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Johnson R, Stephens AV, Mester R, Knyazev S, Kohn LA, Freund MK, Bondhus L, Hill BL, Schwarz T, Zaitlen N, Arboleda VA, A Bastarache L, Pasaniuc B, Butte MJ. Electronic health record signatures identify undiagnosed patients with common variable immunodeficiency disease. Sci Transl Med 2024; 16:eade4510. [PMID: 38691621 DOI: 10.1126/scitranslmed.ade4510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/10/2024] [Indexed: 05/03/2024]
Abstract
Human inborn errors of immunity include rare disorders entailing functional and quantitative antibody deficiencies due to impaired B cells called the common variable immunodeficiency (CVID) phenotype. Patients with CVID face delayed diagnoses and treatments for 5 to 15 years after symptom onset because the disorders are rare (prevalence of ~1/25,000), and there is extensive heterogeneity in CVID phenotypes, ranging from infections to autoimmunity to inflammatory conditions, overlapping with other more common disorders. The prolonged diagnostic odyssey drives excessive system-wide costs before diagnosis. Because there is no single causal mechanism, there are no genetic tests to definitively diagnose CVID. Here, we present PheNet, a machine learning algorithm that identifies patients with CVID from their electronic health records (EHRs). PheNet learns phenotypic patterns from verified CVID cases and uses this knowledge to rank patients by likelihood of having CVID. PheNet could have diagnosed more than half of our patients with CVID 1 or more years earlier than they had been diagnosed. When applied to a large EHR dataset, followed by blinded chart review of the top 100 patients ranked by PheNet, we found that 74% were highly probable to have CVID. We externally validated PheNet using >6 million records from disparate medical systems in California and Tennessee. As artificial intelligence and machine learning make their way into health care, we show that algorithms such as PheNet can offer clinical benefits by expediting the diagnosis of rare diseases.
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Affiliation(s)
- Ruth Johnson
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alexis V Stephens
- Department of Pediatrics, Division of Immunology, Allergy and Rheumatology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Rachel Mester
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Sergey Knyazev
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lisa A Kohn
- Department of Pediatrics, Division of Immunology, Allergy and Rheumatology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Malika K Freund
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Leroy Bondhus
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brian L Hill
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Noah Zaitlen
- Department of Neurology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lisa A Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA 37203
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Manish J Butte
- Department of Pediatrics, Division of Immunology, Allergy and Rheumatology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
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Rivière JG, Soler Palacín P, Butte MJ. Proceedings from the inaugural Artificial Intelligence in Primary Immune Deficiencies (AIPID) conference. J Allergy Clin Immunol 2024; 153:637-642. [PMID: 38224784 DOI: 10.1016/j.jaci.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
Here, we summarize the proceedings of the inaugural Artificial Intelligence in Primary Immune Deficiencies conference, during which experts and advocates gathered to advance research into the applications of artificial intelligence (AI), machine learning, and other computational tools in the diagnosis and management of inborn errors of immunity (IEIs). The conference focused on the key themes of expediting IEI diagnoses, challenges in data collection, roles of natural language processing and large language models in interpreting electronic health records, and ethical considerations in implementation. Innovative AI-based tools trained on electronic health records and claims databases have discovered new patterns of warning signs for IEIs, facilitating faster diagnoses and enhancing patient outcomes. Challenges in training AIs persist on account of data limitations, especially in cases of rare diseases, overlapping phenotypes, and biases inherent in current data sets. Furthermore, experts highlighted the significance of ethical considerations, data protection, and the necessity for open science principles. The conference delved into regulatory frameworks, equity in access, and the imperative for collaborative efforts to overcome these obstacles and harness the transformative potential of AI. Concerted efforts to successfully integrate AI into daily clinical immunology practice are still needed.
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Affiliation(s)
- Jacques G Rivière
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Infantil i de la Dona, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Soler Palacín
- Infection and Immunity in Pediatric Patients Research Group, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Infantil i de la Dona, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, Calif; Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, Calif; Department of Human Genetics, University of California Los Angeles, Los Angeles, Calif.
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3
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Garcia-Prat M, Batlle-Masó L, Parra-Martínez A, Franco-Jarava C, Martinez-Gallo M, Aguiló-Cucurull A, Perurena-Prieto J, Castells N, Urban B, Dieli-Crimi R, Soler-Palacín P, Colobran R. Role of Skewed X-Chromosome Inactivation in Common Variable Immunodeficiency. J Clin Immunol 2024; 44:54. [PMID: 38265673 DOI: 10.1007/s10875-024-01659-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
The term common variable immunodeficiency (CVID) encompasses a clinically diverse group of disorders, mainly characterized by hypogammaglobulinemia, insufficient specific antibody production, and recurrent infections. The genetics of CVID is complex, and monogenic defects account for only a portion of cases, typically <30%. Other proposed mechanisms include digenic, oligogenic, or polygenic inheritance and epigenetic dysregulation. In this study, we aimed to assess the role of skewed X-chromosome inactivation (XCI) in CVID. Within our cohort of 131 genetically analyzed CVID patients, we selected female patients with rare variants in CVID-associated genes located on the X-chromosome. Four patients harboring heterozygous variants in BTK (n = 2), CD40LG (n = 1), and IKBKG (n = 1) were included in the study. We assessed XCI status using the HUMARA assay and an NGS-based method to quantify the expression of the 2 alleles in mRNA. Three of the 4 patients (75%) exhibited skewed XCI, and the mutated allele was predominantly expressed in all cases. Patient 1 harbored a hypomorphic variant in BTK (p.Tyr418His), patient 3 had a pathogenic variant in CD40LG (c.288+1G>A), and patient 4 had a hypomorphic variant in IKBKG (p.Glu57Lys) and a heterozygous splice variant in TNFRSF13B (TACI) (c.61+2T>A). Overall, the analysis of our cohort suggests that CVID in a small proportion of females (1.6% in our cohort) is caused by skewed XCI and highly penetrant gene variants on the X-chromosome. Additionally, skewed XCI may contribute to polygenic effects (3.3% in our cohort). These results indicate that skewed XCI may represent another piece in the complex puzzle of CVID genetics.
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Affiliation(s)
- Marina Garcia-Prat
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Children's Hospital, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
| | - Laura Batlle-Masó
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Children's Hospital, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain
| | - Alba Parra-Martínez
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Children's Hospital, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
| | - Clara Franco-Jarava
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Mónica Martinez-Gallo
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Aina Aguiló-Cucurull
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Janire Perurena-Prieto
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Neus Castells
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Medicine Genetics Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Blanca Urban
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Romina Dieli-Crimi
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Pere Soler-Palacín
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain.
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Children's Hospital, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain.
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain.
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Catalonia, Spain.
- Translational Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain.
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain.
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain.
- Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Bellaterra, Catalonia, Spain.
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Nyström S, Hultberg J, Blixt E, Nilsdotter-Augustinsson Å, Larsson M. Plasma Levels of mir-34a-5p Correlate with Systemic Inflammation and Low Naïve CD4 T Cells in Common Variable Immunodeficiency. J Clin Immunol 2023; 44:21. [PMID: 38129593 PMCID: PMC10739380 DOI: 10.1007/s10875-023-01618-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE Common variable immunodeficiency (CVID) is a primary antibody deficiency that commonly manifests as recurrent infections. Many CVID patients also suffer from immune dysregulation, an inflammatory condition characterized by polyclonal lymphocytic tissue infiltration and associated with increased morbidity and mortality. The genetic cause is unknown in most CVID patients and epigenetic alterations may contribute to the broad range of clinical manifestations. MicroRNAs are small non-coding RNAs that are involved in epigenetic modulation and may contribute to the clinical phenotype in CVID. METHODS Here, we determined the circulating microRNAome and plasma inflammatory proteins of a cohort of CVID patients with various levels of immune dysregulation and compared them to healthy controls. A set of deregulated microRNAs was validated by qPCR and correlated to inflammatory proteins and clinical findings. RESULTS Levels of microRNA-34a correlated with 11 proteins such as CXCL9, TNF, and IL10, which were predicted to be biologically connected. Moreover, there was a negative correlation between mir-34 levels and the number of naïve CD4 T cells in CVID. CONCLUSION Collectively, our data show that microRNAs correlate with the inflammatory response in CVID. Further investigations are needed to elucidate the role of miRNAs in the development of CVID-related immune dysregulation.
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Affiliation(s)
- Sofia Nyström
- Department of Clinical Immunology and Transfusion Medicine, and Department of Biomedical and Clinical Sciences, Linköping University, S-58185, Linköping, Sweden.
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
| | - Jonas Hultberg
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Emelie Blixt
- Department of Clinical Immunology and Transfusion Medicine, and Department of Biomedical and Clinical Sciences, Linköping University, S-58185, Linköping, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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5
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Urnikyte A, Masiulyte A, Pranckeniene L, Kučinskas V. Disentangling archaic introgression and genomic signatures of selection at human immunity genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105528. [PMID: 37977419 DOI: 10.1016/j.meegid.2023.105528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/04/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were to infer the genetic signatures of positive selection that may be involved in adaptation to infectious diseases and to investigate the function of Neanderthal alleles identified within a set of 50 Lithuanian genomes. Introgressed regions were identified using the machine learning tool ArchIE. Recent positive selection signatures were analysed using iHS. We detected high-scoring signals of positive selection at innate immunity genes (EMB, PARP8, HLAC, and CDSN) and evaluated their interactions with the structural proteins of pathogens. Interactions with human immunodeficiency virus (HIV) 1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. Overall, genomic regions introgressed from Neanderthals were shown to be enriched in genes related to immunity, keratinocyte differentiation, and sensory perception.
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Affiliation(s)
- Alina Urnikyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Abigaile Masiulyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania
| | - Laura Pranckeniene
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Vaidutis Kučinskas
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
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6
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Hultberg J, Blixt E, Göransson R, Adolfsson J, Govender M, Larsson M, Nilsdotter-Augustinsson Å, Ernerudh J, Nyström S. In-depth immune profiling reveals advanced B- and T-cell differentiation to be associated with Th1-driven immune dysregulation in common variable immunodeficiency. Clin Immunol 2023; 257:109816. [PMID: 37918468 DOI: 10.1016/j.clim.2023.109816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Common variable immunodeficiency (CVID) is an inborn error of immunity characterized by low levels of antibodies. In addition to infections, many patients also suffer from T-helper 1-driven immune dysregulation, which is associated with increased mortality. The aim of this study was to perform in-depth characterization of the T and the B cell compartments in a well-defined cohort of patients affected by CVID and correlate the findings to the level of clinical immune dysregulation. We used mass cytometry, targeted proteomics, flow cytometry and functional assays to delineate the immunological phenotype of 15 CVID-affected patients with different levels of immune dysregulation. Unbiased clustering of T cell mass cytometry data correlated with CVID-related immune dysregulation and plasma protein profiles. Expanded CXCR3+ T-bet-expressing B cells correlated with effector memory CD4+ T cell clusters, and increased plasma levels of CXCR3-ligands. Our findings indicate an interplay between B cells and T cells in CVID-related immune dysregulation and provide a better understanding of the underlying pathological mechanisms.
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Affiliation(s)
- Jonas Hultberg
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Emelie Blixt
- Department of Clinical Immunology and Transfusion Medicine, and Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Robin Göransson
- Department of Clinical Immunology and Transfusion Medicine, and Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Jörgen Adolfsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Melissa Govender
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine, and Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Sofia Nyström
- Department of Clinical Immunology and Transfusion Medicine, and Department of Biomedical and Clinical Sciences, Linköping University, Sweden.
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7
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Liu Z, Lu C, Qing P, Cheng R, Li Y, Guo X, Chen Y, Ying Z, Yu H, Liu Y. Genetic characteristics of common variable immunodeficiency patients with autoimmunity. Front Genet 2023; 14:1209988. [PMID: 38028622 PMCID: PMC10679925 DOI: 10.3389/fgene.2023.1209988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background: The pathogenesis of common variable immunodeficiency disorder (CVID) is complex, especially when combined with autoimmunity. Genetic factors may be potential explanations for this complex situation, and whole genome sequencing (WGS) provide the basis for this potential. Methods: Genetic information of patients with CVID with autoimmunity, together with their first-degree relatives, was collected through WGS. The association between genetic factors and clinical phenotypes was studied using genetic analysis strategies such as sporadic and pedigree. Results: We collected 42 blood samples for WGS (16 CVID patients and 26 first-degree relatives of healthy controls). Through pedigree, sporadic screening strategies and low-frequency deleterious screening of rare diseases, we obtained 9,148 mutation sites, including 8,171 single-nucleotide variants (SNVs) and 977 Insertion-deletions (InDels). Finally, we obtained a total of 28 candidate genes (32 loci), of which the most common mutant was LRBA. The most common autoimmunity in the 16 patients was systematic lupus erythematosis. Through KEGG pathway enrichment, we identified the top ten signaling pathways, including "primary immunodeficiency", "JAK-STAT signaling pathway", and "T-cell receptor signaling pathway". We used PyMOL to predict and analyse the three-dimensional protein structures of the NFKB1, RAG1, TIRAP, NCF2, and MYB genes. In addition, we constructed a PPI network by combining candidate mutants with genes associated with CVID in the OMIM database via the STRING database. Conclusion: The genetic background of CVID includes not only monogenic origins but also oligogenic effects. Our study showed that immunodeficiency and autoimmunity may overlap in genetic backgrounds. Clinical Trial Registration: identifier ChiCTR2100044035.
