1
|
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.
Collapse
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
| |
Collapse
|
2
|
Ameratunga R, Edwards ESJ, Lehnert K, Leung E, Woon ST, Lea E, Allan C, Chan L, Steele R, Longhurst H, Bryant VL. The Rapidly Expanding Genetic Spectrum of Common Variable Immunodeficiency-Like Disorders. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:1646-1664. [PMID: 36796510 DOI: 10.1016/j.jaip.2023.01.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 02/16/2023]
Abstract
The understanding of common variable immunodeficiency disorders (CVID) is in evolution. CVID was previously a diagnosis of exclusion. New diagnostic criteria have allowed the disorder to be identified with greater precision. With the advent of next-generation sequencing (NGS), it has become apparent that an increasing number of patients with a CVID phenotype have a causative genetic variant. If a pathogenic variant is identified, these patients are removed from the overarching diagnosis of CVID and are deemed to have a CVID-like disorder. In populations where consanguinity is more prevalent, the majority of patients with severe primary hypogammaglobulinemia will have an underlying inborn error of immunity, usually an early-onset autosomal recessive disorder. In nonconsanguineous societies, pathogenic variants are identified in approximately 20% to 30% of patients. These are often autosomal dominant mutations with variable penetrance and expressivity. To add to the complexity of CVID and CVID-like disorders, some genetic variants such as those in TNFSF13B (transmembrane activator calcium modulator cyclophilin ligand interactor) predispose to, or enhance, disease severity. These variants are not causative but can have epistatic (synergistic) interactions with more deleterious mutations to worsen disease severity. This review is a description of the current understanding of genes associated with CVID and CVID-like disorders. This information will assist clinicians in interpreting NGS reports when investigating the genetic basis of disease in patients with a CVID phenotype.
Collapse
Affiliation(s)
- Rohan Ameratunga
- Department of Clinical immunology, Auckland Hospital, Auckland, New Zealand; Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
| | - Emily S J Edwards
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, and Allergy and Clinical Immunology Laboratory, Department of Immunology, Monash University, Melbourne, VIC, Australia
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand
| | - Edward Lea
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand
| | - Caroline Allan
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand
| | - Lydia Chan
- Department of Clinical immunology, Auckland Hospital, Auckland, New Zealand
| | - Richard Steele
- Department of Virology and Immunology, Auckland Hospital, Auckland, New Zealand; Department of Respiratory Medicine, Wellington Hospital, Wellington, New Zealand
| | - Hilary Longhurst
- Department of Medicine, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Vanessa L Bryant
- Department of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Department of Clinical Immunology and Allergy, Royal Melbourne Hospital, Parkville, VIC, Australia
| |
Collapse
|
3
|
Yazdanpanah N, Rezaei N. Autoimmune disorders associated with common variable immunodeficiency: prediction, diagnosis, and treatment. Expert Rev Clin Immunol 2022; 18:1265-1283. [PMID: 36197300 DOI: 10.1080/1744666x.2022.2132938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency. Due to the wide spectrum of the CVID manifestations, the differential diagnosis becomes complicated, ends in a diagnostic delay and increased morbidity and mortality rates. Autoimmunity is one of the important complications associated with CVID. While immunoglobulin replacement therapy has considerably decreased the mortality rate in CVID patients, mainly infection-related mortality, other complications such as autoimmunity appeared prevalent and, in some cases, life threatening. AREAS COVERED In this article, genetics, responsible immune defects, autoimmune manifestations in different organs, and the diagnosis and treatment processes in CVID patients are reviewed, after searching the literature about these topics. EXPERT OPINION Considering the many phenotypes of CVID and the fact that it remained undiagnosed until older ages, it is important to include various manifestations of CVID in the differential diagnosis. Due to the different manifestations of CVID, including autoimmune diseases, interdisciplinary collaboration of physicians from different fields is highly recommended, as discussed in the manuscript. Meanwhile, it is important to determine which patients could benefit from genetic diagnostic studies since such studies are not necessary for establishing the diagnosis of CVID.
