1
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Huang X, Huang J, Li X, Fan J, Zhou D, Qu HQ, Glessner JT, Ji D, Jia Q, Ding Z, Wang N, Wei W, Lyu X, Li MJ, Liu Z, Liu W, Wei Y, Hakonarson H, Xia Q, Li J. Target genes regulated by CLEC16A intronic region associated with common variable immunodeficiency. J Allergy Clin Immunol 2024; 153:1668-1680. [PMID: 38191060 DOI: 10.1016/j.jaci.2023.12.023] [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: 08/17/2022] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND CLEC16A intron 19 has been identified as a candidate locus for common variable immunodeficiency (CVID). OBJECTIVES This study sought to elucidate the molecular mechanism by which variants at the CLEC16A intronic locus may contribute to the pathogenesis of CVID. METHODS The investigators performed fine-mapping of the CLEC16A locus in a CVID cohort, then deleted the candidate functional SNP in T-cell lines by the CRISPR-Cas9 technique and conducted RNA-sequencing to identify target gene(s). The interactions between the CLEC16A locus and its target genes were identified using circular chromosome conformation capture. The transcription factor complexes mediating the chromatin interactions were determined by proteomic approach. The molecular pathways regulated by the CLEC16A locus were examined by RNA-sequencing and reverse phase protein array. RESULTS This study showed that the CLEC16A locus is an enhancer regulating expression of multiple target genes including a distant gene ATF7IP2 through chromatin interactions. Distinct transcription factor complexes mediate the chromatin interactions in an allele-specific manner. Disruption of the CLEC16A locus affects the AKT signaling pathway, as well as the molecular response of CD4+ T cells to immune stimulation. CONCLUSIONS Through multiomics and targeted experimental approaches, this study elucidated the underlying target genes and signaling pathways involved in the genetic association of CLEC16A with CVID, and highlighted plausible molecular targets for developing novel therapeutics.
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Affiliation(s)
- Xubo Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jinxia Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiumei Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jingxian Fan
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Desheng Zhou
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Hui-Qi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Dandan Ji
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qi Jia
- International School of Information Science Engineering, Dalian University of Technology, Dalian, China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan, China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan, China
| | - Wei Wei
- Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xing Lyu
- Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mulin Jun Li
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Liu
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China; Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Yongjie Wei
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Qianghua Xia
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Jin Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China.
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2
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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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3
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Wang LA, Larson A, Abbott JK. The Immune Status of Patients with 16p11.2 Deletion Syndrome. J Clin Immunol 2023; 43:1792-1795. [PMID: 37814083 DOI: 10.1007/s10875-023-01597-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Affiliation(s)
- Laura A Wang
- Children's Hospital of Colorado and University of Colorado, 13123 E 16th Ave, Aurora, CO, USA.
| | - Austin Larson
- Children's Hospital of Colorado and University of Colorado, 13123 E 16th Ave, Aurora, CO, USA
| | - Jordan K Abbott
- Children's Hospital of Colorado and University of Colorado, 13123 E 16th Ave, Aurora, CO, USA
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4
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Ito T, Iwamoto S, Hirayama M, Yamada Y, Azuma E. Transient hypogammaglobulinemia of infancy may be associated with reduced switched memory B cells and del (16) (p11.2p12). Clin Case Rep 2021; 9:e3837. [PMID: 34188919 PMCID: PMC8218327 DOI: 10.1002/ccr3.3837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 11/16/2022] Open
Abstract
Transient hypogammaglobulinemia of infancy may be associated with chromosome del (16)(p11.2) that has reportedly been associated with other forms of primary immunodeficiency (Clin Immunol, 2009, 131, 24; J Allergy Clin Immunol, 2015;135, 1569).