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Affiliation(s)
- Zhihui Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Chenyang Lu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Pingying Qing
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Ruijuan Cheng
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yujie Li
- Novogene Co. Ltd., Beijing, China
| | - Xue Guo
- Novogene Co. Ltd., Beijing, China
| | - Ye Chen
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiye Ying
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
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8
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Gray PE, David C. Inborn Errors of Immunity and Autoimmune Disease. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:1602-1622. [PMID: 37119983 DOI: 10.1016/j.jaip.2023.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/01/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
Autoimmunity may be a manifestation of inborn errors of immunity, specifically as part of the subgroup of primary immunodeficiency known as primary immune regulatory disorders. However, although making a single gene diagnosis can have important implications for prognosis and management, picking patients to screen can be difficult, against a background of a high prevalence of autoimmune disease in the population. This review compares the genetics of common polygenic and rare monogenic autoimmunity, and explores the molecular mechanisms, phenotypes, and inheritance of autoimmunity associated with primary immune regulatory disorders, highlighting the emerging importance of gain-of-function and non-germline somatic mutations. A novel framework for identifying rare monogenic cases of common diseases in children is presented, highlighting important clinical and immunologic features that favor single gene disease and guides clinicians in selecting appropriate patients for genomic screening. In addition, there will be a review of autoimmunity in non-genetically defined primary immunodeficiency such as common variable immunodeficiency, and of instances where primary autoimmunity can result in clinical phenocopies of inborn errors of immunity.
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Affiliation(s)
- Paul Edgar Gray
- Sydney Children's Hospital, Randwick, NSW, Australia; Western Sydney University, Penrith, NSW, Australia.
| | - Clementine David
- Sydney Children's Hospital, Randwick, NSW, Australia; The School of Women's & Children's Health, University of New South Wales, Randwick, NSW, Australia
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Sacco KA, Gazzin A, Notarangelo LD, Delmonte OM. Granulomatous inflammation in inborn errors of immunity. Front Pediatr 2023; 11:1110115. [PMID: 36891233 PMCID: PMC9986611 DOI: 10.3389/fped.2023.1110115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/22/2023] Open
Abstract
Granulomas have been defined as inflammatory infiltrates formed by recruitment of macrophages and T cells. The three-dimensional spherical structure typically consists of a central core of tissue resident macrophages which may merge into multinucleated giant cells surrounded by T cells at the periphery. Granulomas may be triggered by infectious and non-infectious antigens. Cutaneous and visceral granulomas are common in inborn errors of immunity (IEI), particularly among patients with chronic granulomatous disease (CGD), combined immunodeficiency (CID), and common variable immunodeficiency (CVID). The estimated prevalence of granulomas in IEI ranges from 1%-4%. Infectious agents causing granulomas such Mycobacteria and Coccidioides presenting atypically may be 'sentinel' presentations for possible underlying immunodeficiency. Deep sequencing of granulomas in IEI has revealed non-classical antigens such as wild-type and RA27/3 vaccine-strain Rubella virus. Granulomas in IEI are associated with significant morbidity and mortality. The heterogeneity of granuloma presentation in IEI presents challenges for mechanistic approaches to treatment. In this review, we discuss the main infectious triggers for granulomas in IEI and the major forms of IEI presenting with 'idiopathic' non-infectious granulomas. We also discuss models to study granulomatous inflammation and the impact of deep-sequencing technology while searching for infectious triggers of granulomatous inflammation. We summarize the overarching goals of management and highlight the therapeutic options reported for specific granuloma presentations in IEI.
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Affiliation(s)
- Keith A Sacco
- Department of Pulmonology, Section of Allergy-Immunology, Phoenix Children's Hospital, Phoenix, AZ, United States
| | - Andrea Gazzin
- Laboratory of Clinical Immunology and Microbiology, Immune Deficiency Genetics Section, National Institutes of Health, Bethesda, MD, United States
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Immune Deficiency Genetics Section, National Institutes of Health, Bethesda, MD, United States
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Immune Deficiency Genetics Section, National Institutes of Health, Bethesda, MD, United States
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10
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"Common variable immunodeficiency: Challenges for diagnosis". J Immunol Methods 2022; 509:113342. [PMID: 36027932 DOI: 10.1016/j.jim.2022.113342] [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: 03/17/2022] [Revised: 07/21/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022]
Abstract
Common variable immunodeficiency is a heterogeneous condition characterized by B cell dysfunction with reduced serum immunoglobulin levels and a highly variable spectrum of clinical manifestations ranging from recurrent infections to autoimmune disease. The diagnosis of CVID is often challenging due to the diverse clinical presentation of patients and the existence of multiple diagnostic criteria without a universally adopted consensus. Laboratory evaluation to assist with diagnosis currently includes serum immunoglobulin testing, immunophenotyping, assessment of vaccine response, and genetic testing. Additional emerging techniques include investigation of the B cell repertoire and the use of machine learning algorithms. Advances in our understanding of common variable immunodeficiency will ultimately contribute to earlier diagnosis and novel interventions with the goal of improving prognosis for these patients.
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11
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Kabir A, Alizadehfar R, Tsoukas CM. Good's Syndrome: Time to Move on From Reviewing the Past. Front Immunol 2022; 12:815710. [PMID: 35095915 PMCID: PMC8790113 DOI: 10.3389/fimmu.2021.815710] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/22/2021] [Indexed: 01/06/2023] Open
Abstract
For seven decades, the pathophysiology of Good’s syndrome (GS) has remained a mystery, with few attempts to solve it. Initially described as an association between hypogammaglobulinemia and thymoma, controversy exists whether this is a unique disease, or a subgroup of Common Variable Immune Deficiency (CVID). Recently, some distinguishing aspects of both syndromes have come to light reflecting fundamental differences in their underlying pathophysiology. GS and CVID differ in demographic features and immune phenotype. GS is found almost exclusively in adults and is characterized by a significantly reduced or absence of peripheral B cells. In CVID, which also occurs in children, most patients have normal or slightly reduced peripheral B cells, with a distinguishing feature of low memory B cells. Similarly, differences in T cell dysregulation and manifestations of hematologic cytopenias may further distinguish GS from CVID. Knowledge of the clinical phenotype of this rare adult immune deficiency stems from individual case reports, retrospective, and cross-sectional data on a few cohorts with a limited number of well characterized patients. The understanding of pathophysiology in GS is hampered by the incomplete and inconsistent reporting of clinical and laboratory data, with a limited knowledge of its natural history. In this mini review, we discuss current state of the art data and identify research gaps. In order to resolve controversies and fill in knowledge gaps, we propose a coordinated paradigm shift from incidence reporting to robust investigative studies, addressing mechanisms of disease. We hope this novel approach sets a clear direction to solve the current controversies.
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Affiliation(s)
- Aunonna Kabir
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Reza Alizadehfar
- Department of Medicine, Divisions of Allergy and Clinical Immunology, and Pediatrics, McGill University, Montreal, QC, Canada
| | - Christos M Tsoukas
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Medicine, Division of Allergy and Clinical Immunology, McGill University, Montreal, QC, Canada.,Division of Experimental Medicine, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
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12
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Comprehensive Assessment of Skin Disorders in Patients with Common Variable Immunodeficiency (CVID). J Clin Immunol 2022; 42:653-664. [PMID: 35084691 DOI: 10.1007/s10875-022-01211-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/16/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Common variable immunodeficiency (CVID) is an inborn error of immunity (IEI) characterized by various clinical manifestations such as hypogammaglobulinemia, recurrent infections, and autoimmune diseases. Among different clinical manifestations, skin manifestations have been less reported in these patients. METHODS In this study, we investigated the prevalence of dermatologic features in 387 CVID patients. Demographic information, clinical manifestations, laboratory data, and genetic findings were collected from medical records. All data were analyzed based on the presence or absence of skin disorders in CVID patients. RESULTS We observed at least one skin manifestation in about 40% of these patients. Among these complications, skin infection (n = 64, 42.1%) was the most frequent presentation, followed by non-infectious skin lesions (n = 54, 35.6%). Among skin infections, abscesses (n = 34, 22.4%) were the most common complication. Skin infections such as cellulitis, impetigo, measles, and warts were also documented. Eczema (n = 34, 22.4%) was the most common complication in atopic lesions, and vitiligo (n = 13, 8.5%) was prevalent in autoimmune/pigmentation disorders. Among all the patients with genetic mutations, one-quarter had a deleterious mutation in the LRBA gene, relating to the autoimmune and atopic skin lesions. CONCLUSION This rate of skin disorders in our cohort demonstrating these manifestations could be significant in CVID patients, and they are not rare. Low data of skin complications in CVID patients could be attributed to insufficient attention of physicians and also might alert dermatologists to perform immunological investigations in children with certain skin manifestations.
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13
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Capitani N, Onnis A, Finetti F, Cassioli C, Plebani A, Brunetti J, Troilo A, D’Elios S, Baronio M, Gazzurelli L, Della Bella C, Billadeau DD, D’Elios MM, Lougaris V, Baldari CT. A CVID-associated variant in the ciliogenesis protein CCDC28B disrupts immune synapse assembly. Cell Death Differ 2022; 29:65-81. [PMID: 34294890 PMCID: PMC8738737 DOI: 10.1038/s41418-021-00837-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/03/2023] Open
Abstract
Ciliogenesis proteins orchestrate vesicular trafficking pathways that regulate immune synapse (IS) assembly in the non-ciliated T-cells. We hypothesized that ciliogenesis-related genes might be disease candidates for common variable immunodeficiency with impaired T-cell function (T-CVID). We identified a heterozygous, predicted pathogenic variant in the ciliogenesis protein CCDC28B present with increased frequency in a large CVID cohort. We show that CCDC28B participates in IS assembly by regulating polarized T-cell antigen receptor (TCR) recycling. This involves the CCDC28B-dependent, FAM21-mediated recruitment of the actin regulator WASH to retromer at early endosomes to promote actin polymerization. The CVID-associated CCDC28BR25W variant failed to interact with FAM21, leading to impaired synaptic TCR recycling. CVID T cells carrying the ccdc28b 211 C > T allele displayed IS defects mapping to this pathway that were corrected by overexpression of the wild-type allele. These results identify a new disease gene in T-CVID and pinpoint CCDC28B as a new player in IS assembly.
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Affiliation(s)
- Nagaja Capitani
- grid.9024.f0000 0004 1757 4641Department of Life Sciences, University of Siena, Siena, Italy
| | - Anna Onnis
- grid.9024.f0000 0004 1757 4641Department of Life Sciences, University of Siena, Siena, Italy
| | - Francesca Finetti
- grid.9024.f0000 0004 1757 4641Department of Life Sciences, University of Siena, Siena, Italy
| | - Chiara Cassioli
- grid.9024.f0000 0004 1757 4641Department of Life Sciences, University of Siena, Siena, Italy
| | - Alessandro Plebani
- grid.7637.50000000417571846Department of Clinical and Experimental Sciences, University of Brescia, and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Jlenia Brunetti
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Arianna Troilo
- grid.8404.80000 0004 1757 2304Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Sofia D’Elios
- grid.5395.a0000 0004 1757 3729Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Manuela Baronio
- grid.7637.50000000417571846Department of Clinical and Experimental Sciences, University of Brescia, and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Luisa Gazzurelli
- grid.7637.50000000417571846Department of Clinical and Experimental Sciences, University of Brescia, and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Chiara Della Bella
- grid.8404.80000 0004 1757 2304Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Daniel D. Billadeau
- grid.66875.3a0000 0004 0459 167XDivision of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Mario Milco D’Elios
- grid.8404.80000 0004 1757 2304Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Vassilios Lougaris
- grid.7637.50000000417571846Department of Clinical and Experimental Sciences, University of Brescia, and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Cosima T. Baldari
- grid.9024.f0000 0004 1757 4641Department of Life Sciences, University of Siena, Siena, Italy
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14
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Varricchi G, Poto R, Ianiro G, Punziano A, Marone G, Gasbarrini A, Spadaro G. Gut Microbiome and Common Variable Immunodeficiency: Few Certainties and Many Outstanding Questions. Front Immunol 2021; 12:712915. [PMID: 34408753 PMCID: PMC8366412 DOI: 10.3389/fimmu.2021.712915] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most common symptomatic primary antibody immunodeficiency, characterized by reduced serum levels of IgG, IgA, and/or IgM. The vast majority of CVID patients have polygenic inheritance. Immune dysfunction in CVID can frequently involve the gastrointestinal tract and lung. Few studies have started to investigate the gut microbiota profile in CVID patients. Overall, the results suggest that in CVID patients there is a reduction of alpha and beta diversity compared to controls. In addition, these patients can exhibit increased plasma levels of lipopolysaccharide (LPS) and markers (sCD14 and sCD25) of systemic immune cell activation. CVID patients with enteropathy exhibit decreased IgA expression in duodenal tissue. Mouse models for CVID unsatisfactorily recapitulate the polygenic causes of human CVID. The molecular pathways by which gut microbiota contribute to systemic inflammation and possibly tumorigenesis in CVID patients remain poorly understood. Several fundamental questions concerning the relationships between gut microbiota and the development of chronic inflammatory conditions, autoimmune disorders or cancer in CVID patients remain unanswered. Moreover, it is unknown whether it is possible to modify the microbiome and the outcome of CVID patients through specific therapeutic interventions.