Collapse
Affiliation(s)
- Niloufar Yazdanpanah
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
4
|
"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.
Collapse
|
5
|
Karimi E, Mahmoudian F, Reyes SOL, Bargir UA, Madkaikar M, Artac H, Sabzevari A, Lu N, Azizi G, Abolhassani H. Approach to genetic diagnosis of inborn errors of immunity through next-generation sequencing. Mol Immunol 2021; 137:57-66. [PMID: 34216999 DOI: 10.1016/j.molimm.2021.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 01/02/2023]
Abstract
Patients with inborn errors of immunity (IEI) present with a heterogeneous clinical and immunological phenotype, therefore a correct molecular diagnosis is crucial for the classification and subsequent therapeutic management. On the other hand, IEI are a group of rare congenital diseases with highly diverse features and, in most cases, an as yet unknown genetic etiology. Next generation sequencing has facilitated genetic examinations of rare inherited disorders during the recent years, thus allowing a suitable molecular diagnosis in the IEI patients. This review aimed to investigate the current findings about these techniques in the field of IEI, suggesting an efficient stepwise approach to molecular diagnosis of inborn errors of immunity.
Collapse
Affiliation(s)
- Esmat Karimi
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, 85721, USA; Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran
| | - Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saul O Lugo Reyes
- Immune Deficiencies Lab, National Institute of Pediatrics, Mexico City, Mexico
| | - Umair Ahmed Bargir
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Manisha Madkaikar
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Faculty of Medicine, Selcuk University, Konya, Turkey
| | - Araz Sabzevari
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Na Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Division of Clinical Immunology, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
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
| |
Collapse
|
9
|
Pfeiffer D, Chen B, Schlicht K, Ginsbach P, Abboud S, Bersano A, Bevan S, Brandt T, Caso V, Debette S, Erhart P, Freitag-Wolf S, Giacalone G, Grau AJ, Hayani E, Jern C, Jiménez-Conde J, Kloss M, Krawczak M, Lee JM, Lemmens R, Leys D, Lichy C, Maguire JM, Martin JJ, Metso AJ, Metso TM, Mitchell BD, Pezzini A, Rosand J, Rost NS, Stenman M, Tatlisumak T, Thijs V, Touzé E, Traenka C, Werner I, Woo D, Del Zotto E, Engelter ST, Kittner SJ, Cole JW, Grond-Ginsbach C, Lyrer PA, Lindgren A. Genetic Imbalance Is Associated With Functional Outcome After Ischemic Stroke. Stroke 2019; 50:298-304. [PMID: 30661490 DOI: 10.1161/strokeaha.118.021856] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background and Purpose- We sought to explore the effect of genetic imbalance on functional outcome after ischemic stroke (IS). Methods- Copy number variation was identified in high-density single-nucleotide polymorphism microarray data of IS patients from the CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) and SiGN (Stroke Genetics Network)/GISCOME (Genetics of Ischaemic Stroke Functional Outcome) networks. Genetic imbalance, defined as total number of protein-coding genes affected by copy number variations in an individual, was compared between patients with favorable (modified Rankin Scale score of 0-2) and unfavorable (modified Rankin Scale score of ≥3) outcome after 3 months. Subgroup analyses were confined to patients with imbalance affecting ohnologs-a class of dose-sensitive genes, or to those with imbalance not affecting ohnologs. The association of imbalance with outcome was analyzed by logistic regression analysis, adjusted for age, sex, stroke subtype, stroke severity, and ancestry. Results- The study sample comprised 816 CADISP patients (age 44.2±10.3 years) and 2498 SiGN/GISCOME patients (age 67.7±14.2 years). Outcome was unfavorable in 122 CADISP and 889 SiGN/GISCOME patients. Multivariate logistic regression analysis revealed that increased genetic imbalance was associated with less favorable outcome in both samples (CADISP: P=0.0007; odds ratio=0.89; 95% CI, 0.82-0.95 and SiGN/GISCOME: P=0.0036; odds ratio=0.94; 95% CI, 0.91-0.98). The association was independent of age, sex, stroke severity on admission, stroke subtype, and ancestry. On subgroup analysis, imbalance affecting ohnologs was associated with outcome (CADISP: odds ratio=0.88; 95% CI, 0.80-0.95 and SiGN/GISCOME: odds ratio=0.93; 95% CI, 0.89-0.98) whereas imbalance without ohnologs lacked such an association. Conclusions- Increased genetic imbalance was associated with poorer functional outcome after IS in both study populations. Subgroup analysis revealed that this association was driven by presence of ohnologs in the respective copy number variations, suggesting a causal role of the deleterious effects of genetic imbalance.