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Affiliation(s)
- Tsuyoshi Ito
- Department of PediatricsToyohashi Municipal HospitalToyohashiJapan
| | - Shotaro Iwamoto
- Department of PediatricsMie University Graduate School of MedicineTsuJapan
| | - Masahiro Hirayama
- Department of PediatricsMie University Graduate School of MedicineTsuJapan
| | - Yasuharu Yamada
- Department of Clinical EngineeringSuzuka University of Medical ScienceSuzukaJapan
| | - Eiichi Azuma
- Department of Clinical EngineeringSuzuka University of Medical ScienceSuzukaJapan
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5
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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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6
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Persistent Activation of Innate Immunity in Patients with Primary Antibody Deficiencies. J Immunol Res 2020; 2020:8317671. [PMID: 33274244 PMCID: PMC7695510 DOI: 10.1155/2020/8317671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/13/2020] [Accepted: 10/19/2020] [Indexed: 12/03/2022] Open
Abstract
Primary antibody deficiencies (PAD) represent a heterogeneous group of disorders, with common variable immunodeficiency being the most common with clinical significance. The main phenotypic defect resides in the inability of B cells to produce antibodies, and the cornerstone of therapy is immunoglobulin replacement treatment in order to fight infections. However, the management of the other inflammatory manifestations is inadequate, reinforcing the hypothesis that a complex genetic background affecting additional cell populations, such as polymorphonuclear cells (PMN) and monocytes, influences the expression of the clinical phenotype of the disease. In this study, we investigated by flow cytometry in different conditions (resting state, and after isolation and incubation, with and without stimuli) the expression pattern of several markers on PMN and monocytes, indicative of their maturation, capacity for chemotaxis, adhesion, opsonization, migration, and phagocytosis in 25 PAD patients, 12 healthy blood donors, and 4 septic patients. In this context, we also analyzed patients before and after the initiation of replacement treatment, as well as an untreated patient in different clinical conditions. Interestingly, we observed that PAD patients exhibit a chronic activation status of the innate immunity compartment, along with several differences in the expression of activation, maturation, and adhesion markers, with respect to different clinical conditions. Moreover, immunoglobulin replacement treatment had a favorable effect on PMN, as it was expressed by a more mature and less activated phenotype on basal state cells, and an enhanced activation capacity after LPS exposure. Thus, we conclude that PAD patients display a persistent innate immune cell activation, which is probably associated with the chronic inflammatory stress, usually observed in these disorders.
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7
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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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8
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Contini C, Firinu D, Serrao S, Manconi B, Olianas A, Cinetto F, Cossu F, Castagnola M, Messana I, Del Giacco S, Cabras T. RP-HPLC-ESI-IT Mass Spectrometry Reveals Significant Variations of the Human Salivary Protein Profile Associated with Predominantly Antibody Deficiencies. J Clin Immunol 2020. [PMID: 31916122 DOI: 10.1007/s10875-020-00743-4.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
PURPOSE Present study is designed to discover potential salivary biomarkers associated with predominantly antibody deficiencies, which include a large spectrum of disorders sharing failure of antibody production, and B cell defects resulting in recurrent infections, autoimmune and inflammatory manifestations, and tumor susceptibility. Understanding and clinical classification of these syndromes is still challenging. METHODS We carried out a study of human saliva based on liquid chromatography-mass spectrometry measurements of intact protein mass values. Salivary protein profiles of patients (n = 23) and healthy controls (n = 30) were compared. RESULTS Patients exhibited lower abundance of α-defensins 1-4, cystatins S1 and S2, and higher abundance of glutathionylated cystatin B and cystatin SN than controls. Patients could be clustered in two groups on the basis of different levels of cystatin SN, S1 and S2, suggesting that these proteins may play different roles in the disease. CONCLUSIONS Quantitative variations of these pro-inflammatory and antimicrobial peptides/proteins may be related to immunodeficiency and infectious condition of the patients. The high incidence of tumors in the group with the highest level of cystatin SN, which is recognized as tumoral marker, appeared an intriguing result deserving of future investigations. Data are available via ProteomeXchange with identifier PXD012688.