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Affiliation(s)
- Gilda Varricchi
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Remo Poto
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
| | - Gianluca Ianiro
- Department of Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Cattolica del Sacro Cuore University, Rome, Italy
| | - Alessandra Punziano
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
| | - Gianni Marone
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy.,Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Antonio Gasbarrini
- Department of Internal Medicine and Gastroenterology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Cattolica del Sacro Cuore University, Rome, Italy
| | - Giuseppe Spadaro
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy.,Center for Basic and Clinical Immunology Research (CISI), University of Naples Federico II, Naples, Italy
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15
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Hargreaves CE, Salatino S, Sasson SC, Charlesworth JEG, Bateman E, Patel AM, Anzilotti C, Broxholme J, Knight JC, Patel SY. Decreased ATM Function Causes Delayed DNA Repair and Apoptosis in Common Variable Immunodeficiency Disorders. J Clin Immunol 2021; 41:1315-1330. [PMID: 34009545 PMCID: PMC8310859 DOI: 10.1007/s10875-021-01050-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/20/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Common variable immunodeficiency disorders (CVID) is characterized by low/absent serum immunoglobulins and susceptibility to bacterial infection. Patients can develop an infections-only phenotype or a complex disease course with inflammatory, autoimmune, and/or malignant complications. We hypothesized that deficient DNA repair mechanisms may be responsible for the antibody deficiency and susceptibility to inflammation and cancer in some patients. METHODS Germline variants were identified following targeted sequencing of n = 252 genes related to DNA repair in n = 38 patients. NanoString nCounter PlexSet assay measured gene expression in n = 20 CVID patients and n = 7 controls. DNA damage and apoptosis were assessed by flow cytometry in n = 34 CVID patients and n = 11 controls. RESULTS Targeted sequencing supported enrichment of rare genetic variants in genes related to DNA repair pathways with novel and rare likely pathogenic variants identified and an altered gene expression signature that distinguished patients from controls and complex patients from those with an infections-only phenotype. Consistent with this, flow cytometric analyses of lymphocytes following DNA damage revealed a subset of CVID patients whose immune cells have downregulated ATM, impairing the recruitment of other repair factors, delaying repair and promoting apoptosis. CONCLUSION These data suggest that germline genetics and altered gene expression predispose a subset of CVID patients to increased sensitivity to DNA damage and reduced DNA repair capacity.
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Affiliation(s)
- Chantal E Hargreaves
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK.
| | - Silvia Salatino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Sarah C Sasson
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK
| | - James E G Charlesworth
- Oxford University Clinical Academic Graduate School, Medical Sciences Office, John Radcliffe Hospital, University of Oxford, OX3 9DU, Oxford, UK
| | - Elizabeth Bateman
- Department of Immunology, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 7LE, UK
| | - Arzoo M Patel
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK
| | - Consuelo Anzilotti
- Clinical Immunology Department, Oxford University Hospitals Trust, Oxford, OX3 9DU, UK
| | - John Broxholme
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Smita Y Patel
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK
- Clinical Immunology Department, Oxford University Hospitals Trust, Oxford, OX3 9DU, UK
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16
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Guevara-Hoyer K, Jiménez-Huete A, Vasconcelos J, Neves E, Sánchez-Ramón S. Variable immunodeficiency score upfront analytical link (VISUAL), a proposal for combined prognostic score at diagnosis of common variable immunodeficiency. Sci Rep 2021; 11:12211. [PMID: 34108596 PMCID: PMC8190250 DOI: 10.1038/s41598-021-91791-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
The broad and heterogeneous clinical spectrum that characterizes common variable immunodeficiency (CVID) is associated with quite different disease course and prognosis, highlighting the need to develop tools that predict complications. We developed a multianalyte VISUAL score (variable immunodeficiency score upfront analytical link) aimed to predict severity using individual CVID patient data at baseline of a cohort of 50 CVID patients from two different centers in Portugal and Spain. We retrospectively applied VISUAL to the CVID clinical severity scores proposed by Ameratunga and Grimbacher after 15 years follow-up of our cohort. VISUAL score at CVID diagnosis showed adequate performance for predicting infectious and non-infectious severe complications (Cluster B). Compared to switched memory B lymphocyte phenotype alone, VISUAL provided a more accurate identification of clinically meaningful outcome, with significantly higher sensitivity (85% vs 55%, p = 0.01), and negative predictive value (77% vs 58%) and AUC of the ROC curves (0.72 vs 0.64), with optimal cut-off level of 10. For every increase of 1 point in the VISUAL scale, the odds of being in the higher risk category (Cluster B) increased in 1.3 (p = 0.005) for Ameratunga's severity score and 1.26 (p = 0.004) for Grimbacher's severity score. At diagnosis of CVID, VISUAL score ≥ 10 showed 8.94-fold higher odds of severe prognosis than below this threshold. Kaplan-Meier estimates for the VISUAL ≥ 10 points showed significantly earlier progression to Cluster B than those with VISUAL < 10 (p = 0.0002). This prognostic laboratory score might allow close monitoring and more aggressive treatment in patients with scores ≥ 10 on a personalized basis approach. Further studies are needed to prospectively validate VISUAL score.
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Affiliation(s)
- Kissy Guevara-Hoyer
- grid.411068.a0000 0001 0671 5785Department of Immunology, IML and IdSSC, Hospital Clínico San Carlos, Madrid, Spain ,grid.4795.f0000 0001 2157 7667Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain ,Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain
| | - Adolfo Jiménez-Huete
- grid.413297.a0000 0004 1768 8622Department of Neurology, Hospital Ruber Internacional, Madrid, Spain
| | - Julia Vasconcelos
- grid.5808.50000 0001 1503 7226Department of Immunology, Centro Hospitalar e Universitário do Porto, Porto, Portugal
| | - Esmeralda Neves
- grid.5808.50000 0001 1503 7226Department of Immunology, Centro Hospitalar e Universitário do Porto, Porto, Portugal
| | - Silvia Sánchez-Ramón
- grid.411068.a0000 0001 0671 5785Department of Immunology, IML and IdSSC, Hospital Clínico San Carlos, Madrid, Spain ,grid.4795.f0000 0001 2157 7667Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain ,Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain
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17
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Abraham RS, Butte MJ. The New "Wholly Trinity" in the Diagnosis and Management of Inborn Errors of Immunity. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 9:613-625. [PMID: 33551037 DOI: 10.1016/j.jaip.2020.11.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022]
Abstract
The field of immunology has a rich and diverse history, and the study of inborn errors of immunity (IEIs) represents both the "cake" and the "icing on top of the cake," as it has enabled significant advances in our understanding of the human immune system. This explosion of knowledge has been facilitated by a unique partnership, a triumvirate formed by the physician who gathers detailed immunological and clinical phenotypic information from, and shares results with, the patient; the laboratory scientist/immunologist who performs diagnostic testing, as well as advanced functional correlative studies; and the genomics scientist/genetic counselor, who conducts and interprets varied genetic analyses, all of which are essential for dissecting constitutional genetic disorders. Although the basic principles of clinical care have not changed in recent years, the practice of clinical immunology has changed to reflect the prodigious advances in diagnostics, genomics, and therapeutics. An "omic/tics"-centric approach to IEI reflects the tremendous strides made in the field in the new millennium with recognition of new disorders, characterization of the molecular underpinnings, and development and implementation of personalized treatment strategies. This review brings renewed attention to bear on the indispensable "trinity" of phenotypic, genomic, and immunological analyses in the diagnosis, management, and treatment of IEIs.
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Affiliation(s)
- Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics and the Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Calif.
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18
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Zhang J, van Oostrom D, Li J, Savelkoul HFJ. Innate Mechanisms in Selective IgA Deficiency. Front Immunol 2021; 12:649112. [PMID: 33981304 PMCID: PMC8107477 DOI: 10.3389/fimmu.2021.649112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Selective IgA deficiency (SIgAD), characterized by a serum IgA level below 0.07 mg/ml, while displaying normal serum levels of IgM and IgG antibodies, is the most frequently occurring primary immunodeficiency that reveals itself after the first four years after birth. These individuals with SIgAD are for the majority healthy and even when they are identified they are usually not investigated further or followed up. However, recent studies show that newborns and young infants already display clinical manifestations of this condition due to aberrancies in their immune defense. Interestingly, there is a huge heterogeneity in the clinical symptoms of the affected individuals. More than 50% of the affected individuals do not have clinical symptoms, while the individuals that do show clinical symptoms can suffer from mild to severe infections, allergies and autoimmune diseases. However, the reason for this heterogeneity in the manifestation of clinical symptoms of the individuals with SIgAD is unknown. Therefore, this review focusses on the characteristics of innate immune system driving T-cell independent IgA production and providing a mechanism underlying the development of SIgAD. Thereby, we focus on some important genes, including TNFRSF13B (encoding TACI), associated with SIgAD and the involvement of epigenetics, which will cover the methylation degree of TNFRSF13B, and environmental factors, including the gut microbiota, in the development of SIgAD. Currently, no specific treatment for SIgAD exists and novel therapeutic strategies could be developed based on the discussed information.
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Affiliation(s)
- Jingyan Zhang
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Dèlenn van Oostrom
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
| | - JianXi Li
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Huub F. J. Savelkoul
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
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19
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The impact of rare and low-frequency genetic variants in common variable immunodeficiency (CVID). Sci Rep 2021; 11:8308. [PMID: 33859323 PMCID: PMC8050305 DOI: 10.1038/s41598-021-87898-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Next Generation Sequencing (NGS) has uncovered hundreds of common and rare genetic variants involved in complex and rare diseases including immune deficiencies in both an autosomal recessive and autosomal dominant pattern. These rare variants however, cannot be classified clinically, and common variants only marginally contribute to disease susceptibility. In this study, we evaluated the multi-gene panel results of Common Variable Immunodeficiency (CVID) patients and argue that rare variants located in different genes play a more prominent role in disease susceptibility and/or etiology. We performed NGS on DNA extracted from the peripheral blood leukocytes from 103 patients using a panel of 19 CVID-related genes: CARD11, CD19, CD81, ICOS, CTLA4, CXCR4, GATA2, CR2, IRF2BP2, MOGS, MS4A1, NFKB1, NFKB2, PLCG2, TNFRSF13B, TNFRSF13C, TNFSF12, TRNT1 and TTC37. Detected variants were evaluated and classified based on their impact, pathogenicity classification and population frequency as well as the frequency within our study group. NGS revealed 112 different (a total of 227) variants with under 10% population frequency in 103 patients of which 22(19.6%) were classified as benign, 29(25.9%) were classified as likely benign, 4(3.6%) were classified as likely pathogenic and 2(1.8%) were classified as pathogenic. Moreover, 55(49.1%) of the variants were classified as variants of uncertain significance. We also observed different variant frequencies when compared to population frequency databases. Case-control data is not sufficient to unravel the genetic etiology of immune deficiencies. Thus, it is important to understand the incidence of co-occurrence of two or more rare variants to aid in illuminating their potential roles in the pathogenesis of immune deficiencies.
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20
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van Wilder P, Odnoletkova I, Mouline M, de Vries E. Immunoglobulin Replacement Therapy is critical and cost-effective in increasing life expectancy and quality of life in patients suffering from Common Variable Immunodeficiency Disorders (CVID): A health-economic assessment. PLoS One 2021; 16:e0247941. [PMID: 33661975 PMCID: PMC7932530 DOI: 10.1371/journal.pone.0247941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Common variable immunodeficiency disorders (CVID), the most common form of primary antibody deficiency, are rare conditions associated with considerable morbidity and mortality. The clinical benefit of immunoglobulin replacement therapy (IgGRT) is substantial: timely treatment with appropriate doses significantly reduces mortality and the incidence of CVID-complications such as major infections and bronchiectasis. Unfortunately, CVID-patients still face a median diagnostic delay of 4 years. Their disease burden, expressed in annual loss of disability-adjusted life years, is 3-fold higher than in the general population. Hurdles to treatment access and reimbursement by healthcare payers may exist because the value of IgGRT is poorly documented. This paper aims to demonstrate cost-effectiveness and cost-utility (on life expectancy and quality) of IgGRT in CVID. METHODS AND FINDINGS With input from a literature search, we built a health-economic model for cost-effectiveness and cost-utility assessment of IgGRT in CVID. We compared a mean literature-based dose (≥450mg/kg/4wks) to a zero-or-low dose (0 to ≤100 mg/kg/4wks) in a simulated cohort of adult patients from time of diagnosis until death; we also estimated the economic impact of diagnostic delay in this simulated cohort. Compared to no or minimal treatment, IgGRT showed an incremental benefit of 17 life-years (LYs) and 11 quality-adjusted life-years (QALYs), resulting in an incremental cost-effectiveness ratio (ICER) of €29,296/LY and €46,717/QALY. These results were robust in a sensitivity analysis. Reducing diagnostic delay by 4 years provided an incremental benefit of six LYs and four QALYs compared to simulated patients with delayed IgGRT initiation, resulting in an ICER of €30,374/LY and €47,495/QALY. CONCLUSIONS The health-economic model suggests that early initiation of IgGRT compared to no or delayed IgGRT is highly cost-effective. CVID-patients' access to IgGRT should be facilitated, not only because of proven clinical efficacy, but also due to the now demonstrated cost-effectiveness.