Collapse
Affiliation(s)
- Dorothea Pfeiffer
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Bowang Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China (B.C.)
| | - Kristina Schlicht
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Philip Ginsbach
- School of Informatics, University of Edinburgh, United Kingdom (P.G.)
| | - Sherine Abboud
- Laboratory of Experimental Neurology, Université Libre de Bruxelles, Brussels, Belgium (S.A.)
| | - Anna Bersano
- Cerebrovascular Unit IRCCS Foundation C. Besta Neurological Institute, Milan, Italy (A.B.)
| | - Steve Bevan
- School of Life Science, University of Lincoln, United Kingdom (S.B.)
| | - Tobias Brandt
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.).,Suva/Swiss National Accident Insurance Fund, Lucerne, Switzerland (T.B.)
| | - Valeria Caso
- Stroke Unit, Perugia University Hospital, Italy (V.C.)
| | - Stéphanie Debette
- Inserm, Bordeaux Population Health Research Center, UMR 1219, University of Bordeaux, France (S.D.).,Department of Neurology, Bordeaux University Hospital, France (S.D.)
| | - Philipp Erhart
- Department of Vascular and Endovascular Surgery, University Hospital Heidelberg, Germany (P.E.)
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Giacomo Giacalone
- Department of Neurology, San Raffaele University Hospital, Milan, Italy (G.G.)
| | - Armin J Grau
- Department of Neurology, Klinikum Ludwigshafen, Germany (A.J.G.)
| | - Eyad Hayani
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Christina Jern
- The Sahlgrenska Academy, University of Gothenburg, Sweden (C.J.).,Sahlgrenska University Hospital, Sweden (C.J.)
| | | | - Manja Kloss
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein Campus Kiel, Germany (K.S., S.F.-W., M. Krawczak)
| | - Jin-Moo Lee
- Department of Neurology, Washington University School of Medicine, St Louis, MO (J.-M.L.)
| | - Robin Lemmens
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute, KU Leuven, University of Leuven, Belgium (R.L.).,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium (R.L.).,Department of Neurology, University Hospitals Leuven, Belgium (R.L.)
| | - Didier Leys
- Department of Neurology, University of Lille, France (D.L.)
| | | | - Jane M Maguire
- Faculty of Health, University of Technology Sydney, Australia (J.M.M.).,Hunter Medical Research Institute, Priority Research Centre for Stroke and Traumatic Brain Injury, University of Newcastle, Australia (J.M.M.)
| | - Juan J Martin
- Department of Neurology, Sanatorio Allende, Cordoba, Argentina (J.J.M.)
| | - Antti J Metso
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.)
| | - Tiina M Metso
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.)