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Affiliation(s)
- Cristina Contini
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Univ. Monserrato, ss 554, 09042, Monserrato, CA, Italy
| | - Davide Firinu
- Department of Medical Sciences and Public Health, University of Cagliari, Cittadella Univ. Monserrato, Monserrato, 09042, CA, Italy
| | - Simone Serrao
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Univ. Monserrato, ss 554, 09042, Monserrato, CA, Italy
| | - Barbara Manconi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Univ. Monserrato, ss 554, 09042, Monserrato, CA, Italy.
| | - Alessandra Olianas
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Univ. Monserrato, ss 554, 09042, Monserrato, CA, Italy
| | - Francesco Cinetto
- Ca' Foncello Hospital - Treviso, Department of Medicine - DIMED, University of Padova, Padova, Italy
| | - Fausto Cossu
- Pediatric HSCT Unit, Pediatric Clinic of University, Ospedale Microcitemico, Cagliari, Italy
| | - Massimo Castagnola
- Proteomics and Metabolomics Laboratory, IRCCS - Fondazione Santa Lucia, Rome, Italy
| | - Irene Messana
- CNR-SCITEC Istituto di Scienze e Tecnologie Chimiche, c/o Istituto di Biochimica e Biochimica Clinica Università Cattolica, L.go F. Vito, 1, 00168, Rome, Italy
| | - Stefano Del Giacco
- Department of Medical Sciences and Public Health, University of Cagliari, Cittadella Univ. Monserrato, Monserrato, 09042, CA, Italy
| | - Tiziana Cabras
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Univ. Monserrato, ss 554, 09042, Monserrato, CA, Italy
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9
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RP-HPLC-ESI-IT Mass Spectrometry Reveals Significant Variations of the Human Salivary Protein Profile Associated with Predominantly Antibody Deficiencies. J Clin Immunol 2020; 40:329-339. [PMID: 31916122 DOI: 10.1007/s10875-020-00743-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Present study is designed to discover potential salivary biomarkers associated with predominantly antibody deficiencies, which include a large spectrum of disorders sharing failure of antibody production, and B cell defects resulting in recurrent infections, autoimmune and inflammatory manifestations, and tumor susceptibility. Understanding and clinical classification of these syndromes is still challenging. METHODS We carried out a study of human saliva based on liquid chromatography-mass spectrometry measurements of intact protein mass values. Salivary protein profiles of patients (n = 23) and healthy controls (n = 30) were compared. RESULTS Patients exhibited lower abundance of α-defensins 1-4, cystatins S1 and S2, and higher abundance of glutathionylated cystatin B and cystatin SN than controls. Patients could be clustered in two groups on the basis of different levels of cystatin SN, S1 and S2, suggesting that these proteins may play different roles in the disease. CONCLUSIONS Quantitative variations of these pro-inflammatory and antimicrobial peptides/proteins may be related to immunodeficiency and infectious condition of the patients. The high incidence of tumors in the group with the highest level of cystatin SN, which is recognized as tumoral marker, appeared an intriguing result deserving of future investigations. Data are available via ProteomeXchange with identifier PXD012688.