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Affiliation(s)
- Philippe van Wilder
- Research Centre in Health Economics, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium
| | - Irina Odnoletkova
- Research Centre in Health Economics, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium
| | - Mehdi Mouline
- Research Centre in Health Economics, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium
| | - Esther de Vries
- Dept Tranzo, Tilburg School of Social and Behavioral Sciences, Tilburg University, Tilburg, The Netherlands
- Laboratory of Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
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21
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Edwards ESJ, Bosco JJ, Ojaimi S, O'Hehir RE, van Zelm MC. Beyond monogenetic rare variants: tackling the low rate of genetic diagnoses in predominantly antibody deficiency. Cell Mol Immunol 2021; 18:588-603. [PMID: 32801365 PMCID: PMC8027216 DOI: 10.1038/s41423-020-00520-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Predominantly antibody deficiency (PAD) is the most prevalent form of primary immunodeficiency, and is characterized by broad clinical, immunological and genetic heterogeneity. Utilizing the current gold standard of whole exome sequencing for diagnosis, pathogenic gene variants are only identified in less than 20% of patients. While elucidation of the causal genes underlying PAD has provided many insights into the cellular and molecular mechanisms underpinning disease pathogenesis, many other genes may remain as yet undefined to enable definitive diagnosis, prognostic monitoring and targeted therapy of patients. Considering that many patients display a relatively late onset of disease presentation in their 2nd or 3rd decade of life, it is questionable whether a single genetic lesion underlies disease in all patients. Potentially, combined effects of other gene variants and/or non-genetic factors, including specific infections can drive disease presentation. In this review, we define (1) the clinical and immunological variability of PAD, (2) consider how genetic defects identified in PAD have given insight into B-cell immunobiology, (3) address recent technological advances in genomics and the challenges associated with identifying causal variants, and (4) discuss how functional validation of variants of unknown significance could potentially be translated into increased diagnostic rates, improved prognostic monitoring and personalized medicine for PAD patients. A multidisciplinary approach will be the key to curtailing the early mortality and high morbidity rates in this immune disorder.
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Affiliation(s)
- Emily S J Edwards
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
| | - Julian J Bosco
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University and Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia
| | - Samar Ojaimi
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
- Department of Infectious Diseases, Monash Health, Clayton, VIC, Australia
- Centre for Inflammatory Diseases, Monash Health, Clayton, VIC, Australia
- Department of Allergy and Immunology, Monash Health, Clayton, VIC, Australia
| | - Robyn E O'Hehir
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University and Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia
| | - Menno C van Zelm
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia.
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia.
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University and Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia.
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22
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Binversie EE, Baker LA, Engelman CD, Hao Z, Moran JJ, Piazza AM, Sample SJ, Muir P. Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture. PLoS One 2020; 15:e0244075. [PMID: 33382735 PMCID: PMC7774950 DOI: 10.1371/journal.pone.0244075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/02/2020] [Indexed: 11/19/2022] Open
Abstract
Anterior cruciate ligament (ACL) rupture is an important condition of the human knee. Second ruptures are common and societal costs are substantial. Canine cranial cruciate ligament (CCL) rupture closely models the human disease. CCL rupture is common in the Labrador Retriever (5.79% prevalence), ~100-fold more prevalent than in humans. Labrador Retriever CCL rupture is a polygenic complex disease, based on genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers. Dissection of genetic variation in complex traits can be enhanced by studying structural variation, including copy number variants (CNVs). Dogs are an ideal model for CNV research because of reduced genetic variability within breeds and extensive phenotypic diversity across breeds. We studied the genetic etiology of CCL rupture by association analysis of CNV regions (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were called from SNPs using three different programs (PennCNV, CNVPartition, and QuantiSNP). After quality control, CNV calls were combined to create CNVRs using ParseCNV and an association analysis was performed. We found no strong effect CNVRs but found 46 small effect (max(T) permutation P<0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were deletions and 21 were duplications. Of the 46 CCL rupture associated CNVRs, we identified 39 unique regions. Thirty four were identified by a single calling algorithm, 3 were identified by two calling algorithms, and 2 were identified by all three algorithms. For 42 of the associated CNVRs, frequency in the population was <10% while 4 occurred at a frequency in the population ranging from 10–25%. Average CNVR length was 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were associated with case status. CNVRs did not overlap previous canine CCL rupture risk loci identified by GWAS. Associated CNVRs contained 152 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using pathway analysis, a cluster of 19 homeobox domain transcript regulator genes was associated with CCL rupture (P = 6.6E-13). This gene cluster influences cranial-caudal body pattern formation during embryonic limb development. Clustered genes were found in 3 CNVRs on chromosome 14 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion CNVRs, the association was strengthened (P = 8.7E-16). This study suggests a component of the polygenic risk of CCL rupture in Labrador Retrievers is associated with small effect CNVs and may include aspects of stifle morphology regulated by homeobox domain transcript regulator genes.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lauren A. Baker
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Corinne D. Engelman
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zhengling Hao
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John J. Moran
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander M. Piazza
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susannah J. Sample
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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23
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van de Ven AAJM, Alfaro TM, Robinson A, Baumann U, Bergeron A, Burns SO, Condliffe AM, Fevang B, Gennery AR, Haerynck F, Jacob J, Jolles S, Malphettes M, Meignin V, Milota T, van Montfrans J, Prasse A, Quinti I, Renzoni E, Stolz D, Warnatz K, Hurst JR. Managing Granulomatous-Lymphocytic Interstitial Lung Disease in Common Variable Immunodeficiency Disorders: e-GLILDnet International Clinicians Survey. Front Immunol 2020; 11:606333. [PMID: 33324422 PMCID: PMC7726128 DOI: 10.3389/fimmu.2020.606333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
Background Granulomatous-lymphocytic interstitial lung disease (GLILD) is a rare, potentially severe pulmonary complication of common variable immunodeficiency disorders (CVID). Informative clinical trials and consensus on management are lacking. Aims The European GLILD network (e-GLILDnet) aims to describe how GLILD is currently managed in clinical practice and to determine the main uncertainties and unmet needs regarding diagnosis, treatment and follow-up. Methods The e-GLILDnet collaborators developed and conducted an online survey facilitated by the European Society for Immunodeficiencies (ESID) and the European Respiratory Society (ERS) between February-April 2020. Results were analyzed using SPSS. Results One hundred and sixty-one responses from adult and pediatric pulmonologists and immunologists from 47 countries were analyzed. Respondents treated a median of 27 (interquartile range, IQR 82-maximum 500) CVID patients, of which a median of 5 (IQR 8-max 200) had GLILD. Most respondents experienced difficulties in establishing the diagnosis of GLILD and only 31 (19%) had access to a standardized protocol. There was little uniformity in diagnostic or therapeutic interventions. Fewer than 40% of respondents saw a definite need for biopsy in all cases or performed bronchoalveolar lavage for diagnostics. Sixty-six percent used glucocorticosteroids for remission-induction and 47% for maintenance therapy; azathioprine, rituximab and mycophenolate mofetil were the most frequently prescribed steroid-sparing agents. Pulmonary function tests were the preferred modality for monitoring patients during follow-up. Conclusions These data demonstrate an urgent need for clinical studies to provide more evidence for an international consensus regarding management of GLILD. These studies will need to address optimal procedures for definite diagnosis and a better understanding of the pathogenesis of GLILD in order to provide individualized treatment options. Non-availability of well-established standardized protocols risks endangering patients.
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Affiliation(s)
- Annick A. J. M. van de Ven
- Departments of Internal Medicine and Allergology, Rheumatology and Clinical Immunology, University Medical Center Groningen, Netherlands
| | - Tiago M. Alfaro
- Pneumology Unit, Centro Hospital e Universitário de Coimbra, Coimbra, Portugal and Centre of Pneumology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | | | - Ulrich Baumann
- Department of Paediatric Pulmonology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Anne Bergeron
- Université de Paris, Assistance Publique Hôpitaux de Paris (APHP), Hôpital Saint Louis, Paris, France
| | - Siobhan O. Burns
- Institute of Immunity and Transplantation, University College London, Dept of Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Alison M. Condliffe
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield Medical School, Sheffield, United Kingdom
| | - Børre Fevang
- Centre for Rare Disorders and Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Andrew R. Gennery
- Translational and Clinical Research Institute, Newcastle University and Great North Children’s Hospital, Newcastle upon Tyne, United Kingdom
| | - Filomeen Haerynck
- Department of Pediatric Pulmonology and Immunology, Centre for Primary Immune deficiency Ghent, PID research lab, Ghent University Hospital, Belgium
| | - Joseph Jacob
- UCL Respiratory, University College London, London, United Kingdom
- Centre for Medical Image Computing, University College London, London, United Kingdom
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, United Kingdom
| | - Marion Malphettes
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Université Paris Diderot, Paris, France
| | - Véronique Meignin
- Department of Pathology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Tomas Milota
- Department of Immunology, Second Faculty of Medicine Charles University and Motol University Hospital, Prague, Czech Republic
| | - Joris van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, Netherlands
| | - Antje Prasse
- Department of Pulmonology, Hannover Medical School and DZL BREATH, and Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Renzoni
- Interstitial Lung Disease Unit, Royal Brompton Hospital, London, United Kingdom
| | - Daiana Stolz
- Clinic for Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - John R. Hurst
- UCL Respiratory, University College London, London, United Kingdom
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24
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Tavakol M, Jamee M, Azizi G, Sadri H, Bagheri Y, Zaki-Dizaji M, Mahdavi FS, Jadidi-Niaragh F, Tajfirooz S, Kamali AN, Aghamahdi F, Noorian S, Kojidi HT, Mosavian M, Matani R, Dolatshahi E, Porrostami K, Elahimehr N, Fatemi-Abhari M, Sharifi L, Arjmand R, Haghi S, Zainaldain H, Yazdani R, Shaghaghi M, Abolhassani H, Aghamohammadi A. Diagnostic Approach to the Patients with Suspected Primary Immunodeficiency. Endocr Metab Immune Disord Drug Targets 2020; 20:157-171. [PMID: 31456526 DOI: 10.2174/1871530319666190828125316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/16/2019] [Accepted: 08/04/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Primary immunodeficiency diseases (PIDs) are a group of more than 350 disorders affecting distinct components of the innate and adaptive immune systems. In this review, the classic and advanced stepwise approach towards the diagnosis of PIDs are simplified and explained in detail. RESULTS Susceptibility to recurrent infections is the main hallmark of almost all PIDs. However, noninfectious complications attributable to immune dysregulation presenting with lymphoproliferative and/or autoimmune disorders are not uncommon. Moreover, PIDs could be associated with misleading presentations including allergic manifestations, enteropathies, and malignancies. CONCLUSION Timely diagnosis is the most essential element in improving outcome and reducing the morbidity and mortality in PIDs. This wouldn't be possible unless the physicians keep the diagnosis of PID in mind and be sufficiently aware of the approach to these patients.
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Affiliation(s)
- Marzieh Tavakol
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Allergy and Clinical Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahnaz Jamee
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Homa Sadri
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Allergy and Clinical Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Yasser Bagheri
- Clinical Research Development Unit (CRDU), 5 azar Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | | | | | - Sanaz Tajfirooz
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Ali N Kamali
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Fatemeh Aghamahdi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Pediatric Endocrinology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Shahab Noorian
- Department of Pediatric Endocrinology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Habibeh Taghavi Kojidi
- Department of Pediatric Endocrinology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Mosavian
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Gastroenterology and Hepatology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Rahman Matani
- Department of Gastroenterology and Hepatology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Elahe Dolatshahi
- Department of Rheumatology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Kumars Porrostami
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nasrin Elahimehr
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Marzie Fatemi-Abhari
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Laleh Sharifi
- Uro- Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Arjmand
- Department of Infectious Disease, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Sabahat Haghi
- Department of Hematology & Oncology, School of Medicine, Alborz university of medical sciences, Karaj, Iran
| | - Hamed Zainaldain
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Shaghaghi
- Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins Hospital, Baltimore, MD, United States
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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25
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Current genetic landscape in common variable immune deficiency. Blood 2020; 135:656-667. [PMID: 31942606 DOI: 10.1182/blood.2019000929] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/14/2019] [Indexed: 12/14/2022] Open
Abstract
Using whole-exome sequencing to examine the genetic causes of immune deficiency in 235 common variable immunodeficiency (CVID) patients seen in the United States (Mount Sinai, New York), 128 patients from Sweden, and 208 from Iran revealed 68 known disease-causing genes underlying this heterogeneous immune defect. The patients at the time of study ranged from 4 to 90 years of age. Overall, 31%, 36%, and 54% of the patients in the US, Swedish, or Iranian cohorts had mutations. The multiplicity of genes identified in the 571 subjects reflects the complex requirements of B-cell antigen signaling, activation, survival, migration, maturation, and maintenance of antibody-secreting memory B-cell populations to the plasma cell stage. For the US and Swedish cohorts, CVID subjects with noninfectious complications, lymphoid infiltrations, inflamatory conditions, or autoimmunity were somewhat more likely to have an identifiable gene, but in both cohorts, numerous subjects with these medical conditions had no potential gene that could be assigned. Specific clinical patterns of illnesses were also not linked to any given gene defect as there was considerable overlap in clinical presentations. These observations led to a new perspective on the complexity of the immunologic phenotype found in CVID syndrome.