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore (B.D.M.).,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD (B.D.M.)
| | - Alessandro Pezzini
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Italy (A.P., E.D.Z.)
| | - Jonathan Rosand
- Center for Genomic Medicine (J.R.), Massachusetts General Hospital, Boston
| | - Natalia S Rost
- Department of Neurology (N.S.R.), Massachusetts General Hospital, Boston
| | - Martin Stenman
- Department of Clinical Sciences Lund, Neurology, Lund University, Sweden (M.S., A.L.).,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden (M.S., A.L.)
| | - Turgut Tatlisumak
- Department of Neurology, Helsinki University Central Hospital, Finland (A.J.M., T.M.M., T.T.).,Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Sweden (T.T.).,Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden (T.T.)
| | - Vincent Thijs
- Stroke Division, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Heidelberg, Victoria, Australia (V.T.).,Department of Neurology, Austin Health, Heidelberg, Victoria, Australia (V.T.)
| | - Emmanuel Touzé
- Paris Descartes University, INSERM UMR S894, Department of Neurology, Sainte-Anne Hospital, Paris, France (E.T.).,Normandie Université, Université Caen-Normandie, Inserm U1237, CHU Côte de Nacre, Service de Neurologie, Caen, France (E.T.)
| | - Christopher Traenka
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.)
| | - Inge Werner
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Daniel Woo
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, OH (D.W.)
| | - Elisabetta Del Zotto
- Department of Clinical and Experimental Sciences, Neurology Clinic, University of Brescia, Italy (A.P., E.D.Z.)
| | - Stefan T Engelter
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.).,Neurorehabilitation Unit, University of Basel, Switzerland (S.T.E.).,University Center for Medicine of Aging, Felix Platter Hospital, Basel, Switzerland (S.T.E.)
| | - Steven J Kittner
- Department of Neurology, Veterans Affairs Medical Center, Baltimore, MD (S.J.K., J.W.C.); and Department of Neurology University of Maryland School of Medicine, Baltimore (S.J.K., J.W.C.)
| | - John W Cole
- Department of Neurology, Veterans Affairs Medical Center, Baltimore, MD (S.J.K., J.W.C.); and Department of Neurology University of Maryland School of Medicine, Baltimore (S.J.K., J.W.C.)
| | - Caspar Grond-Ginsbach
- From the Department of Neurology, Heidelberg University Hospital, Germany (D.P., T.B., E.H., M. Kloss, I.W., C.G.-G.)
| | - Philippe A Lyrer
- Department of Neurology and Stroke Center, University Hospital Basel, Switzerland (C.T., S.T.E., P.A.L.)
| | - Arne Lindgren
- Department of Clinical Sciences Lund, Neurology, Lund University, Sweden (M.S., A.L.).,Department of Neurology and Rehabilitation Medicine, Skåne University Hospital, Lund, Sweden (M.S., A.L.)
| | | |
Collapse
|
10
|
de Valles-Ibáñez G, Esteve-Solé A, Piquer M, González-Navarro EA, Hernandez-Rodriguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez Á, Martín-Nalda A, Martínez-Gallo M, García-Prat M, Del Pino-Molina L, Cuscó I, Codina-Solà M, Batlle-Masó L, Solís-Moruno M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobran R, Yagüe J, Alsina L, Juan M, Casals F. Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond. Front Immunol 2018; 9:636. [PMID: 29867916 PMCID: PMC5960686 DOI: 10.3389/fimmu.2018.00636] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2018] [Indexed: 12/16/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency characterized by recurrent infections, hypogammaglobulinemia and poor response to vaccines. Its diagnosis is made based on clinical and immunological criteria, after exclusion of other diseases that can cause similar phenotypes. Currently, less than 20% of cases of CVID have a known underlying genetic cause. We have analyzed whole-exome sequencing and copy number variants data of 36 children and adolescents diagnosed with CVID and healthy relatives to estimate the proportion of monogenic cases. We have replicated an association of CVID to p.C104R in TNFRSF13B and reported the second case of homozygous patient to date. Our results also identify five causative genetic variants in LRBA, CTLA4, NFKB1, and PIK3R1, as well as other very likely causative variants in PRKCD, MAPK8, or DOCK8 among others. We experimentally validate the effect of the LRBA stop-gain mutation which abolishes protein production and downregulates the expression of CTLA4, and of the frameshift indel in CTLA4 producing expression downregulation of the protein. Our results indicate a monogenic origin of at least 15–24% of the CVID cases included in the study. The proportion of monogenic patients seems to be lower in CVID than in other PID that have also been analyzed by whole exome or targeted gene panels sequencing. Regardless of the exact proportion of CVID monogenic cases, other genetic models have to be considered for CVID. We propose that because of its prevalence and other features as intermediate penetrancies and phenotypic variation within families, CVID could fit with other more complex genetic scenarios. In particular, in this work, we explore the possibility of CVID being originated by an oligogenic model with the presence of heterozygous mutations in interacting proteins or by the accumulation of detrimental variants in particular immunological pathways, as well as perform association tests to detect association with rare genetic functional variation in the CVID cohort compared to healthy controls.