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10
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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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11
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Tian S, Huang P, Gu Y, Yang J, Wu R, Zhao J, Liu AJ, Zhang W. Systems Biology Analysis of the Effect and Mechanism of Qi-Jing-Sheng-Bai Granule on Leucopenia in Mice. Front Pharmacol 2019; 10:408. [PMID: 31105563 PMCID: PMC6494967 DOI: 10.3389/fphar.2019.00408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
Qi-Jing-Sheng-Bai granule (QJSB) is a newly developed traditional Chinese medicine (TCM) formula. Clinically, it has been used for the treatment of leucopenia. However, its pharmacological mechanism needs more investigation. In this study, we firstly tested the effects of QJSB on leucopenia using mice induced by cyclophosphamide. Our results suggested that QJSB significantly raised the number of peripheral white blood cells, platelets and nucleated bone marrow cells. Additionally, it markedly enhanced the cell viability and promoted the colony formation of bone marrow mononuclear cells. Furthermore, it reversed the serum cytokines IL-6 and G-CSF disorders. Then, using transcriptomics datasets and metabonomic datasets, we integrated transcriptomics-based network pharmacology and metabolomics technologies to investigate the mechanism of action of QJSB. We found that QJSB regulated a series of biological processes such as hematopoietic cell lineage, homeostasis of number of cells, lymphocyte differentiation, metabolic processes (including lipid, amino acid, and nucleotide metabolism), B cell receptor signaling pathway, T cell activation and NOD-like receptor signaling pathway. In a summary, QJSB has protective effects to leucopenia in mice probably through accelerating cell proliferation and differentiation, regulating metabolism response pathways and modulating immunologic function at a system level.
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Affiliation(s)
- Saisai Tian
- School of Pharmacy, The Second Military Medical University, Shanghai, China
| | - Pengli Huang
- Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu Gu
- Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jian Yang
- School of Pharmacy, The Second Military Medical University, Shanghai, China
| | - Ran Wu
- Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Jing Zhao
- Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ai-Jun Liu
- School of Pharmacy, The Second Military Medical University, Shanghai, China.,Department of Pharmacy, Shanghai Pulmonary Hospital, Shanghai, China
| | - Weidong Zhang
- School of Pharmacy, The Second Military Medical University, Shanghai, China.,Institute of Interdisciplinary Complex Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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12
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Jouda J, Wöhr M, Del Rey A. Immunity and ultrasonic vocalization in rodents. Ann N Y Acad Sci 2018; 1437:68-82. [PMID: 30062701 DOI: 10.1111/nyas.13931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/14/2022]
Abstract
Ultrasonic vocalizations (USVs) serve important communicative functions in rodents. Different types of USVs can be triggered in the sender, for example, by maternal separation, social interactions, or exposure to predators, and they evoke affiliative or alarming behaviors in recipients. This review focusses on studies evaluating possible links between immunity and USVs. Most studies have been performed in a murine model of maternal immune activation and subsequent evaluation of effects in the offspring. This model has received large attention in recent years because it mimics behavioral abnormalities observed in certain human neuropsychiatric disorders, including autism spectrum disorder. Although there is still some controversy, the results indicate that stimulation of the immune system of mice and rats during pregnancy affects ultrasonic calling in pups. Few studies are available on immunization during adulthood and USVs. In most cases, immune stimulation led to disease, complicating conclusions about a possible direct link between vocalization and immunity. Although much work is still needed, this is certainly a rather new and promising aspect of interactions between the immune system and behavior.
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Affiliation(s)
- Jamela Jouda
- Department of Biology, College of Science, Al-Mustansiriyah University, Baghdad, Iraq
| | - Markus Wöhr
- Behavioral Neuroscience, Experimental and Biological Psychology, Philipps-University of Marburg, Marburg, Germany.,Center for Mind, Brain and Behavior, Philipps-University of Marburg, Marburg, Germany
| | - Adriana Del Rey
- Immunophysiology, Division of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University of Marburg, Marburg, Germany
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13
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Shores DR, Everett AD. Children as Biomarker Orphans: Progress in the Field of Pediatric Biomarkers. J Pediatr 2018; 193:14-20.e31. [PMID: 29031860 PMCID: PMC5794519 DOI: 10.1016/j.jpeds.2017.08.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/04/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Darla R Shores
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD.
| | - Allen D Everett
- Division of Cardiology, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD
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14
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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.