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26
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Global Distribution of Common Variable Immunodeficiency (CVID) in the Light of the UNDP Human Development Index (HDI): A Preliminary Perspective of a Rare Disease. J Immunol Res 2020; 2020:8416124. [PMID: 32953893 PMCID: PMC7481957 DOI: 10.1155/2020/8416124] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 11/18/2022] Open
Abstract
Common variable immunodeficiency (CVID), although the most common primary immunodeficiency in humans, is a rare disease. We explored the spatial global distribution and country-wise prevalence of CVID, based on published data and those available from databases. As a country's medical progress is linked to its technological and socio-economic developmental status, we expected that observed CVID prevalence was linked to human wellbeing. To assess this, we examined the correlation of observed CVID prevalence and the UNDP Human Development Index (HDI), which is a key measure of human development. Seventy-four data sets from 47 countries were available (most of them no older than 10 years). Analyses revealed that observed CVID prevalence ranged from 0.001 to 3.374 per 100,000 (mean 0.676 ± 0.83) and was highest in “high” HDI countries (Spearman′s rho = 0.757). Observed prevalence was particularly high in countries where immunodeficiencies are systematically documented in registers. In “low” and “middle” HDI countries, CVID awareness is extremely poor. Assuming that true CVID prevalence does not differ among countries, this study, though preliminary, provides evidence that the discrepancy between observed and (unknown) true prevalence can be clearly linked to the countries' developmental status. As a potential alternative explanation, we briefly discuss the possibility that variation in CVID prevalence is related to human genetic lineage.
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27
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Guevara-Hoyer K, Vasconcelos J, Marques L, Fernandes AA, Ochoa-Grullón J, Marinho A, Sequeira T, Gil C, Rodríguez de la Peña A, Serrano García I, Recio MJ, Fernández-Arquero M, Pérez de Diego R, Ramos JT, Neves E, Sánchez-Ramón S. Variable immunodeficiency study: Evaluation of two European cohorts within a variety of clinical phenotypes. Immunol Lett 2020; 223:78-88. [PMID: 32344018 DOI: 10.1016/j.imlet.2020.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/02/2020] [Accepted: 03/16/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Given the wide heterogeneity of common variable immunodeficiency (CVID), several groups have proposed clinical and immunological classifications to better define follow-up and prognostic algorithms. The present study aims to validate recent clinical and laboratory algorithms, based on different combinations of CVID biomarkers, to provide more personalized treatment and follow-up strategies. METHODS We analysed clinical and immunological features of 80 patients with suspected or diagnosed CVID, in two reference centres of Portugal and Spain. Clinical manifestations were categorized into clinical phenotyping proposed by Chapel et al. [1] that included cytopenia; polyclonal lymphocytic infiltration; unexplained enteropathy; and no disease-related complications. RESULTS 76% of patients in our cohort entered one of the four categories of clinical phenotyping, without overlap (cytopenia; polyclonal lymphocytic infiltration; unexplained enteropathy; and no disease-related complications). The most prominent phenotype was "cytopenia" (40%) followed by "polyclonal lymphocytic infiltration" (19%). The remaining 24% patients of our cohort had overlap of 2 clinical phenotypes (cytopenia and unexplained enteropathy mainly). A delay of CVID diagnosis in more than 6 years presented 3.7-fold higher risk of developing lymphoproliferation and/or malignancy (p < 0.05), and was associated with increased CD8+CD45RO + T-lymphocytes (p < 0.05). An association between decreased switched-memory B cells with lymphoproliferation and malignancy was observed (p < 0.03 and p < 0.05, respectively). CD4 + T-lymphocytopenia correlated with autoimmune phenotype, with 30% prevalence (p < 0.05). HLA-DR7 expression was related to CVID onset in early life in our patients (13 vs 25 years), and DQ2.5 or DQ2.2 with unexplained enteropathy (p < 0.05). CONCLUSIONS The phenotypic and genetic study is crucial for an adequate clinical orientation of CVID patients. In these two independent cohorts of patients, classification based in clinical and laboratory algorithms, provides more personalized treatment and follow-up strategies.
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Affiliation(s)
- Kissy Guevara-Hoyer
- Department of Immunology, IML and IdSSC, Hospital Clínico San Carlos, Madrid, Spain; Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain; Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain
| | - Julia Vasconcelos
- Department of Immunology, Centro Hospitalar e Universitário Do Porto, Porto, Portugal
| | - Laura Marques
- Department of Pediatrics, Centro Hospitalar e Universitário Do Porto, Porto, Portugal
| | | | - Juliana Ochoa-Grullón
- Department of Immunology, IML and IdSSC, Hospital Clínico San Carlos, Madrid, Spain; Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain; Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain
| | - Antonio Marinho
- Clinical Immunology Unit, Centro Hospitalar e Universitário Do Porto, Porto, Portugal
| | - Teresa Sequeira
- Clinical Immunology Unit, Centro Hospitalar e Universitário Do Porto, Porto, Portugal
| | - Celia Gil
- Department of Pediatrics, Hospital Clínico San Carlos, Madrid, Spain
| | | | - Irene Serrano García
- Department of Epidemiology and Preventive Medicine, Hospital Clínico San Carlos, Madrid, Spain
| | - M José Recio
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain; Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain
| | - Miguel Fernández-Arquero
- Department of Immunology, IML and IdSSC, Hospital Clínico San Carlos, Madrid, Spain; Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain; Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain
| | - Rebeca Pérez de Diego
- Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain; Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, Madrid, Spain
| | - José Tomas Ramos
- Department of Pediatrics, Hospital Clínico San Carlos, Madrid, Spain
| | - Esmeralda Neves
- Department of Immunology, Centro Hospitalar e Universitário Do Porto, Porto, Portugal
| | - Silvia Sánchez-Ramón
- Department of Immunology, IML and IdSSC, Hospital Clínico San Carlos, Madrid, Spain; Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain; Immunodeficiency Interdepartmental Group (GIID), Madrid, Spain.
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28
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Gruber C, Bogunovic D. Incomplete penetrance in primary immunodeficiency: a skeleton in the closet. Hum Genet 2020; 139:745-757. [PMID: 32067110 PMCID: PMC7275875 DOI: 10.1007/s00439-020-02131-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/02/2020] [Indexed: 12/11/2022]
Abstract
Primary immunodeficiencies (PIDs) comprise a diverse group of over 400 genetic disorders that result in clinically apparent immune dysfunction. Although PIDs are classically considered as Mendelian disorders with complete penetrance, we now understand that absent or partial clinical disease is often noted in individuals harboring disease-causing genotypes. Despite the frequency of incomplete penetrance in PID, no conceptual framework exists to categorize and explain these occurrences. Here, by reviewing decades of reports on incomplete penetrance in PID we identify four recurrent themes of incomplete penetrance, namely genotype quality, (epi)genetic modification, environmental influence, and mosaicism. For each of these principles, we review what is known, underscore what remains unknown, and propose future experimental approaches to fill the gaps in our understanding. Although the content herein relates specifically to inborn errors of immunity, the concepts are generalizable across genetic diseases.
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Affiliation(s)
- Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Department of Pediatrics, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
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29
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Suratannon N, van Wijck RTA, Broer L, Xue L, van Meurs JBJ, Barendregt BH, van der Burg M, Dik WA, Chatchatee P, Langerak AW, Swagemakers SMA, Goos JAC, Mathijssen IMJ, Dalm VASH, Suphapeetiporn K, Heezen KC, Drabwell J, Uitterlinden AG, van der Spek PJ, van Hagen PM. Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency. Front Immunol 2020; 11:614. [PMID: 32373116 PMCID: PMC7179678 DOI: 10.3389/fimmu.2020.00614] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Genetic tests for primary immunodeficiency disorders (PIDs) are expensive, time-consuming, and not easily accessible in developing countries. Therefore, we studied the feasibility of a customized single nucleotide variant (SNV) microarray that we developed to detect disease-causing variants and copy number variation (CNV) in patients with PIDs for only 40 Euros. Methods: Probes were custom-designed to genotype 9,415 variants of 277 PID-related genes, and were added to the genome-wide Illumina Global Screening Array (GSA). Data analysis of GSA was performed using Illumina GenomeStudio 2.0, Biodiscovery Nexus 10.0, and R-3.4.4 software. Validation of genotype calling was performed by comparing the GSA with whole-genome sequencing (WGS) data of 56 non-PID controls. DNA samples of 95 clinically diagnosed PID patients, of which 60 patients (63%) had a genetically established diagnosis (by Next-Generation Sequencing (NGS) PID panels or Sanger sequencing), were analyzed to test the performance of the GSA. The additional SNVs detected by GSA were validated by Sanger sequencing. Results: Genotype calling of the customized array had an accuracy rate of 99.7%. The sensitivity for detecting rare PID variants was high (87%). The single sample replication in two runs was high (94.9%). The customized GSA was able to generate a genetic diagnosis in 37 out of 95 patients (39%). These 37 patients included 29 patients in whom the genetic variants were confirmed by conventional methods (26 patients by SNV and 3 by CNV analysis), while in 8 patients a new genetic diagnosis was established (6 patients by SNV and 2 patients suspected for leukemia by CNV analysis). Twenty-eight patients could not be detected due to the limited coverage of the custom probes. However, the diagnostic yield can potentially be increased when newly updated variants are added. Conclusion: Our robust customized GSA seems to be a promising first-line rapid screening tool for PIDs at an affordable price, which opens opportunities for low-cost genetic testing in developing countries. The technique is scalable, allows numerous new genetic variants to be added, and offers the potential for genetic testing not only in PIDs, but also in many other genetic diseases.
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Affiliation(s)
- Narissara Suratannon
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Rogier T A van Wijck
- Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Linda Broer
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Laixi Xue
- Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Joyce B J van Meurs
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Barbara H Barendregt
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - Willem A Dik
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Sigrid M A Swagemakers
- Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Pathology & Clinical Bioinformatics, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Virgil A S H Dalm
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Kim C Heezen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Jose Drabwell
- International Patient Organization for Primary Immunodeficiencies (IPOPI), Downderry, United Kingdom
| | - André G Uitterlinden
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Peter J van der Spek
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - P Martin van Hagen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Yakaboski E, Fuleihan RL, Sullivan KE, Cunningham-Rundles C, Feuille E. Lymphoproliferative Disease in CVID: a Report of Types and Frequencies from a US Patient Registry. J Clin Immunol 2020; 40:524-530. [PMID: 32185577 DOI: 10.1007/s10875-020-00769-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/08/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE Lymphoproliferative disease in common variable immunodeficiency disease (CVID) is heterogeneous in pathogenesis and ranges from non-malignant lymphoid hyperplasia to lymphoma. METHODS The United States Immunodeficiency Network (USIDNET) patient registry was queried for lymphoproliferative diseases reported in CVID patients. Diagnoses included as possible manifestations of lymphoproliferation included lymphadenopathy, lymphoid hyperplasia, lymphocytic inflammation, lymphocytosis, and gammopathy. RESULTS Among 1091 CVID patients, lymphoproliferative conditions were reported in 17.2% (N = 188). These conditions included lymphadenopathy (N = 192, 12.3%), lymphoid hyperplasia or lymphocytic inflammation (N = 50, 4.6%), lymphocytosis (N = 3, 0.3%), and gammopathies (N = 3, 0.3%). Of the 188 patients with lymphoproliferative conditions, 15 (8%) also had a diagnosis of lymphoma, while the remaining 173 (92%) did not. Nine (4.8%) had a diagnosis of non-lymphomatous malignancy including basal cell carcinoma (N = 3, 1.6%), thyroid carcinoma (N = 2, 1.1%), gynecologic cancer (N = 2, 1.1%), testicular cancer (N = 1), and vocal cord carcinoma (N = 1). CVID patients with lymphoma were older than patients with lymphoproliferative disease who did not have a diagnosis of lymphoma at the time of analysis (median age 49 vs. 35 years, p = 0.005). CVID patients with lymphoproliferative disease had 2.5 times higher odds of having chronic lung disease compared with those with lymphoma (OR = 0.4, p = 0.049). There were no significant differences in the frequency of autoimmune, gastrointestinal, hepatic, or granulomatous disease between these populations. CONCLUSIONS While CVID patients are at increased risk for lymphoma, lymphoproliferation may be observed in the absence of a concurrent hematologic or solid tumor malignancy.
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Affiliation(s)
- Elizabeth Yakaboski
- Massachusetts General Hospital, 55 Fruit St, Bulfinch 165, Boston, MA, 02114, USA.
| | - Ramsay L Fuleihan
- Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
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31
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Hultberg J, Ernerudh J, Larsson M, Nilsdotter-Augustinsson Å, Nyström S. Plasma protein profiling reflects T H1-driven immune dysregulation in common variable immunodeficiency. J Allergy Clin Immunol 2020; 146:417-428. [PMID: 32057767 DOI: 10.1016/j.jaci.2020.01.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Common variable immunodeficiency (CVID) is a disorder characterized by antibody deficiency. A significant fraction of the patients suffer from immune dysregulation, which leads to increased morbidity and mortality. The pathogenesis of this condition is poorly understood. OBJECTIVE Our aim was to find out whether the plasma protein signature in CVID is associated with clinical characteristics and lymphocyte aberrations. METHODS A highly sensitive proximity extension assay was used for targeted profiling of 145 plasma proteins in 29 patients with CVID. Phenotyping of peripheral lymphocytes was done by flow cytometry. The findings were correlated with the burden of immune dysregulation. RESULTS Unsupervised clustering of plasma protein profiles identified 2 distinct groups of patients with CVID that differed significantly in terms of the degree of complications due to immune dysregulation and in terms of the frequency of activated B- and T-cell subpopulations. Pathway analysis identified IFN-γ and IL-1β as the top enriched upstream regulators associated with higher grade of immune dysregulation. In addition, CVID was found to be associated with increased plasma levels of the B-cell-attracting chemokine CXCL13. CONCLUSION Clustering based on plasma protein profiles delineated a subgroup of patients with CVID with activated T cells and clinical complications due to immune dysregulation. Thus, data indicate that CVID-associated immune dysregulation is a TH1-mediated inflammatory process driven by the IFN-γ pathway.
