Mutation in IRF2BP2 is responsible for a familial form of common variable immunodeficiency disorder
Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might...
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| Published in | Journal of allergy and clinical immunology Vol. 138; no. 2; pp. 544 - 550.e4 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
01.08.2016
Elsevier Limited |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0091-6749 1097-6825 1097-6825 |
| DOI | 10.1016/j.jaci.2016.01.018 |
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| Abstract | Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint.
We sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders.
A family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, and in vitro plasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines.
Exome sequencing identified a novel heterozygous mutation in IRF2BP2 (c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablasts in vitro, and IRF2BP2 transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants in TACI, BAFFR, ICOS, CD21, LRBA, and CD27 as genetically dissimilar from polygenic CVID.
A novel IRFBP2 mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases. |
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| AbstractList | Background Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint. Objective We sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders. Methods A family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, and in vitro plasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines. Results Exome sequencing identified a novel heterozygous mutation in IRF2BP2 (c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablasts in vitro, and IRF2BP2 transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants in TACI, BAFFR, ICOS, CD21, LRBA, and CD27 as genetically dissimilar from polygenic CVID. Conclusion A novel IRFBP2 mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases. Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint. We sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders. A family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, and in vitro plasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines. Exome sequencing identified a novel heterozygous mutation in IRF2BP2 (c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablasts in vitro, and IRF2BP2 transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants in TACI, BAFFR, ICOS, CD21, LRBA, and CD27 as genetically dissimilar from polygenic CVID. A novel IRFBP2 mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases. Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint.BACKGROUNDGenome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint.We sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders.OBJECTIVEWe sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders.A family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, and in vitro plasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines.METHODSA family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, and in vitro plasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines.Exome sequencing identified a novel heterozygous mutation in IRF2BP2 (c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablasts in vitro, and IRF2BP2 transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants in TACI, BAFFR, ICOS, CD21, LRBA, and CD27 as genetically dissimilar from polygenic CVID.RESULTSExome sequencing identified a novel heterozygous mutation in IRF2BP2 (c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablasts in vitro, and IRF2BP2 transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants in TACI, BAFFR, ICOS, CD21, LRBA, and CD27 as genetically dissimilar from polygenic CVID.A novel IRFBP2 mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases.CONCLUSIONA novel IRFBP2 mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases. Background Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint. Objective We sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders. Methods A family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, and in vitro plasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines. Results Exome sequencing identified a novel heterozygous mutation in IRF2BP2 (c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablasts in vitro , and IRF2BP2 transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants in TACI , BAFFR , ICOS , CD21 , LRBA , and CD27 as genetically dissimilar from polygenic CVID. Conclusion A novel IRFBP2 mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases. Background Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint. Objective We sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders. Methods A family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, andin vitroplasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines. Results Exome sequencing identified a novel heterozygous mutation inIRF2BP2(c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablastsin vitro, andIRF2BP2transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants inTACI,BAFFR,ICOS,CD21,LRBA, andCD27as genetically dissimilar from polygenic CVID. Conclusion A novelIRFBP2mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases. |
| Author | Henrickson, Sarah E. Pandey, Rahul Glessner, Joseph Jyonouchi, Soma Orange, Jordan S. Hakonarson, Hakon Li, Dong Monaco-Shawver, Linda Heimall, Jennifer Hou, Cuiping Otieno, Frederick G. van Montfrans, Joris Chinn, Ivan K. Calabrese, Leonard Tian, Lifeng Keller, Michael D. |
| AuthorAffiliation | 2 The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA 5 Baylor Genomics Institute, Baylor College of Medicine, Houston, TX, USA 6 Department of Rheumatologic and Immunologic Disease, Cleveland Clinic, Cleveland, OH, USA 4 Division of Immunology, Allergy, and Rheumatology, Texas Children’s Hospital, Houston, TX, USA 7 Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center, Utrecht, The Netherlands 3 Division of Allergy & Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA 1 Division of Allergy & Immunology, Children’s National Medical Center, Washington, DC, USA |
| AuthorAffiliation_xml | – name: 3 Division of Allergy & Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA – name: 1 Division of Allergy & Immunology, Children’s National Medical Center, Washington, DC, USA – name: 5 Baylor Genomics Institute, Baylor College of Medicine, Houston, TX, USA – name: 6 Department of Rheumatologic and Immunologic Disease, Cleveland Clinic, Cleveland, OH, USA – name: 7 Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center, Utrecht, The Netherlands – name: 2 The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA – name: 4 Division of Immunology, Allergy, and Rheumatology, Texas Children’s Hospital, Houston, TX, USA |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27016798$$D View this record in MEDLINE/PubMed |
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| Copyright | 2016 American Academy of Allergy, Asthma & Immunology American Academy of Allergy, Asthma & Immunology Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved. Copyright Elsevier Limited Aug 01, 2016 |
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| Keywords | CVID Common variable immunodeficiency primary antibody deficiency immunoglobulin SNP IRF2BP2 CNV SVM machine learning EBV-LCL EBV-immortalized lymphoblastoid cell line Support vector machine Copy number variation Common variable immunodeficiency disorder Single nucleotide polymorphism |
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| License | Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved. |
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| Snippet | Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable... Background Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common... |
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| SubjectTerms | Adolescent Adult Aged Algorithms Allergy and Immunology B-Lymphocyte Subsets - immunology B-Lymphocyte Subsets - metabolism Biomarkers Carrier Proteins - genetics Carrier Proteins - metabolism Cell Differentiation - genetics Cell Differentiation - immunology Classification Common variable immunodeficiency Common Variable Immunodeficiency - diagnosis Common Variable Immunodeficiency - genetics Common Variable Immunodeficiency - immunology Deoxyribonucleic acid DNA Epstein-Barr virus Exome Family Female Flow cytometry Genes Genetic Association Studies Genetic Predisposition to Disease Genetic testing Genotype High-Throughput Nucleotide Sequencing Humans immunoglobulin Immunoglobulin Isotypes - blood Immunoglobulin Isotypes - immunology Immunoglobulins Immunophenotyping IRF2BP2 Lymphocytes machine learning Male Middle Aged Mutation Nuclear Proteins - genetics Nuclear Proteins - metabolism Patients Pedigree Phenotype primary antibody deficiency Studies T-Lymphocyte Subsets - immunology T-Lymphocyte Subsets - metabolism Young Adult |
| Title | Mutation in IRF2BP2 is responsible for a familial form of common variable immunodeficiency disorder |
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