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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
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15
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Chinen J, Notarangelo LD, Shearer WT. Advances in clinical immunology in 2015. J Allergy Clin Immunol 2016; 138:1531-1540. [PMID: 27931534 PMCID: PMC5157931 DOI: 10.1016/j.jaci.2016.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/02/2016] [Accepted: 10/07/2016] [Indexed: 12/17/2022]
Abstract
Advances in clinical immunology in the past year included the report of practice parameters for the diagnosis and management of primary immunodeficiencies to guide the clinician in the approach to these relatively uncommon disorders. We have learned of new gene defects causing immunodeficiency and of new phenotypes expanding the spectrum of conditions caused by genetic mutations such as a specific regulator of telomere elongation (RTEL1) mutation causing isolated natural killer cell deficiency and mutations in ras-associated RAB (RAB27) resulting in immunodeficiency without albinism. Advances in diagnosis included the increasing use of whole-exome sequencing to identify gene defects and the measurement of serum free light chains to identify secondary hypogammaglobulinemias. For several primary immunodeficiencies, improved outcomes have been reported after definitive therapy with hematopoietic stem cell transplantation and gene therapy.
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Affiliation(s)
- Javier Chinen
- Immunology, Allergy and Rheumatology Section, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Tex.
| | - Luigi D Notarangelo
- Division of Immunology, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - William T Shearer
- Immunology, Allergy and Rheumatology Section, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Tex
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16
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Jørgensen SF, Trøseid M, Kummen M, Anmarkrud JA, Michelsen AE, Osnes LT, Holm K, Høivik ML, Rashidi A, Dahl CP, Vesterhus M, Halvorsen B, Mollnes TE, Berge RK, Moum B, Lundin KEA, Fevang B, Ueland T, Karlsen TH, Aukrust P, Hov JR. Altered gut microbiota profile in common variable immunodeficiency associates with levels of lipopolysaccharide and markers of systemic immune activation. Mucosal Immunol 2016; 9:1455-1465. [PMID: 26982597 DOI: 10.1038/mi.2016.18] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/08/2016] [Indexed: 02/04/2023]
Abstract
Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency characterized by low immunoglobulin (Ig)G and IgA, and/or IgM. In addition to bacterial infections, a large subgroup has noninfectious inflammatory and autoimmune complications. We performed 16S ribosomal RNA-based profiling of stool samples in 44 CVID patients, 45 patients with inflammatory bowel disease (disease controls), and 263 healthy controls. We measured plasma lipopolysaccharide (LPS) and markers of immune cell activation (i.e., soluble (s) CD14 and sCD25) in an expanded cohort of 104 patients with CVID and in 30 healthy controls. We found a large shift in the microbiota of CVID patients characterized by a reduced within-individual bacterial diversity (alpha diversity, P<0.001) without obvious associations to antibiotics use. Plasma levels of both LPS (P=0.001) and sCD25 (P<0.0001) were elevated in CVID, correlating negatively with alpha diversity and positively with a dysbiosis index calculated from the taxonomic profile. Low alpha diversity and high dysbiosis index, LPS, and immune markers were most pronounced in the subgroup with inflammatory and autoimmune complications. Low level of IgA was associated with decreased alpha diversity, but not independently from sCD25 and LPS. Our findings suggest a link between immunodeficiency, systemic immune activation, LPS, and altered gut microbiota.