Collapse
Affiliation(s)
- Guillem de Valles-Ibáñez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ana Esteve-Solé
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Mònica Piquer
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - E Azucena González-Navarro
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Bioinformatics Studies, ESCI-UPF, Barcelona, Spain
| | - Eva González-Roca
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ana María Plaza-Martin
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Ángela Deyà-Martínez
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina García-Prat
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Lucía Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Ivón Cuscó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Marta Codina-Solà
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Laura Batlle-Masó
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Manuel Solís-Moruno
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Juan Ignacio Aróstegui
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Manel Juan
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| |
Collapse
|
11
|
Heimall JR, Hagin D, Hajjar J, Henrickson SE, Hernandez-Trujillo HS, Tan Y, Kobrynski L, Paris K, Torgerson TR, Verbsky JW, Wasserman RL, Hsieh EWY, Blessing JJ, Chou JS, Lawrence MG, Marsh RA, Rosenzweig SD, Orange JS, Abraham RS. Use of Genetic Testing for Primary Immunodeficiency Patients. J Clin Immunol 2018; 38:320-329. [PMID: 29675737 DOI: 10.1007/s10875-018-0489-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/16/2018] [Indexed: 12/11/2022]
Abstract
Genetic testing plays a critical role in diagnosis for many primary immunodeficiency diseases. The goals of this report are to outline some of the challenges that clinical immunologists face routinely in the use of genetic testing for patient care. In addition, we provide a review of the types of genetic testing used in the diagnosis of PID, including their strengths and limitations. We describe the strengths and limitations of different genetic testing approaches for specific clinical contexts that raise concern for specific PID disorders in light of the challenges reported by the clinical immunologist members of the CIS in a recent membership survey. Finally, we delineate the CIS's recommendations for the use of genetic testing in light of these issues.
Collapse
Affiliation(s)
- Jennifer R Heimall
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, University of Pennsylvania, Wood Building 3rd Floor, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - David Hagin
- Allergy and Immunology Division, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Joud Hajjar
- Department of Pediatrics, Section of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX, USA
| | - Sarah E Henrickson
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, University of Pennsylvania, Wood Building 3rd Floor, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Wherry Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Hillary S Hernandez-Trujillo
- Division of Infectious Disease & Immunology, Connecticut Children's Medical Center, Hartford, CT, USA
- CT Asthma and Allergy Center, West Hartford, CT, USA
| | - Yuval Tan
- The Charles Bronfman Institute of Personalized Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kenneth Paris
- Division of Allergy-Immunology, LSU Health Sciences Center, Children's Hospital, New Orleans, LA, USA
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James W Verbsky
- Pediatrics and Microbiology and Molecular Genetics Section of Pediatric Rheumatology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Elena W Y Hsieh
- Department of Immunology and Microbiology, Department of Pediatrics, Division of Allergy and Immunology, University of Colorado, School of Medicine, Aurora, CO, USA
| | - Jack J Blessing
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Janet S Chou
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Monica G Lawrence
- Division of Asthma, Allergy and Clinical Immunology, University of Virginia Health System, Charlottesville, VA, USA
| | - Rebecca A Marsh
- Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Jordan S Orange
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
12
|
Richardson AM, Moyer AM, Hasadsri L, Abraham RS. Diagnostic Tools for Inborn Errors of Human Immunity (Primary Immunodeficiencies and Immune Dysregulatory Diseases). Curr Allergy Asthma Rep 2018; 18:19. [PMID: 29470720 DOI: 10.1007/s11882-018-0770-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an overview of diagnostic testing in primary immunodeficiency and immune dysregulatory disorders (PIDDs), particularly focusing on flow cytometry and genetic techniques, utilizing specific examples of PIDDs. RECENT FINDINGS Flow cytometry remains a vital tool in the diagnosis and monitoring of immunological diseases. Its utility ranges from cellular analysis and specific protein quantitation to functional assays and signaling pathway analysis. Mass cytometry combines flow cytometry and mass spectrometry to dramatically increase the throughput of multivariate single-cell analysis. Next-generation sequencing in combination with other molecular techniques and processing algorithms has become more widely available and identified the diverse and heterogeneous genetic underpinnings of these disorders. As the spectrum of disease is further clarified by increasing immunological, genetic, and epigenetic knowledge, the careful application of these diagnostic tools and bioinformatics will assist not only in our understanding of these complex disorders, but also enable the implementation of personalized therapeutic approaches for disease management.
