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Erman B, Aba U, Ipsir C, Pehlivan D, Aytekin C, Cildir G, Cicek B, Bozkurt C, Tekeoglu S, Kaya M, Aydogmus C, Cipe F, Sucak G, Eltan SB, Ozen A, Barıs S, Karakoc-Aydiner E, Kıykım A, Karaatmaca B, Kose H, Uygun DFK, Celmeli F, Arikoglu T, Ozcan D, Keskin O, Arık E, Aytekin ES, Cesur M, Kucukosmanoglu E, Kılıc M, Yuksek M, Bıcakcı Z, Esenboga S, Ayvaz DÇ, Sefer AP, Guner SN, Keles S, Reisli I, Musabak U, Demirbas ND, Haskologlu S, Kilic SS, Metin A, Dogu F, Ikinciogulları A, Tezcan I. Genetic Evaluation of the Patients with Clinically Diagnosed Inborn Errors of Immunity by Whole Exome Sequencing: Results from a Specialized Research Center for Immunodeficiency in Türkiye. J Clin Immunol 2024; 44:157. [PMID: 38954121 PMCID: PMC11219406 DOI: 10.1007/s10875-024-01759-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
Molecular diagnosis of inborn errors of immunity (IEI) plays a critical role in determining patients' long-term prognosis, treatment options, and genetic counseling. Over the past decade, the broader utilization of next-generation sequencing (NGS) techniques in both research and clinical settings has facilitated the evaluation of a significant proportion of patients for gene variants associated with IEI. In addition to its role in diagnosing known gene defects, the application of high-throughput techniques such as targeted, exome, and genome sequencing has led to the identification of novel disease-causing genes. However, the results obtained from these different methods can vary depending on disease phenotypes or patient characteristics. In this study, we conducted whole-exome sequencing (WES) in a sizable cohort of IEI patients, consisting of 303 individuals from 21 different clinical immunology centers in Türkiye. Our analysis resulted in likely genetic diagnoses for 41.1% of the patients (122 out of 297), revealing 52 novel variants and uncovering potential new IEI genes in six patients. The significance of understanding outcomes across various IEI cohorts cannot be overstated, and we believe that our findings will make a valuable contribution to the existing literature and foster collaborative research between clinicians and basic science researchers.
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Affiliation(s)
- Baran Erman
- Institute of Child Health, Hacettepe University, Ankara, Turkey.
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey.
| | - Umran Aba
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Canberk Ipsir
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Damla Pehlivan
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Caner Aytekin
- Pediatric Immunology, SBU Ankara Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Gökhan Cildir
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia
| | - Begum Cicek
- Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Ceren Bozkurt
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Sidem Tekeoglu
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Melisa Kaya
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Cigdem Aydogmus
- Department of Pediatric Allergy and Clinical Immunology, University of Health Sciences, Istanbul Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Funda Cipe
- Department of Pediatric Allergy and Clinical Immunology, Altinbas University School of Medicine, Istanbul, Turkey
| | - Gulsan Sucak
- Medical Park Bahçeşehir Hospital, Clinic of Hematology and Transplantation, İstanbul, Turkey
| | - Sevgi Bilgic Eltan
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ahmet Ozen
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Safa Barıs
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ayca Kıykım
- Pediatric Allergy and Immunology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Betul Karaatmaca
- Department of Pediatric Allergy and Immunology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Hulya Kose
- Department of Pediatric Immunology, Diyarbakir Children Hospital, Diyarbakır, Turkey
| | - Dilara Fatma Kocacık Uygun
- Division of Allergy Immunology, Department of Pediatrics, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Fatih Celmeli
- Republic of Turkey Ministry of Health Antalya Training and Research Hospital Pediatric Immunology and Allergy Diseases, Antalya, Turkey
| | - Tugba Arikoglu
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Dilek Ozcan
- Division of Pediatric Allergy and Immunology, Faculty of Medicine, Balcali Hospital, Cukurova University, Adana, Turkey
| | - Ozlem Keskin
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Elif Arık
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Elif Soyak Aytekin
- Department of Pediatric Allergy and Immunology, Etlik City Hospital, Ankara, Turkey
| | - Mahmut Cesur
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ercan Kucukosmanoglu
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Mehmet Kılıc
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, University of Firat, Elazığ, Turkey
| | - Mutlu Yuksek
- Department of Pediatric Immunology and Allergy, Faculty of Medicine, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | - Zafer Bıcakcı
- Department of Pediatric Hematology, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Saliha Esenboga