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Affiliation(s)
- S F Jørgensen
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Transplantation Medicine, Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - M Trøseid
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Transplantation Medicine, Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - M Kummen
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - J A Anmarkrud
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - A E Michelsen
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - L T Osnes
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - K Holm
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - M L Høivik
- Department of Gastroenterology, Oslo University Hospital Ullevål, Oslo, Norway
| | - A Rashidi
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - C P Dahl
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Cardiology, Oslo University Hospital, Oslo, Norway
| | - M Vesterhus
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Medicine, National Centre for Ultrasound in Gastroenterology, Haukeland University Hospital, Bergen, Norway
| | - B Halvorsen
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - T E Mollnes
- K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Research Laboratory, Nordland Hospital, Bodø, and Faculty of Health Sciences, K.G. Jebsen TREC, University of Tromsø, Tromsø, Norway.,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - R K Berge
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Heart Disease, Haukeland University Hospital, Bergen, Norway
| | - B Moum
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterology, Oslo University Hospital Ullevål, Oslo, Norway
| | - K E A Lundin
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Transplantation Medicine, Section of Gastroenterology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - B Fevang
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Transplantation Medicine, Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - T Ueland
- K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Transplantation Medicine, Section of Gastroenterology, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K G Jebsen Thrombosis Research and Expertise Centre, University of Tromsø, Tromsø, Norway
| | - T H Karlsen
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Transplantation Medicine, Section of Gastroenterology, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of clinical medicine, University of Bergen, Bergen, Norway
| | - P Aukrust
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Department of Transplantation Medicine, Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - J R Hov
- Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,K G Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Transplantation Medicine, Section of Gastroenterology, Oslo University Hospital Rikshospitalet, Oslo, Norway
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17
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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]
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18
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Schatorjé E, van der Flier M, Seppänen M, Browning M, Morsheimer M, Henriet S, Neves JF, Vinh DC, Alsina L, Grumach A, Soler-Palacin P, Boyce T, Celmeli F, Goudouris E, Hayman G, Herriot R, Förster-Waldl E, Seidel M, Simons A, de Vries E. Primary immunodeficiency associated with chromosomal aberration - an ESID survey. Orphanet J Rare Dis 2016; 11:110. [PMID: 27484815 PMCID: PMC4971718 DOI: 10.1186/s13023-016-0492-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/27/2016] [Indexed: 11/21/2022] Open
Abstract
Background Patients with syndromic features frequently suffer from recurrent respiratory infections, but little is known about the spectrum of immunological abnormalities associated with their underlying chromosomal aberrations outside the well-known examples of Down and DiGeorge syndromes. Therefore, we performed this retrospective, observational survey study. Methods All members of the European Society for Immunodeficiencies (ESID) were invited to participate by reporting their patients with chromosomal aberration (excluding Down and DiGeorge syndromes) in combination with one or more identified immunological abnormalities potentially relating to primary immunodeficiency. An online questionnaire was used to collect the patient data. Results Forty-six patients were included from 16 centers (24 males, 22 females; median age 10.4 years [range 1.0–69.2 years]; 36 pediatric, 10 adult patients). A variety of chromosomal aberrations associated with immunological abnormalities potentially relating to primary immune deficiency was reported. The most important clinical presentation prompting the immunological evaluation was ‘recurrent ear-nose-throat (ENT) and airway infections’. Immunoglobulin isotype and/or IgG-subclass deficiencies were the most prevalent immunological abnormalities reported. Conclusions Our survey yielded a wide variety of chromosomal aberrations associated with immunological abnormalities potentially relating to primary immunodeficiency. Although respiratory tract infections can often also be ascribed to other causes (e.g. aspiration or structural abnormalities), we show that a significant proportion of patients also have an antibody deficiency requiring specific treatment (e.g. immunoglobulin replacement, antibiotic prophylaxis). Therefore, it is important to perform immunological investigations in patients with chromosomal aberrations and recurrent ENT or airway infections, to identify potential immunodeficiency that can be specifically treated. Electronic supplementary material The online version of this article (doi:10.1186/s13023-016-0492-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ellen Schatorjé
- Department Pediatrics, Jeroen Bosch Hospital, P.O. Box 90153, 5200 ME, 's-Hertogenbosch, The Netherlands
| | - Michiel van der Flier
- Department of Pediatrics, Amalia Children's Hospital and Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Mikko Seppänen
- Immunodeficiency Unit, Inflammation Center and Center for Rare Diseases, Children's Hospital, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | | | | | - Stefanie Henriet
- Department of Pediatrics, Amalia Children's Hospital and Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - João Farela Neves
- Primary Immunodeficiencies unit Hospital Dona Estefania, Centro Hospitalar de Lisboa Central, Lisbon, Portugal
| | | | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Deu, Barcelona, Spain
| | | | - Pere Soler-Palacin
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Fatih Celmeli
- Antalya Education and Research Hospital Department of Pediatric Immunology and Allergy, Antalya, Turkey
| | | | - Grant Hayman
- Epsom & St Helier University Hospitals NHS Trust, Carshalton, UK
| | | | - Elisabeth Förster-Waldl
- Department of Pediatrics and Adolescent Medicine, Center for Congenital Immunodeficiencies, Medical University Vienna, Wien, Austria
| | - Markus Seidel
- Pediatric Hematology-Oncology, Medical University Graz, Graz, Austria
| | - Annet Simons
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
| | - Esther de Vries
- Department Pediatrics, Jeroen Bosch Hospital, P.O. Box 90153, 5200 ME, 's-Hertogenbosch, The Netherlands. .,Department Tranzo, Tilburg University, Tilburg, The Netherlands.