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Affiliation(s)
- Jonas Hultberg
- Division of Molecular Virology, Department of Biomedicine and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Immunology and Transfusions Medicine, and Department of Biomedicine and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusions Medicine, and Department of Biomedicine and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Marie Larsson
- Division of Molecular Virology, Department of Biomedicine and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Department of Infectious Diseases, and Department of Biomedicine and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sofia Nyström
- Division of Molecular Virology, Department of Biomedicine and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Immunology and Transfusions Medicine, and Department of Biomedicine and Clinical Sciences, Linköping University, Linköping, Sweden.
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32
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Christiansen M, Offersen R, Jensen JMB, Petersen MS, Larsen CS, Mogensen TH. Identification of Novel Genetic Variants in CVID Patients With Autoimmunity, Autoinflammation, or Malignancy. Front Immunol 2020; 10:3022. [PMID: 32047491 PMCID: PMC6996488 DOI: 10.3389/fimmu.2019.03022] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
Common variable immunodeficiency (CVID) is a primary immunodeficiency characterized by recurrent bacterial infections and defined by reduced levels of IgG, IgA, and/or IgM, insufficient response to polysaccharide vaccination, and an abnormal B-cell immunophenotype with a significantly reduced fraction of isotype-switched memory B cells. In addition to this infectious phenotype, at least one third of the patients experience autoimmune, autoinflammatory, granulomatous, and/or malignant complications. The very heterogeneous presentation strongly suggests a collection of different disease entities with somewhat different pathogeneses and most likely diverse genetic etiologies. Major progress has been made during recent years with the advent and introduction of next-generation sequencing, initially for research purposes, but more recently in clinical practice. In the present study, we performed whole exome sequencing on 20 CVID patients with autoimmunity, autoinflammation, and/or malignancy from the Danish CVID cohort with the aim to identify gene variants with a certain, possible, or potential disease-causing role in CVID. Through bioinformatics analyses, we identified variants with possible/probable disease-causing potential in nine of the patients. Of these, three patients had four variants in three different genes classified as likely pathogenic (NFKB1, TNFAIP3, and TTC37), whereas in six patients, we identified seven variants of possible pathogenic potential classified as variants of unknown significance (STAT3, IL17F, IRAK4, DDX41, NLRC3, TNFRSF1A, and PLCG2). In the remaining 11 patients, we did not identify possible genetic causes. Genetic findings were correlated to clinical disease presentation, clinical immunological phenotype, and disease complications. We suggest that the variants identified in the present work should lay the ground for future studies to functionally validate their disease-causing potential and to investigate at the mechanistic and molecular level their precise role in CVID pathogenesis. Overall, we believe that the present work contributes important new insights into the genetic basis of CVID and particular in the subset of CVID patients with a complex phenotype involving not only infection, but also autoimmunity, autoinflammation, and malignancy.
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Affiliation(s)
- Mette Christiansen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Rasmus Offersen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Carsten S Larsen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Trine H Mogensen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Silva SL, Fonseca M, Pereira MLM, Silva SP, Barbosa RR, Serra-Caetano A, Blanco E, Rosmaninho P, Pérez-Andrés M, Sousa AB, Raposo AASF, Gama-Carvalho M, Victorino RMM, Hammarstrom L, Sousa AE. Monozygotic Twins Concordant for Common Variable Immunodeficiency: Strikingly Similar Clinical and Immune Profile Associated With a Polygenic Burden. Front Immunol 2019; 10:2503. [PMID: 31824477 PMCID: PMC6882918 DOI: 10.3389/fimmu.2019.02503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/07/2019] [Indexed: 01/10/2023] Open
Abstract
Monozygotic twins provide a unique opportunity to better understand complex genetic diseases and the relative contribution of heritable factors in shaping the immune system throughout life. Common Variable Immunodeficiency Disorders (CVID) are primary antibody defects displaying wide phenotypic and genetic heterogeneity, with monogenic transmission accounting for only a minority of the cases. Here, we report a pair of monozygotic twins concordant for CVID without a family history of primary immunodeficiency. They featured a remarkably similar profile of clinical manifestations and immunological alterations at diagnosis (established at age 37) and along the subsequent 15 years of follow-up. Interestingly, whole-exome sequencing failed to identify a monogenic cause for CVID, but unraveled a combination of heterozygous variants, with a predicted deleterious impact. These variants were found in genes involved in relevant immunological pathways, such as JUN, PTPRC, TLR1, ICAM1, and JAK3. The potential for combinatorial effects translating into the observed disease phenotype is inferred from their roles in immune pathways, namely in T and B cell activation. The combination of these genetic variants is also likely to impose a significant constraint on environmental influences, resulting in a similar immunological phenotype in both twins, despite exposure to different living conditions. Overall, these cases stress the importance of integrating NGS data with clinical and immunological phenotypes at the single-cell level, as provided by multi-dimensional flow-cytometry, in order to understand the complex genetic landscape underlying the vast majority of patients with CVID, as well as those with other immunodeficiencies.
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Affiliation(s)
- Susana L Silva
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Mariana Fonseca
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Marcelo L M Pereira
- Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Sara P Silva
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Rita R Barbosa
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Serra-Caetano
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Elena Blanco
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Salamanca, Spain.,Biomedical Research Networking Centre on Cancer-CIBER-CIBERONC, Number CB16/12/00400, Institute of Health Carlos III, Madrid, Spain
| | - Pedro Rosmaninho
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Martin Pérez-Andrés
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Salamanca, Spain.,Biomedical Research Networking Centre on Cancer-CIBER-CIBERONC, Number CB16/12/00400, Institute of Health Carlos III, Madrid, Spain
| | - Ana Berta Sousa
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Alexandre A S F Raposo
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Rui M M Victorino
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | | | - Ana E Sousa
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
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Cunningham-Rundles C. Common variable immune deficiency: Dissection of the variable. Immunol Rev 2019; 287:145-161. [PMID: 30565247 DOI: 10.1111/imr.12728] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/16/2018] [Indexed: 12/28/2022]
Abstract
Starting about 60 years ago, a number of reports appeared that outlined the severe clinical course of a few adult subjects with profound hypogammaglobinemia. Puzzled by the lack of family history and adult onset of symptoms in most, the name "acquired" hypogammaglobinemia was given, but later altered to the current name common variable immune deficiency. Pathology reports remarked on the loss of lymph node architecture and paucity of plasma cells in lymphoid tissues in these subjects. While characterized by reduced serum IgG and IgA and often IgM, and thus classified among the B-cell defects, an increasing number of cellular defects in these patients have been recognized over time. In the early years, severe respiratory tract infections commonly led to a shortened life span, but the wide spread availability of immune globulin concentrates for the last 25 years has improved survival. However, chronic non-infectious inflammatory and autoimmune conditions have now emerged as challenging clinical problems; these require further immunologic understanding and additional therapeutic measures. Recent study of this phenotypic syndrome have provided an increasingly fertile ground for the identification of autosomal recessive and now more commonly, autosomal dominant gene defects which lead to the loss of B-cell development in this syndrome.
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35
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Disorders of CTLA-4 expression, how they lead to CVID and dysregulated immune responses. Curr Opin Allergy Clin Immunol 2019; 19:578-585. [DOI: 10.1097/aci.0000000000000590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Brasil S, Pascoal C, Francisco R, dos Reis Ferreira V, A. Videira P, Valadão G. Artificial Intelligence (AI) in Rare Diseases: Is the Future Brighter? Genes (Basel) 2019; 10:genes10120978. [PMID: 31783696 PMCID: PMC6947640 DOI: 10.3390/genes10120978] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
The amount of data collected and managed in (bio)medicine is ever-increasing. Thus, there is a need to rapidly and efficiently collect, analyze, and characterize all this information. Artificial intelligence (AI), with an emphasis on deep learning, holds great promise in this area and is already being successfully applied to basic research, diagnosis, drug discovery, and clinical trials. Rare diseases (RDs), which are severely underrepresented in basic and clinical research, can particularly benefit from AI technologies. Of the more than 7000 RDs described worldwide, only 5% have a treatment. The ability of AI technologies to integrate and analyze data from different sources (e.g., multi-omics, patient registries, and so on) can be used to overcome RDs’ challenges (e.g., low diagnostic rates, reduced number of patients, geographical dispersion, and so on). Ultimately, RDs’ AI-mediated knowledge could significantly boost therapy development. Presently, there are AI approaches being used in RDs and this review aims to collect and summarize these advances. A section dedicated to congenital disorders of glycosylation (CDG), a particular group of orphan RDs that can serve as a potential study model for other common diseases and RDs, has also been included.
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Affiliation(s)
- Sandra Brasil
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Carlota Pascoal
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Rita Francisco
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Vanessa dos Reis Ferreira
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- Correspondence:
| | - Paula A. Videira
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Gonçalo Valadão
- Instituto de Telecomunicações, 1049-001 Lisboa, Portugal;
- Departamento de Ciências e Tecnologias, Autónoma Techlab–Universidade Autónoma de Lisboa, 1169-023 Lisboa, Portugal
- Electronics, Telecommunications and Computers Engineering Department, Instituto Superior de Engenharia de Lisboa, 1959-007 Lisboa, Portugal
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Ameratunga R, Lehnert K, Woon ST. All Patients With Common Variable Immunodeficiency Disorders (CVID) Should Be Routinely Offered Diagnostic Genetic Testing. Front Immunol 2019; 10:2678. [PMID: 31824486 PMCID: PMC6883368 DOI: 10.3389/fimmu.2019.02678] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/30/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
- Rohan Ameratunga
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand.,Department of Clinical Immunology, Auckland City Hospital, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand
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38
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Mohammed AD, Khan MAW, Chatzistamou I, Chamseddine D, Williams-Kang K, Perry M, Enos R, Murphy A, Gomez G, Aladhami A, Oskeritzian CA, Jolly A, Chang Y, He S, Pan Z, Kubinak JL. Gut Antibody Deficiency in a Mouse Model of CVID Results in Spontaneous Development of a Gluten-Sensitive Enteropathy. Front Immunol 2019; 10:2484. [PMID: 31708923 PMCID: PMC6820504 DOI: 10.3389/fimmu.2019.02484] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/04/2019] [Indexed: 12/14/2022] Open
Abstract
Primary immunodeficiencies are heritable disorders of immune function. CD19 is a B cell co-receptor important for B cell development, and CD19 deficiency is a known genetic risk factor for a rare form of primary immunodeficiency known as “common variable immunodeficiency” (CVID); an antibody deficiency resulting in low levels of serum IgG and IgA. Enteropathies are commonly observed in CVID patients but the underlying reason for this is undefined. Here, we utilize CD19−/− mice as a model of CVID to test the hypothesis that antibody deficiency negatively impacts gut physiology under steady-state conditions. As anticipated, immune phenotyping experiments demonstrate that CD19−/− mice develop a severe B cell deficiency in gut-associated lymphoid tissues that result in significant reductions to antibody concentrations in the gut lumen. Antibody deficiency was associated with defective anti-commensal IgA responses and the outgrowth of anaerobic bacteria in the gut. Expansion of anaerobic bacteria coincides with the development of a chronic inflammatory condition in the gut of CD19−/− mice that results in an intestinal malabsorption characterized by defects in lipid metabolism and transport. Administration of the antibiotic metronidazole to target anaerobic members of the microbiota rescues mice from disease indicating that intestinal malabsorption is a microbiota-dependent phenomenon. Finally, intestinal malabsorption in CD19−/− mice is a gluten-sensitive enteropathy as exposure to a gluten-free diet also significantly reduces disease severity in CD19−/− mice. Collectively, these results support an effect of antibody deficiency on steady-state gut physiology that compliment emerging data from human studies linking IgA deficiency with non-infectious complications associated with CVID. They also demonstrate that CD19−/− mice are a useful model for studying the role of B cell deficiency and gut dysbiosis on gluten-sensitive enteropathies; a rapidly emerging group of diseases in humans with an unknown etiology.