Collapse
Affiliation(s)
- Annely M Richardson
- Division of Allergic Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.
| |
Collapse
|
13
|
Kienzler AK, Hargreaves CE, Patel SY. The role of genomics in common variable immunodeficiency disorders. Clin Exp Immunol 2017; 188:326-332. [PMID: 28236292 DOI: 10.1111/cei.12947] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2017] [Indexed: 01/16/2023] Open
Abstract
The advent of next-generation sequencing (NGS) and 'omic' technologies has revolutionized the field of genetics, and its implementation in health care has the potential to realize precision medicine. Primary immunodeficiencies (PID) are a group of rare diseases which have benefited from NGS, with a massive increase in causative genes identified in the past few years. Common variable immunodeficiency disorders (CVID) are a heterogeneous form of PID and the most common form of antibody failure in children and adults. While a monogenic cause of disease has been identified in a small subset of CVID patients, a genomewide association study and whole genome sequencing have found that, in the majority, a polygenic cause is likely. Other NGS technologies such as RNA sequencing and epigenetic studies have contributed further to our understanding of the contribution of altered gene expression in CVID pathogenesis. We believe that to unravel further the complexities of CVID, a multi-omic approach, combining DNA sequencing with gene expression, methylation, proteomic and metabolomics data, will be essential to identify novel disease-associated pathways and therapeutic targets.
Collapse
Affiliation(s)
- A-K Kienzler
- NIHR Oxford Biomedical Research Centre, Clinical Immunology Group, Oxford, UK
| | - C E Hargreaves
- NIHR Oxford Biomedical Research Centre, Clinical Immunology Group, Oxford, UK
| | - S Y Patel
- NIHR Oxford Biomedical Research Centre, Clinical Immunology Group, Oxford, UK
| |
Collapse
|
14
|
Indications to Epigenetic Dysfunction in the Pathogenesis of Common Variable Immunodeficiency. Arch Immunol Ther Exp (Warsz) 2016; 65:101-110. [DOI: 10.1007/s00005-016-0414-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/10/2016] [Indexed: 12/12/2022]
|
15
|
Understanding the genetic and epigenetic basis of common variable immunodeficiency disorder through omics approaches. Biochim Biophys Acta Gen Subj 2016; 1860:2656-63. [PMID: 27316315 DOI: 10.1016/j.bbagen.2016.06.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/26/2016] [Accepted: 06/09/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND Common variable immunodeficiency disorder (CVID) is the most frequently encountered symptomatic primary immunodeficiency, characterized by highly heterogeneous immunological features and clinical presentations. As better targeted therapies are importantly needed for CVID, improved understanding of the genetic and epigenetic basis for the development of CVID presents the most promising venue for improvement. SCOPE OF REVIEW Several genomic and epigenomic studies of CVID have recently been carried out on cohorts of sporadic cases of CVID. Using high-throughput