miguel Berenguel Carla Gianelli Carla Gianelli Carla Gianelli Elisabet Matas Pérez Teresa del Rosal Ana Méndez Echevarría Ángel Robles Marhuenda Marta Feito Rodríguez Maria Teresa Caballero Molina Maria Teresa Caballero Molina Lorena Magallares García Brenda Sánchez Garrido Samantha Hita Díaz Luis Allende Martínez Luis Allende Martínez Pilar Nozal Aranda Pilar Nozal Aranda Pilar Nozal Aranda Carmen Cámara Hijón Carmen Cámara Hijón Carmen Cámara Hijón Eduardo López Granados Eduardo López Granados Eduardo López Granados Rebeca Rodríguez Pena Rebeca Rodríguez Pena Rebeca Rodríguez Pena María Bravo García-Morato María Bravo García-Morato María Bravo García-Morato |
| author_facet | Laura Miguel Berenguel Carla Gianelli Carla Gianelli Carla Gianelli Elisabet Matas Pérez Teresa del Rosal Ana Méndez Echevarría Ángel Robles Marhuenda Marta Feito Rodríguez Maria Teresa Caballero Molina Maria Teresa Caballero Molina Lorena Magallares García Brenda Sánchez Garrido Samantha Hita Díaz Luis Allende Martínez Luis Allende Martínez Pilar Nozal Aranda Pilar Nozal Aranda Pilar Nozal Aranda Carmen Cámara Hijón Carmen Cámara Hijón Carmen Cámara Hijón Eduardo López Granados Eduardo López Granados Eduardo López Granados Rebeca Rodríguez Pena Rebeca Rodríguez Pena Rebeca Rodríguez Pena María Bravo García-Morato María Bravo García-Morato María Bravo García-Morato |
| author_sort | Laura Miguel Berenguel |
| collection | DOAJ |
| description | BackgroundSplicing is the molecular mechanism to produce mature messenger RNA (mRNA) before its translation into protein. It is estimated that 50% of disease-causing mutations disrupt splicing, mostly of them affecting canonical positions. However, variants occurring in coding regions or deep-intronic variants can also affect splicing. In these cases, interpretation of the results may be challenging and molecular validation is required.MethodsThe study includes 23 patients with splicing variants out of a cohort of 187 patients diagnosed with inborn errors of immunity (IEI). Clinical features and immunophenotypes are shown. Reverse transcription-polymerase chain reaction (RT-PCR) is the molecular assay employed for pathogenicity validation.ResultsWe detected 23 patients of 20 pedigrees with splicing variants in IEI genes, which constitutes the 12.3% of our cohort. In total, 21 splicing variants were analyzed, 10 of which had previously been reported in the literature and 11 novel ones. Among the 23 patients, 16 showed variants at canonical splice sites. Molecular validation was required only in the cases of genes of uncertain significance (GUS), high homology pseudogenes or incompatible clinical phenotype. Seven patients showed variants outside canonical positions. All of them needed molecular validation, with the exception of two patients, whose variants had previously been well characterized in the medical literature.ConclusionThis study shows the proportion of splicing variants in a cohort of IEI patients, providing their clinical phenotypic characteristics and the methodology used to validate the splicing defects. Based on the results, an algorithm is proposed to clarify when a splicing variant should be validated by complementary methodology and when, by contrast, it can be directly considered disease causing. |
| format | Article |
| id | doaj-art-574d0fce45064113a869336ebfabc08a |
| institution | Kabale University |
| issn | 1664-3224 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj-art-574d0fce45064113a869336ebfabc08a2025-01-29T06:46:12ZengFrontiers Media S.A.Frontiers in Immunology1664-32242025-01-011510.3389/fimmu.2024.14994151499415Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarksLaura Miguel Berenguel0Carla Gianelli1Carla Gianelli2Carla Gianelli3Elisabet Matas Pérez4Teresa del Rosal5Ana Méndez Echevarría6Ángel Robles Marhuenda7Marta Feito Rodríguez8Maria Teresa Caballero Molina9Maria Teresa Caballero Molina10Lorena Magallares García11Brenda Sánchez Garrido12Samantha Hita Díaz13Luis Allende Martínez14Luis Allende Martínez15Pilar Nozal Aranda16Pilar Nozal Aranda17Pilar Nozal Aranda18Carmen Cámara Hijón19Carmen Cámara Hijón20Carmen Cámara Hijón21Eduardo López Granados22Eduardo López Granados23Eduardo López Granados24Rebeca Rodríguez Pena25Rebeca Rodríguez Pena26Rebeca Rodríguez Pena27María Bravo García-Morato28María Bravo García-Morato29María Bravo García-Morato30Department of Immunology, La Paz University Hospital, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainCenter for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, SpainLymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainDepartment of Pediatric Infectious Diseases, La Paz University Hospital, Madrid, SpainDepartment of Pediatric Infectious Diseases, La Paz University Hospital, Madrid, SpainDepartment of Internal Medicine, La Paz University Hospital, Madrid, SpainDepartment of Dermatology, La Paz University Hospital, Madrid, SpainDepartment of Allergy, La Paz University Hospital, Madrid, SpainCenter for Biomedical