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Deniz Çagdaş Ayvaz
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
- Section of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Asena Pınar Sefer
- Department of Pediatric Allergy and Immunology, Şanlıurfa Training and Research Hospital, Şanlıurfa, Turkey
| | - Sukrü Nail Guner
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Sevgi Keles
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ismail Reisli
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ugur Musabak
- Department of Immunology and Allergy, Baskent University School of Medicine, Ankara, Turkey
| | - Nazlı Deveci Demirbas
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Sule Haskologlu
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Sara Sebnem Kilic
- Division of Pediatric Immunology-Rheumatology, Bursa Uludag University Faculty of Medicine, Bursa, Turkey
- Translational Medicine, Bursa Uludag University, Bursa, Turkey
| | - Ayse Metin
- Department of Pediatric Allergy and Immunology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Figen Dogu
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Aydan Ikinciogulları
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Ilhan Tezcan
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
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Du HQ, Zhao XD. Current understanding of ELF4 deficiency: a novel inborn error of immunity. World J Pediatr 2024; 20:444-450. [PMID: 38733460 DOI: 10.1007/s12519-024-00807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/12/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND ELF4 deficiency has been recently recognized as a novel disorder within the spectrum of inborn errors of immunity (IEIs), specifically categorized as a "disease of immune dysregulation." Cases of this condition, reported by our team and others, are very limited worldwide. As such, our current knowledge of this new disease remains preliminary. This review aims to provide a brief overview of the clinical manifestations, pathogenesis, and treatment strategies for this novel IEI. DATA SOURCES A comprehensive review was conducted after an extensive literature search in the PubMed/Medline database and websites concerning transcriptional factor ELF4 and reports concerning patients with ELF4 deficiency. Our search strategy was "ELF4 OR ETS-related transcription factor Elf-4 OR EL4-like factor 4 OR myeloid Elf-1-like factor" as of the time of manuscript submission. RESULTS The current signature manifestations of ELF4 deficiency disorder are recurrent and prolonged oral ulcer, abdominal pain, and diarrhea in pediatric males. In some cases, immunodeficiency and autoimmunity can also be prominent. Targeted Sanger sequencing or whole exome sequencing can be used to detect variation in ELF4 gene. Western blotting for ELF4 expression of the patient's cells can confirm the pathogenic effect of the variant. To fully confirm the pathogenicity of the variant, further functional test is strongly advised. Glucocorticoid and biologics are the mainstream management of ELF4 deficiency disorder. CONCLUSIONS Pediatric males presenting with recurring ulcerations in digestive tract epithelium with or without recurrent fever should be suspected of DEX. When atypical presentations are prominent, variations in ELF4 gene should be carefully evaluated functionally due to the complex nature of ELF4 function. Experience of treating DEX includes use of glucocorticoid and biologics and more precise treatment needs more patients to identify and further mechanistic study.
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Affiliation(s)
- Hong-Qiang Du
- Department of Rheumatology & Immunology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Zhongshan Er Road 136Yuzhong District, Chongqing, China
| | - Xiao-Dong Zhao
- Department of Rheumatology & Immunology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Zhongshan Er Road 136Yuzhong District, Chongqing, China.
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Peng X, Kaviany S. Approach to Diagnosing Inborn Errors of Immunity. Rheum Dis Clin North Am 2023; 49:731-739. [PMID: 37821192 DOI: 10.1016/j.rdc.2023.06.001] [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] [Indexed: 10/13/2023]
Abstract
Inborn errors of immunity are now understood to encompass manifold features including but not limited to immunodeficiency, autoimmunity, autoinflammation, atopy, bone marrow defects, and/or increased malignancy risk. As such, it is essential to maintain a high index of suspicion, as these disorders are not limited to specific demographics such as children or those with recurrent infections. Clinical presentations and standard immunophenotyping are informative for suggesting potential underlying etiologies, but integration of data from multimodal approaches including genomics is often required to achieve diagnosis.
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Affiliation(s)
- Xiao Peng
- McKusick-Nathans, Department of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Blalock 1008, Baltimore, MD 21287, USA
| | - Saara Kaviany
- The University of Chicago & Biological Sciences, Department of Pediatrics, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA.