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Affiliation(s)
- Ahmed Dawood Mohammed
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States.,School of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Md A Wadud Khan
- Biology Department, University of Texas at Arlington, Arlington, TX, United States
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Douja Chamseddine
- Biology Department, University of Texas at Arlington, Arlington, TX, United States
| | - Katie Williams-Kang
- Biology Department, University of Texas at Arlington, Arlington, TX, United States
| | - Mason Perry
- Biology Department, University of Texas at Arlington, Arlington, TX, United States
| | - Reilly Enos
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Angela Murphy
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Gregorio Gomez
- Department of Biomedical Sciences, College of Medicine, University of Houston, Houston, TX, United States
| | - Ahmed Aladhami
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Carole A Oskeritzian
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Amy Jolly
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Yan Chang
- College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, TX, United States
| | - Shuqian He
- College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, TX, United States
| | - Zui Pan
- College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, TX, United States
| | - Jason L Kubinak
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
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39
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Aggarwal V, Banday AZ, Jindal AK, Das J, Rawat A. Recent advances in elucidating the genetics of common variable immunodeficiency. Genes Dis 2019; 7:26-37. [PMID: 32181273 PMCID: PMC7063417 DOI: 10.1016/j.gendis.2019.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/19/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
Common variable immunodeficiency disorders (CVID), a heterogeneous group of inborn errors of immunity, is the most common symptomatic primary immunodeficiency disorder. Patients with CVID have highly variable clinical presentation. With the advent of whole genome sequencing and genome wide association studies (GWAS), there has been a remarkable improvement in understanding the genetics of CVID. This has also helped in understanding the pathogenesis of CVID and has drastically improved the management of these patients. A multi-omics approach integrating the DNA sequencing along with RNA sequencing, proteomics, epigenetic and metabolomics profile is the need of the hour to unravel specific CVID associated disease pathways and novel therapeutic targets. In this review, we elaborate various techniques that have helped in understanding the genetics of CVID.
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Affiliation(s)
- Vaishali Aggarwal
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aaqib Zaffar Banday
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ankur Kumar Jindal
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jhumki Das
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Rawat
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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40
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Abstract
Primary immunodeficiency diseases are a heterogeneous group of rare inherited disorders of innate or adaptive immune system function. Patients with primary immunodeficiencies typically present with recurrent and severe infections in infancy or young adulthood. More recently, the co-occurrence of autoimmune, benign lymphoproliferative, atopic, and malignant complications has been described. The diagnosis of a primary immunodeficiency disorder requires a thorough assessment of a patient's underlying immune system function. Historically, this has been accomplished at the time of symptomatic presentation by measuring immunoglobulins, complement components, protective antibody titers, or immune cell counts in the peripheral blood. Although these data can be used to critically assess the degree of immune dysregulation in the patient, this approach fall short in at least 2 regards. First, this assessment often occurs after the patient has suffered life-threatening infectious or autoinflammatory complications. Second, these data fail to uncover an underlying molecular cause of the patient's primary immune dysfunction, prohibiting the use of molecularly targeted therapeutic interventions. Within the last decade, the field of primary immunodeficiency diagnostics has been revolutionized by 2 major molecular advancements: (1) the onset of newborn screening in 2008, and (2) the onset of next-generation sequencing in 2010. In this article, the techniques of newborn screening and next-generation sequencing are reviewed and their respective impacts on the field of primary immunodeficiency disorders are discussed with a specific emphasis on severe combined immune deficiency and common variable immune deficiency.
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Affiliation(s)
- Jocelyn R Farmer
- Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, USA.
| | - Vinay S Mahajan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, USA
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41
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Focus on Chronic Variable Immunodeficiency for Primary Care Practitioners, the Gatekeepers to Optimal Health Outcomes for Primary Immunodeficiency Syndromes. CURRENT PEDIATRICS REPORTS 2019. [DOI: 10.1007/s40124-019-00202-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Abstract
Purpose of Review
This review sought to assess the extent and causes of suboptimal healthcare outcomes for chronic variable immunodeficiency (CVID).
Recent Findings
Significant improvements in diagnostic technology and treatment protocols over time were found, leading to reduced morbidity and mortality for those accessing therapies. Treatments continue to be largely non-curative with financing (mainly insurance coverage) an obstacle. Symptom recognition by primary care practitioners (PCP) remains a gating factor to treatment and a widespread and persistent barrier to optimal health outcomes.
Summary
CVID is a subtype of primary immunodeficiency (PIDD) associated with under-diagnosis. It has emerged as a health issue more prevalent than historically known. No symptom-recognition framework for early detection of CVID has been generally accepted; those proposed for primary immunodeficiencies have shown low sensitivity, low specificity or both. Positive trends in cases diagnosed have been aided by awareness campaigns and international collaborations. However, treatments for CVID will not realize full potential without effective, accepted frameworks for timely identification in the clinic.
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42
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Martínez-Cano J, Campos-Sánchez E, Cobaleda C. Epigenetic Priming in Immunodeficiencies. Front Cell Dev Biol 2019; 7:125. [PMID: 31355198 PMCID: PMC6635466 DOI: 10.3389/fcell.2019.00125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022] Open
Abstract
Immunodeficiencies (IDs) are disorders of the immune system that increase susceptibility to infections and cancer, and are therefore associated with elevated morbidity and mortality. IDs can be primary (not caused by other condition or exposure) or secondary due to the exposure to different agents (infections, chemicals, aging, etc.). Most primary immunodeficiencies (PIDs) are of genetic origin, caused by mutations affecting genes with key roles in the development or function of the cells of the immune system. A large percentage of PIDs are associated with a defective development and/or function of lymphocytes and, especially, B cells, the ones in charge of generating the different types of antibodies. B-cell development is a tightly regulated process in which many different factors participate. Among the regulators of B-cell differentiation, a correct epigenetic control of cellular identity is essential for normal cell function. With the advent of next-generation sequencing (NGS) techniques, more and more alterations in different types of epigenetic regulators are being described at the root of PIDs, both in humans and in animal models. At the same time, it is becoming increasingly clear that epigenetic alterations triggered by the exposure to environmental agents have a key role in the development of secondary immunodeficiencies (SIDs). Due to their largely reversible nature, epigenetic modifications are quickly becoming key therapeutic targets in other diseases where their contribution has been known for more time, like cancer. Here, we establish a parallelism between IDs and the nowadays accepted role of epigenetics in cancer initiation and progression, and propose that epigenetics forms a "third axis" (together with genetics and external agents) to be considered in the etiology of IDs, and linking PIDs and SIDs at the molecular level. We therefore postulate that IDs arise due to a variable contribution of (i) genetic, (ii) environmental, and (iii) epigenetic causes, which in fact form a continuum landscape of all possible combinations of these factors. Additionally, this implies the possibility of a fully epigenetically triggered mechanism for some IDs. This concept would have important prophylactic and translational implications, and would also imply a more blurred frontier between primary and secondary immunodeficiencies.
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Affiliation(s)
- Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid), Madrid, Spain
| | - Elena Campos-Sánchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid), Madrid, Spain
| | - César Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid), Madrid, Spain
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43
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Gupta S, Pattanaik D, Krishnaswamy G. Common Variable Immune Deficiency and Associated Complications. Chest 2019; 156:579-593. [PMID: 31128118 DOI: 10.1016/j.chest.2019.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/05/2019] [Accepted: 05/13/2019] [Indexed: 12/25/2022] Open
Abstract
Common variable immunodeficiency disorders refer to a relatively common primary immune deficiency group of diseases that present with infectious and inflammatory complications secondary to defects in antibody production and sometimes in cellular immunity. The disorder often presents in middle age or later with recurrent sinopulmonary infections, bronchiectasis, or a plethora of noninfectious complications such as autoimmune disorders, granulomatous interstitial lung disease, GI diseases, malignancies (including lymphoma), and multisystem granulomatous disease resembling sarcoidosis. Infusion of immunoglobulin by IV or subcutaneous is the mainstay of therapy. Management of complications is often difficult as immune suppression may be necessary in these conditions and entails the use of medications and biologicals which may further increase the risk for infections. Specifically, bronchiectasis, granulomatous lymphocytic interstitial lung disease, repeated sinopulmonary infections, and malignancies are sequelae of antibody deficiency that may present to the pulmonologist. This review will provide an updated understanding of the molecular aspects, differential diagnosis, presentations, and the management of common variable immunodeficiency disorders.
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Affiliation(s)
- Siddhi Gupta
- Department of Medicine, Division of Infectious Disease, Wake Forest School of Medicine, Winston Salem, NC
| | - Debendra Pattanaik
- Division of Allergy, Immunology and Rheumatology, University of Tennessee Health Science Center, Memphis TN
| | - Guha Krishnaswamy
- Department of Medicine, Division of Infectious Disease, Wake Forest School of Medicine, Winston Salem, NC; Division of Infectious Disease, Pulmonary, Allergy and Immunology, Wake Forest School of Medicine, Winston Salem, NC; Department of Medicine, Division of Allergy and Immunology, W.G. (Bill) Hefner VA Medical Center, Salisbury, NC.
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44
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Eskandarian Z, Fliegauf M, Bulashevska A, Proietti M, Hague R, Smulski CR, Schubert D, Warnatz K, Grimbacher B. Assessing the Functional Relevance of Variants in the IKAROS Family Zinc Finger Protein 1 ( IKZF1) in a Cohort of Patients With Primary Immunodeficiency. Front Immunol 2019; 10:568. [PMID: 31057532 PMCID: PMC6477086 DOI: 10.3389/fimmu.2019.00568] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/04/2019] [Indexed: 12/13/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency. Patients with CVID are prone to recurrent bacterial infection due to the failure of adequate immunoglobulin production. Monogenetic defects have been identified in ~25% of CVID patients. Recently, mutations in IKZF1, encoding the zinc-finger transcription factor IKAROS which is broadly expressed in hematopoietic cells, have been associated with a CVID-like phenotype. Herein we describe 11 patients with heterozygous IKZF1 variants from eight different families with autosomal dominant CVID and two siblings with an IKZF1 variant presenting with inflammatory bowel disease (IBD). This study shows that mutations affecting the DNA binding domain of IKAROS can impair the interaction with the target DNA sequence thereby preventing heterochromatin and pericentromeric localization (HC-PC) of the protein. Our results also indicate an impairment of pericentromeric localization of IKAROS by overexpression of a truncated variant, caused by an immature stop codon in IKZF1. We also describe an additional variant in TNFSF10, encoding Tumor Necrosis Factor Related Apoptosis Inducing Ligand (TRAIL), additionally presented in individuals of Family A. Our results indicate that this variant may impair the TRAIL-induced apoptosis in target cell lines and prohibit the NFκB activation by TRAIL and may act as a modifier in Family A.
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Affiliation(s)
- Zoya Eskandarian
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Manfred Fliegauf
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany
| | - Alla Bulashevska
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Michele Proietti
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Rosie Hague
- Royal Hospital for Children, Glasgow, United Kingdom
| | - Cristian Roberto Smulski
- Department of Medical Physics, Centro Atómico Bariloche, CONICET, San Carlos de Bariloche, Argentina
| | - Desirée Schubert
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Klaus Warnatz
- Clinic for Rheumatology and Clinical Immunology, Faculty of Medicine, CCI, Medical Center, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,Satellite Center Freiburg, RESIST-Cluster of Excellence 2155, Hanover Medical School, Freiburg, Germany.,Satellite Center Freiburg, German Center for Infection Research, Freiburg, Germany.,Institute of Immunity and Transplantation, Royal Free Hospital, University College London, London, United Kingdom
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45
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Shulzhenko N, Dong X, Vyshenska D, Greer RL, Gurung M, Vasquez-Perez S, Peremyslova E, Sosnovtsev S, Quezado M, Yao M, Montgomery-Recht K, Strober W, Fuss IJ, Morgun A. CVID enteropathy is characterized by exceeding low mucosal IgA levels and interferon-driven inflammation possibly related to the presence of a pathobiont. Clin Immunol 2018; 197:139-153. [PMID: 30240602 PMCID: PMC6289276 DOI: 10.1016/j.clim.2018.09.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/02/2018] [Accepted: 09/16/2018] [Indexed: 12/20/2022]
Abstract
Common variable immunodeficiency (CVID), the most common symptomatic primary antibody deficiency, is accompanied in some patients by a duodenal inflammation and malabsorption syndrome known as CVID enteropathy (E-CVID).The goal of this study was to investigate the immunological abnormalities in CVID patients that lead to enteropathy as well as the contribution of intestinal microbiota to this process.We found that, in contrast to noE-CVID patients (without enteropathy), E-CVID patients have exceedingly low levels of IgA in duodenal tissues. In addition, using transkingdom network analysis of the duodenal microbiome, we identified Acinetobacter baumannii as a candidate pathobiont in E-CVID. Finally, we found that E-CVID patients exhibit a pronounced activation of immune genes and down-regulation of epithelial lipid metabolism genes. We conclude that in the virtual absence of mucosal IgA, pathobionts such as A. baumannii, may induce inflammation that re-directs intestinal molecular pathways from lipid metabolism to immune processes responsible for enteropathy.
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Affiliation(s)
- Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.
| | - Xiaoxi Dong
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Dariia Vyshenska
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Renee L Greer
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Manoj Gurung
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | | | | | | | - Martha Quezado
- Surgical Pathology Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Michael Yao
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States; Washington DC VA Medical Center, Washington DC, United States
| | - Kim Montgomery-Recht
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States; Clinical Research Directorate/Clinical Monitoring Research Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute,United States
| | - Warren Strober
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States
| | - Ivan J Fuss
- Mucosal Immunity Section, NIAID, National Institutes of Health, Bethesda, MD, United States
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, United States.