Network Research on Rare Diseases (CIBERER U754), Madrid, SpainDepartment of Pediatric Gastroenterology, La Paz University Hospital, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, Spain0Immunology Department, 12 de Octubre University Hospital, Madrid, Spain1Research Institute Hospital 12 Octubre (I+12), Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainCenter for Biomedical Network Research on Rare Diseases (CIBERER U754), Madrid, Spain2Complement Alterations in Human Pathology Group, La Paz Institute of Biomedical Research, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainCenter for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, SpainLymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainCenter for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, SpainLymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainCenter for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, SpainLymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research, Madrid, SpainDepartment of Immunology, La Paz University Hospital, Madrid, SpainCenter for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, SpainLymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research, Madrid, SpainBackgroundSplicing is the molecular mechanism to produce mature messenger RNA (mRNA) before its translation into protein. It is estimated that 50% of disease-causing mutations disrupt splicing, mostly of them affecting canonical positions. However, variants occurring in coding regions or deep-intronic variants can also affect splicing. In these cases, interpretation of the results may be challenging and molecular validation is required.MethodsThe study includes 23 patients with splicing variants out of a cohort of 187 patients diagnosed with inborn errors of immunity (IEI). Clinical features and immunophenotypes are shown. Reverse transcription-polymerase chain reaction (RT-PCR) is the molecular assay employed for pathogenicity validation.ResultsWe detected 23 patients of 20 pedigrees with splicing variants in IEI genes, which constitutes the 12.3% of our cohort. In total, 21 splicing variants were analyzed, 10 of which had previously been reported in the literature and 11 novel ones. Among the 23 patients, 16 showed variants at canonical splice sites. Molecular validation was required only in the cases of genes of uncertain significance (GUS), high homology pseudogenes or incompatible clinical phenotype. Seven patients showed variants outside canonical positions. All of them needed molecular validation, with the exception of two patients, whose variants had previously been well characterized in the medical literature.ConclusionThis study shows the proportion of splicing variants in a cohort of IEI patients, providing their clinical phenotypic characteristics and the methodology used to validate the splicing defects. Based on the results, an algorithm is proposed to clarify when a splicing variant should be validated by complementary methodology and when, by contrast, it can be directly considered disease causing.https://www.frontiersin.org/articles/10.3389/fimmu.2024.1499415/fullsplicing mutationsreverse-transcription PCR (RT-PCR)inborn errors of immunitygenetic validation algorithmcanonical sites of splicingdeep-intronic variants |
| spellingShingle | Laura Miguel Berenguel Carla Gianelli Carla Gianelli Carla Gianelli Elisabet Matas Pérez Teresa del Rosal Ana Méndez Echevarría Ángel Robles Marhuenda Marta Feito Rodríguez Maria Teresa Caballero Molina Maria Teresa Caballero Molina Lorena Magallares García Brenda Sánchez Garrido Samantha Hita Díaz Luis Allende Martínez Luis Allende Martínez Pilar Nozal Aranda Pilar Nozal Aranda Pilar Nozal Aranda Carmen Cámara Hijón Carmen Cámara Hijón Carmen Cámara Hijón Eduardo López Granados Eduardo López Granados Eduardo López Granados Rebeca Rodríguez Pena Rebeca Rodríguez Pena Rebeca Rodríguez Pena María Bravo García-Morato María Bravo García-Morato María Bravo García-Morato Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks Frontiers in Immunology splicing mutations reverse-transcription PCR (RT-PCR) inborn errors of immunity genetic validation algorithm canonical sites of splicing deep-intronic variants |
| title | Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks |
| title_full | Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks |
| title_fullStr | Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks |
| title_full_unstemmed | Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks |
| title_short | Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks |
| title_sort | molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity methodological approach and interpretation remarks |
| topic | splicing mutations reverse-transcription PCR (RT-PCR) inborn errors of immunity genetic validation algorithm canonical sites of splicing deep-intronic variants |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2024.1499415/full |
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