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Mauracher AA, Henrickson SE. Leveraging Systems Immunology to Optimize Diagnosis and Treatment of Inborn Errors of Immunity. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:910243. [PMID: 37670772 PMCID: PMC10477056 DOI: 10.3389/fsysb.2022.910243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Inborn errors of immunity (IEI) are monogenic disorders that can cause diverse symptoms, including recurrent infections, autoimmunity and malignancy. While many factors have contributed, the increased availability of next-generation sequencing has been central in the remarkable increase in identification of novel monogenic IEI over the past years. Throughout this phase of disease discovery, it has also become evident that a given gene variant does not always yield a consistent phenotype, while variants in seemingly disparate genes can lead to similar clinical presentations. Thus, it is increasingly clear that the clinical phenotype of an IEI patient is not defined by genetics alone, but is also impacted by a myriad of factors. Accordingly, we need methods to amplify our current diagnostic algorithms to better understand mechanisms underlying the variability in our patients and to optimize treatment. In this review, we will explore how systems immunology can contribute to optimizing both diagnosis and treatment of IEI patients by focusing on identifying and quantifying key dysregulated pathways. To improve mechanistic understanding in IEI we must deeply evaluate our rare IEI patients using multimodal strategies, allowing both the quantification of altered immune cell subsets and their functional evaluation. By studying representative controls and patients, we can identify causative pathways underlying immune cell dysfunction and move towards functional diagnosis. Attaining this deeper understanding of IEI will require a stepwise strategy. First, we need to broadly apply these methods to IEI patients to identify patterns of dysfunction. Next, using multimodal data analysis, we can identify key dysregulated pathways. Then, we must develop a core group of simple, effective functional tests that target those pathways to increase efficiency of initial diagnostic investigations, provide evidence for therapeutic selection and contribute to the mechanistic evaluation of genetic results. This core group of simple, effective functional tests, targeting key pathways, can then be equitably provided to our rare patients. Systems biology is thus poised to reframe IEI diagnosis and therapy, fostering research today that will provide streamlined diagnosis and treatment choices for our rare and complex patients in the future, as well as providing a better understanding of basic immunology.
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Affiliation(s)
- Andrea A. Mauracher
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sarah E. Henrickson
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Mørup SB, Nazaryan-Petersen L, Gabrielaite M, Reekie J, Marquart HV, Hartling HJ, Marvig RL, Katzenstein TL, Masmas TN, Lundgren J, Murray DD, Helleberg M, Borgwardt L. Added Value of Reanalysis of Whole Exome- and Whole Genome Sequencing Data From Patients Suspected of Primary Immune Deficiency Using an Extended Gene Panel and Structural Variation Calling. Front Immunol 2022; 13:906328. [PMID: 35874679 PMCID: PMC9302041 DOI: 10.3389/fimmu.2022.906328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Knowledge of the genetic variation underlying Primary Immune Deficiency (PID) is increasing. Reanalysis of genome-wide sequencing data from undiagnosed patients with suspected PID may improve the diagnostic rate. Methods We included patients monitored at the Department of Infectious Diseases or the Child and Adolescent Department, Rigshospitalet, Denmark, for a suspected PID, who had been analysed previously using a targeted PID gene panel (457 PID-related genes) on whole exome- (WES) or whole genome sequencing (WGS) data. A literature review was performed to extend the PID gene panel used for reanalysis of single nucleotide variation (SNV) and small indels. Structural variant (SV) calling was added on WGS data. Results Genetic data from 94 patients (86 adults) including 36 WES and 58 WGS was reanalysed a median of 23 months after the initial analysis. The extended gene panel included 208 additional PID-related genes. Genetic reanalysis led to a small increase in the proportion of patients with new suspicious PID related variants of uncertain significance (VUS). The proportion of patients with a causal genetic diagnosis was constant. In total, five patients (5%, including three WES and two WGS) had a new suspicious PID VUS identified due to reanalysis. Among these, two patients had a variant added due to the expansion of the PID gene panel, and three patients had a variant reclassified to a VUS in a gene included in the initial PID gene panel. The total proportion of patients with PID related VUS, likely pathogenic, and pathogenic variants increased from 43 (46%) to 47 (50%), as one patient had a VUS detected in both initial- and reanalysis. In addition, we detected new suspicious SNVs and SVs of uncertain significance in PID candidate genes with unknown inheritance and/or as heterozygous variants in genes with autosomal recessive inheritance in 8 patients. Conclusion These data indicate a possible diagnostic gain of reassessing WES/WGS data from patients with suspected PID. Reasons for the possible gain included improved knowledge of genotype-phenotype correlation, expanding the gene panel, and adding SV analyses. Future studies of genotype-phenotype correlations may provide additional knowledge on the impact of the new suspicious VUSs.