array and sequencing technologies, these studies identified several loci associated with the disease. Here, we review the omics approaches used in these studies and resulting discoveries. We also discuss how these findings lead to improved understanding of the molecular basis of CVID and possible future directions to pursue. MAJOR CONCLUSIONS High-throughput omics approaches have been productive in genetic and epigenetic studies of CVID, leading to the identifications of several significantly associated loci of different variant types, as well as genes and pathways elucidating the shared genetic basis of CVID and autoimmunity. Complex polygenic model of inheritance together with interplay between genetic components and environmental factors may account for the etiology of CVID and various associated comorbidities. GENERAL SIGNIFICANCE The genetic and epigenetic basis of CVID when further translated through functional studies will allow for improved understanding of the CVID etiology and will provide new insights into the development of potential new therapeutic approaches for this devastating condition. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
Collapse
|
16
|
Mlynarski EE, Xie M, Taylor D, Sheridan MB, Guo T, Racedo SE, McDonald-McGinn DM, Chow EWC, Vorstman J, Swillen A, Devriendt K, Breckpot J, Digilio MC, Marino B, Dallapiccola B, Philip N, Simon TJ, Roberts AE, Piotrowicz M, Bearden CE, Eliez S, Gothelf D, Coleman K, Kates WR, Devoto M, Zackai E, Heine-Suñer D, Goldmuntz E, Bassett AS, Morrow BE, Emanuel BS. Rare copy number variants and congenital heart defects in the 22q11.2 deletion syndrome. Hum Genet 2016; 135:273-85. [PMID: 26742502 DOI: 10.1007/s00439-015-1623-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022]
Abstract
The 22q11.2 deletion syndrome (22q11DS; velocardiofacial/DiGeorge syndrome; VCFS/DGS; MIM #192430; 188400) is the most common microdeletion syndrome. The phenotypic presentation of 22q11DS is highly variable; approximately 60-75 % of 22q11DS patients have been reported to have a congenital heart defect (CHD), mostly of the conotruncal type, and/or aortic arch defect. The etiology of the cardiac phenotypic variability is not currently known for the majority of patients. We hypothesized that rare copy number variants (CNVs) outside the 22q11.2 deleted region may modify the risk of being born with a CHD in this sensitized population. Rare CNV analysis was performed using Affymetrix SNP Array 6.0 data from 946 22q11DS subjects with CHDs (n = 607) or with normal cardiac anatomy (n = 339). Although there was no significant difference in the overall burden of rare CNVs, an overabundance of CNVs affecting cardiac-related genes was detected in 22q11DS individuals with CHDs. When the rare CNVs were examined with regard to gene interactions, specific cardiac networks, such as Wnt signaling, appear to be overrepresented in 22q11DS CHD cases but not 22q11DS controls with a normal heart. Collectively, these data suggest that CNVs outside the 22q11.2 region may contain genes that modify risk for CHDs in some 22q11DS patients.