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46
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Campos-Sanchez E, Martínez-Cano J, Del Pino Molina L, López-Granados E, Cobaleda C. Epigenetic Deregulation in Human Primary Immunodeficiencies. Trends Immunol 2018; 40:49-65. [PMID: 30509895 DOI: 10.1016/j.it.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are immune disorders resulting from defects in genes involved in immune regulation, and manifesting as an increased susceptibility to infections, autoimmunity, and cancer. However, the molecular basis of some prevalent entities remains poorly understood. Epigenetic control is essential for immune functions, and epigenetic alterations have been identified in different PIDs, including syndromes such as immunodeficiency-centromeric-instability-facial-anomalies, Kabuki, or Wolf-Hirschhorn, among others. Although the epigenetic changes may differ among these PIDs, the reversibility of epigenetic modifications suggests that they might become potential therapeutic targets. Here, we review recent mechanistic advances in our understanding of epigenetic alterations associated with certain PIDs, propose that a fully epigenetically driven mechanism might underlie some PIDs, and discuss the possible prophylactic and therapeutic implications.
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Affiliation(s)
- Elena Campos-Sanchez
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Jorge Martínez-Cano
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain; These authors contributed equally to this work
| | - Lucía Del Pino Molina
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, Hospital Universitario, La Paz Institute of Biomedical Research, 28046, Madrid, Spain; Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, 28046 Madrid, Spain.
| | - Cesar Cobaleda
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC/UAM, Madrid 28049, Spain.
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47
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van Schouwenburg PA, IJspeert H, Pico-Knijnenburg I, Dalm VASH, van Hagen PM, van Zessen D, Stubbs AP, Patel SY, van der Burg M. Identification of CVID Patients With Defects in Immune Repertoire Formation or Specification. Front Immunol 2018; 9:2545. [PMID: 30532750 PMCID: PMC6265514 DOI: 10.3389/fimmu.2018.02545] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/16/2018] [Indexed: 01/08/2023] Open
Abstract
Common variable immune deficiency disorder (CVID) is the most clinically relevant cause of antibody failure. It is a highly heterogeneous disease with different underlying etiologies. CVID has been associated with a quantitative B cell defect, however, little is known about the quality of B cells present. Here, we studied the naïve and antigen selected B-cell receptor (BCR) repertoire in 33 CVID patients using next generation sequencing, to investigate B cells quality. Analysis for each individual patient revealed whether they have a defect in immune repertoire formation [V(D)J recombination] or specification (somatic hypermutation, subclass distribution, or selection). The naïve BCR repertoire was normal in most of the patients, although alterations in repertoire diversity and the junctions were found in a limited number of patients indicating possible defects in early B-cell development or V(D)J recombination in these patients. In contrast, major differences were found in the antigen selected BCR repertoire. Here, most patients (15/17) showed a reduced frequency of somatic hypermutation (SHM), changes in subclass distribution and/or minor alterations in antigen selection. Together these data show that in our CVID cohort only a small number of patients have a defect in formation of the naïve BCR repertoire, whereas the clear majority of patients have disturbances in their antigen selected repertoire, suggesting a defect in repertoire specification in the germinal centers of these patients. This highlights that CVID patients not only have a quantitative B cell defect, but that also the quality of, especially post germinal center B cells, is impaired.
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Affiliation(s)
| | - Hanna IJspeert
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | | | - Virgil A S H Dalm
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Division of Clinical Immunology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - P Martin van Hagen
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Division of Clinical Immunology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - David van Zessen
- Clinical Bioinformatics Unit, Department of Pathology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Andrew P Stubbs
- Clinical Bioinformatics Unit, Department of Pathology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Smita Y Patel
- Nuffield Department of Clinical Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
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48
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Odnoletkova I, Kindle G, Quinti I, Grimbacher B, Knerr V, Gathmann B, Ehl S, Mahlaoui N, Van Wilder P, Bogaerts K, de Vries E. The burden of common variable immunodeficiency disorders: a retrospective analysis of the European Society for Immunodeficiency (ESID) registry data. Orphanet J Rare Dis 2018; 13:201. [PMID: 30419968 PMCID: PMC6233554 DOI: 10.1186/s13023-018-0941-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/22/2018] [Indexed: 01/15/2023] Open
Abstract
Background Common variable immunodeficiency disorders (CVID) are a group of rare innate disorders characterized by specific antibody deficiency and increased rates of infections, comorbidities and mortality. The burden of CVID in Europe has not been previously estimated. We performed a retrospective analysis of the European Society for Immunodeficiencies (ESID) registry data on the subset of patients classified by their immunologist as CVID and treated between 2004 and 2014. The registered deaths and comorbidities were used to calculate the annual average age-standardized rates of Years of Life Lost to premature death (YLL), Years Lost to Disability (YLD) and Disability Adjusted Life Years (DALY=YLL + YLD). These outcomes were expressed as a rate per 105 of the CVID cohort (the individual disease burden), and of the general population (the societal disease burden). Results Data of 2700 patients from 23 countries were analysed. Annual comorbidity rates: bronchiectasis, 21.9%; autoimmunity, 23.2%; digestive disorders, 15.6%; solid cancers, 5.5%; lymphoma, 3.8%, exceeded the prevalence in the general population by a factor of 34.0, 7.6, 8.1, 2.4 and 32.6, respectively. The comorbidities of CVID caused 8722 (6069; 12,363) YLD/105 in this cohort, whereas 44% of disability burden was attributable to infections and bronchiectasis. The total individual burden of CVID was 36,785 (33,078, 41,380) DALY/105. With estimated CVID prevalence of ~ 1/ 25,000, the societal burden of CVID ensued 1.5 (1.3, 1.7) DALY/105 of the general population. In exploratory analysis, increased mortality was associated with solid tumor, HR (95% CI): 2.69 (1.10; 6.57) p = 0.030, lymphoma: 5.48 (2.36; 12.71) p < .0001 and granulomatous-lymphocytic interstitial lung disease: 4.85 (1.63; 14.39) p = 0.005. Diagnostic delay (median: 4 years) was associated with a higher risk of death: 1.04 (1.02; 1.06) p = .0003, bronchiectasis: 1.03 (1.01; 1.04) p = .0001, solid tumor: 1.08 (1.04; 1.11) p < .0001 and enteropathy: 1.02 (1.00; 1.05) p = .0447 and stayed unchanged over four decades (p = .228). Conclusions While the societal burden of CVID may seem moderate, it is severe to the individual patient. Delay in CVID diagnosis may constitute a modifiable risk factor of serious comorbidities and death but showed no improvement. Tools supporting timely CVID diagnosis should be developed with high priority. Electronic supplementary material The online version of this article (10.1186/s13023-018-0941-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irina Odnoletkova
- Plasma Protein Therapeutics Association, Boulevard Brand Whitlock 114b4, 1200, Brussels, Belgium. .,Faculty of Medicine and Health Sciences, Ghent University, C. Heymanslaan 10, 9000, Ghent, Belgium. .,Centre de recherche en Economie de la Santé, Gestion des Institutions de Soins et Sciences Infirmières, Ecole de Santé Publique, University of Brussels (ULB), Brussels, Belgium.
| | - Gerhard Kindle
- The ESID Registry Working Party.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.,University Hospital Policlinico Umberto I, Rome, Italy
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Immunology and Transplantation, Royal Free Hospital, University College London, London, UK
| | - Viviane Knerr
- The ESID Registry Working Party.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Benjamin Gathmann
- The ESID Registry Working Party.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Ehl
- The ESID Registry Working Party.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nizar Mahlaoui
- French National Reference Center for Primary Immune Deficiencies (CEREDIH) and Pediatric Immuno-Haematology and Rheumatology Unit Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM UMR 1163, Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris, France
| | - Philippe Van Wilder
- Centre de recherche en Economie de la Santé, Gestion des Institutions de Soins et Sciences Infirmières, Ecole de Santé Publique, University of Brussels (ULB), Brussels, Belgium
| | - Kris Bogaerts
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), KU Leuven - University of Leuven, I-BioStat, 3000, Leuven, Belgium.,University Hasselt, I-BioStat, 3500, Hasselt, Belgium
| | - Esther de Vries
- Department Tranzo, Tilburg University, PO Box 90153 (RP219), 5000 LE, Tilburg, the Netherlands.,Laboratory for Microbiology and Immunology, Elisabeth Tweesteden Hospital, PO Box 90151 (route 90), 5000LC, Tilburg, the Netherlands
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Tuijnenburg P, Lango Allen H, Burns SO, Greene D, Jansen MH, Staples E, Stephens J, Carss KJ, Biasci D, Baxendale H, Thomas M, Chandra A, Kiani-Alikhan S, Longhurst HJ, Seneviratne SL, Oksenhendler E, Simeoni I, de Bree GJ, Tool ATJ, van Leeuwen EMM, Ebberink EHTM, Meijer AB, Tuna S, Whitehorn D, Brown M, Turro E, Thrasher AJ, Smith KGC, Thaventhiran JE, Kuijpers TW. Loss-of-function nuclear factor κB subunit 1 (NFKB1) variants are the most common monogenic cause of common variable immunodeficiency in Europeans. J Allergy Clin Immunol 2018; 142:1285-1296. [PMID: 29477724 PMCID: PMC6148345 DOI: 10.1016/j.jaci.2018.01.039] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 12/15/2017] [Accepted: 01/03/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND The genetic cause of primary immunodeficiency disease (PID) carries prognostic information. OBJECTIVE We conducted a whole-genome sequencing study assessing a large proportion of the NIHR BioResource-Rare Diseases cohort. METHODS In the predominantly European study population of principally sporadic unrelated PID cases (n = 846), a novel Bayesian method identified nuclear factor κB subunit 1 (NFKB1) as one of the genes most strongly associated with PID, and the association was explained by 16 novel heterozygous truncating, missense, and gene deletion variants. This accounted for 4% of common variable immunodeficiency (CVID) cases (n = 390) in the cohort. Amino acid substitutions predicted to be pathogenic were assessed by means of analysis of structural protein data. Immunophenotyping, immunoblotting, and ex vivo stimulation of lymphocytes determined the functional effects of these variants. Detailed clinical and pedigree information was collected for genotype-phenotype cosegregation analyses. RESULTS Both sporadic and familial cases demonstrated evidence of the noninfective complications of CVID, including massive lymphadenopathy (24%), unexplained splenomegaly (48%), and autoimmune disease (48%), features prior studies correlated with worse clinical prognosis. Although partial penetrance of clinical symptoms was noted in certain pedigrees, all carriers have a deficiency in B-lymphocyte differentiation. Detailed assessment of B-lymphocyte numbers, phenotype, and function identifies the presence of an increased CD21low B-cell population. Combined with identification of the disease-causing variant, this distinguishes between healthy subjects, asymptomatic carriers, and clinically affected cases. CONCLUSION We show that heterozygous loss-of-function variants in NFKB1 are the most common known monogenic cause of CVID, which results in a temporally progressive defect in the formation of immunoglobulin-producing B cells.
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Affiliation(s)
- Paul Tuijnenburg
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands; Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - Hana Lango Allen
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Siobhan O Burns
- Department of Immunology, Royal Free London NHS Foundation Trust, University College London Institute of Immunity and Transplantation, London, United Kingdom
| | - Daniel Greene
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Machiel H Jansen
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands; Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - Emily Staples
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Stephens
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Keren J Carss
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Daniele Biasci
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Helen Baxendale
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Moira Thomas
- Department of Immunology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Anita Chandra
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sorena Kiani-Alikhan
- Department of Immunology, Royal Surrey County Hospital, Guildford, United Kingdom
| | - Hilary J Longhurst
- Department of Immunology, Barts Health NHS Trust, London, United Kingdom
| | - Suranjith L Seneviratne
- Department of Immunology, Royal Free London NHS Foundation Trust, University College London Institute of Immunity and Transplantation, London, United Kingdom
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Ilenia Simeoni
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Godelieve J de Bree
- Department of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Anton T J Tool
- Department of Blood Cell Research, Sanquin Research, Amsterdam, The Netherlands
| | - Ester M M van Leeuwen
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Alexander B Meijer
- Department of Plasma Proteins, Sanquin Research, Amsterdam, The Netherlands
| | - Salih Tuna
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Deborah Whitehorn
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Matthew Brown
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; NHS Blood and Transplant Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Adrian J Thrasher
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust London, London, United Kingdom
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands; Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands; Department of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands.
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Hehir-Kwa JY, Tops BBJ, Kemmeren P. The clinical implementation of copy number detection in the age of next-generation sequencing. Expert Rev Mol Diagn 2018; 18:907-915. [PMID: 30221560 DOI: 10.1080/14737159.2018.1523723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The role of copy number variants (CNVs) in disease is now well established. In parallel NGS technologies, such as long-read technologies, there is continual development and data analysis methods continue to be refined. Clinical exome sequencing data is now a reality for many diagnostic laboratories in both congenital genetics and oncology. This provides the ability to detect and report both SNVs and structural variants, including CNVs, using a single assay for a wide range of patient cohorts. Areas covered: Currently, whole-genome sequencing is mainly restricted to research applications and clinical utility studies. Furthermore, detecting the full-size spectrum of CNVs as well as somatic events remains difficult for both exome and whole-genome sequencing. As a result, the full extent of genomic variants in an individual's genome is still largely unknown. Recently, new sequencing technologies have been introduced which maintain the long-range genomic context, aiding the detection of CNVs and structural variants. Expert commentary: The development of long-read sequencing promises to resolve many CNV and SV detection issues but is yet to become established. The current challenge for clinical CNV detection is how to fully exploit all the data which is generated by high throughput sequencing technologies.
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Affiliation(s)
- Jayne Y Hehir-Kwa
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Bastiaan B J Tops
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Patrick Kemmeren
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
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