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19
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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.
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20
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Keller MD, Pandey R, Li D, Glessner J, Tian L, Henrickson SE, Chinn IK, Monaco-Shawver L, Heimall J, Hou C, Otieno FG, Jyonouchi S, Calabrese L, van Montfrans J, Orange JS, Hakonarson H. Mutation in IRF2BP2 is responsible for a familial form of common variable immunodeficiency disorder. J Allergy Clin Immunol 2016; 138:544-550.e4. [PMID: 27016798 DOI: 10.1016/j.jaci.2016.01.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 01/01/2016] [Accepted: 01/13/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Genome-wide association studies have shown a pattern of rare copy number variations and single nucleotide polymorphisms in patients with common variable immunodeficiency disorder (CVID), which was recognizable by a support vector machine (SVM) algorithm. However, rare monogenic causes of CVID might lack such a genetic fingerprint. OBJECTIVE We sought to identify a unique monogenic cause of familial immunodeficiency and evaluate the use of SVM to identify patients with possible monogenic disorders. METHODS A family with multiple members with a diagnosis of CVID was screened by using whole-exome sequencing. The proband and other subjects with mutations associated with CVID-like phenotypes were screened through the SVM algorithm from our recent CVID genome-wide association study. RT-PCR, protein immunoblots, and in vitro plasmablast differentiation assays were performed on patient and control EBV lymphoblastoids cell lines. RESULTS Exome sequencing identified a novel heterozygous mutation in IRF2BP2 (c.1652G>A:p.[S551N]) in affected family members. Transduction of the mutant gene into control human B cells decreased production of plasmablasts in vitro, and IRF2BP2 transcripts and protein expression were increased in proband versus control EBV-immortalized lymphoblastoid cell lines. The SVM algorithm categorized the proband and subjects with other immunodeficiency-associated gene variants in TACI, BAFFR, ICOS, CD21, LRBA, and CD27 as genetically dissimilar from polygenic CVID. CONCLUSION A novel IRFBP2 mutation was identified in a family with autosomal dominant CVID. Transduction experiments suggest that the mutant protein has an effect on B-cell differentiation and is likely a monogenic cause of the family's CVID phenotype. Successful grouping by the SVM algorithm suggests that our family and other subjects with rare immunodeficiency disorders cluster separately and lack the genetic pattern present in polygenic CVID cases.
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Affiliation(s)
- Michael D Keller
- Division of Allergy and Immunology, Children's National Medical Center, Washington, DC
| | - Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Joseph Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Sarah E Henrickson
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Ivan K Chinn
- Division of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex; Baylor Genomics Institute, Baylor College of Medicine, Houston, Tex
| | - Linda Monaco-Shawver
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Jennifer Heimall
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Cuiping Hou
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Frederick G Otieno
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Soma Jyonouchi
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Leonard Calabrese
- Department of Rheumatologic and Immunologic Disease, Cleveland Clinic, Cleveland, Ohio
| | - Joris van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center, Utrecht, The Netherlands
| | - Jordan S Orange
- Division of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex.
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pa.
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