Collapse
Affiliation(s)
- Elisabeth E Mlynarski
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Molly B Sheridan
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Silvia E Racedo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eva W C Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Jacob Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584, Utrecht, The Netherlands
| | - Ann Swillen
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | | | - Bruno Marino
- Lorillard Spencer Cenci Foundation and Department of Pediatrics, La Sapienza University of Rome, 00165, Rome, Italy
| | | | - Nicole Philip
- Department of Medical Genetics, Timone Children's Hospital, AP-HM and University of Mediterranee, 13005, Marseille, France
| | - Tony J Simon
- Department of Psychiatry and Behavioral Sciences, M.I.N.D. Institute, University of California, Sacramento, CA, 95817, USA
| | - Amy E Roberts
- Department of Cardiology and Division of Genetics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Małgorzata Piotrowicz
- Department of Genetics, Research Institute, Polish Mother's Memorial Hospital, 93-338, Lodz, Poland
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA
| | - Stephan Eliez
- Office Médico- Pédagogique Research Unit, Department of Psychiatry, University of Geneva School of Medicine, 1211, Geneva 8, Switzerland
| | - Doron Gothelf
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, 52621, Tel Aviv, Israel
| | - Karlene Coleman
- Marcus Autism Center, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, and Program in Neuroscience, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Molecular Medicine, University of Rome La Sapienza, 00185, Rome, Italy
| | - Elaine Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Damian Heine-Suñer
- Genetics Department, Hospital Universitari Son Espases, 07020, Palma de Mallorca, Spain
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | | |
Collapse
|
17
|
Anzilotti C, Kienzler AK, Lopez-Granados E, Gooding S, Davies B, Pandit H, Lucas M, Price A, Littlewood T, van der Burg M, Patel SY, Chapel H. Key stages of bone marrow B-cell maturation are defective in patients with common variable immunodeficiency disorders. J Allergy Clin Immunol 2015; 136:487-90.e2. [DOI: 10.1016/j.jaci.2014.12.1943] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/13/2014] [Accepted: 12/17/2014] [Indexed: 02/07/2023]
|
18
|
Lymphoproliferative disease and cancer among patients with common variable immunodeficiency. Leuk Res 2015; 39:389-96. [PMID: 25711943 DOI: 10.1016/j.leukres.2015.02.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/01/2015] [Accepted: 02/02/2015] [Indexed: 01/08/2023]
Abstract
Innate immune deficiencies are a heterogeneous group of genetically inherited diseases affecting the innate and adaptive immune systems that confer susceptibility to infection, autoimmunity, and cancer. This review discusses the latest insights into the links between common variable immunodeficiency (CVI) and malignancies. Although Ig therapy greatly reduces the number of infections and enhances survival, it does not appear to address the development of cancer, especially lymphoma. The reasons for the increased susceptibility to lymphoid malignancies are unclear. These include genetics, immune dysregulation, radiosensitivity and chronic infections such as Helicobacter pylori, EBV, human herpes virus type 8 and cytomegalovirus. Further studies will allow us to better stratify the risk for cancer in these patients, and teach us to better prevent these complications and to better treat them.
Collapse
|
19
|
Chapel H, Prevot J, Gaspar HB, Español T, Bonilla FA, Solis L, Drabwell J. Primary immune deficiencies - principles of care. Front Immunol 2014; 5:627. [PMID: 25566243 PMCID: PMC4266088 DOI: 10.3389/fimmu.2014.00627] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/24/2014] [Indexed: 12/01/2022] Open
Abstract
Primary immune deficiencies (PIDs) are a growing group of over 230 different disorders caused by ineffective, absent or an increasing number of gain of function mutations in immune components, mainly cells and proteins. Once recognized, these rare disorders are treatable and in some cases curable. Otherwise untreated PIDs are often chronic, serious, or even fatal. The diagnosis of PIDs can be difficult due to lack of awareness or facilities for diagnosis, and management of PIDs is complex. This document was prepared by a worldwide multi-disciplinary team of specialists; it aims to set out comprehensive principles of care for PIDs. These include the role of specialized centers, the importance of registries, the need for multinational research, the role of patient organizations, management and treatment options, the requirement for sustained access to all treatments including immunoglobulin therapies and hematopoietic stem cell transplantation, important considerations for developing countries and suggestions for implementation. A range of healthcare policies and services have to be put into place by government agencies and healthcare providers, to ensure that PID patients worldwide have access to appropriate and sustainable medical and support services.
Collapse
Affiliation(s)
| | - Johan Prevot
- International Patient Organisation for Primary Immunodeficiencies (IPOPI) , Downderry , UK
| | | | | | | | - Leire Solis
- International Patient Organisation for Primary Immunodeficiencies (IPOPI) , Downderry , UK
| | - Josina Drabwell
- International Patient Organisation for Primary Immunodeficiencies (IPOPI) , Downderry , UK
| | | |
Collapse
|