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Affiliation(s)
- Sara Bohnstedt Mørup
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lusine Nazaryan-Petersen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hanne V. Marquart
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hans Jakob Hartling
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Terese L. Katzenstein
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tania N. Masmas
- The Child and Adolescent Department, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jens Lundgren
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Daniel D. Murray
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Line Borgwardt
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Fournier B, Mahlaoui N, Moshous D, de Villartay JP. Inborn errors of immunity caused by defects in the DNA damage response pathways: Importance of minimizing treatment-related genotoxicity. Pediatr Allergy Immunol 2022; 33:e13820. [PMID: 35754136 PMCID: PMC9327728 DOI: 10.1111/pai.13820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/11/2022]
Abstract
Several primary immunodeficiencies are caused by defects in the general DNA repair machinery as exemplified by the T-B- radiosensitive SCID condition owing to impaired resolution of programmed DNA double-strand breaks introduced by RAG1/2 during V(D)J recombination. The genome instability generally associated with these conditions results in an increased propensity to develop malignancies requiring genotoxic-based anti-cancer treatments. Moreover, the extent of immune deficiency often calls for hematopoietic stem cell transplantation as a definitive treatment, also requiring genotoxic-based conditioning regimen prior to transplantation. In both cases, the underlying general DNA repair defect may result in catastrophic iatrogenic consequences. It is, therefore, of paramount importance to assess the functionality of the DNA repair apparatus prior to any genotoxic treatment when the exact molecular cause of the disease is unknown. For this purpose, two simple assays can be used on patients derived peripheral blood lymphocytes: (1) the PROMIDISα biomarker, based on the next-generation sequencing analysis of the TCRα repertoire, will highlight specific signatures of DNA repair deficiencies; (2) direct analysis of the sensitivity of peripheral lymphocytes to ionizing radiation will formally identify patients at risk to develop toxicity toward genotoxic-based treatments.
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Affiliation(s)
- Benjamin Fournier
- Pediatric Hematology-Immunology and Rheumatology Department, APHP-Centre Université de Paris (CUP), Necker Hospital, Paris, France
| | - Nizar Mahlaoui
- Pediatric Hematology-Immunology and Rheumatology Department, APHP-Centre Université de Paris (CUP), Necker Hospital, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Despina Moshous
- Pediatric Hematology-Immunology and Rheumatology Department, APHP-Centre Université de Paris (CUP), Necker Hospital, Paris, France.,Laboratory "Genome Dynamics in the Immune System" INSERM UMR 1163, Imagine Institute, Université de Paris Cité, Paris, France
| | - Jean-Pierre de Villartay
- Laboratory "Genome Dynamics in the Immune System" INSERM UMR 1163, Imagine Institute, Université de Paris Cité, Paris, France.,Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
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Khan HA, Butte MJ. Expanding the potential genes of inborn errors of immunity through protein interactions. BMC Genomics 2021; 22:618. [PMID: 34391382 PMCID: PMC8364696 DOI: 10.1186/s12864-021-07909-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/22/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Inborn errors of immunity (IEI) are a group of genetic disorders that impair the immune system, with over 400 genes described so far, and hundreds more to be discovered. To facilitate the search for new genes, we need a way to prioritize among all the genes in the genome those most likely to play an important role in immunity. RESULTS Here we identify a new list of genes by linking known IEI genes to new ones by using open-source databases of protein-protein interactions, post-translational modifications, and transcriptional regulation. We analyze this new set of 2,530 IEI-related genes for their tolerance of genetic variation and by their expression levels in various immune cell types. CONCLUSIONS By merging genes derived from protein interactions of known IEI genes with transcriptional data, we offer a new list of candidate genes that may play a role in as-yet undiscovered IEIs.
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Affiliation(s)
- Humza A Khan
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA.
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Hashim IF, Ahmad Mokhtar AM. Small Rho GTPases and their associated RhoGEFs mutations promote immunological defects in primary immunodeficiencies. Int J Biochem Cell Biol 2021; 137:106034. [PMID: 34216756 DOI: 10.1016/j.biocel.2021.106034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/14/2021] [Accepted: 06/28/2021] [Indexed: 01/10/2023]
Abstract
Primary immunodeficiencies (PIDs) are associated with deleterious mutations of genes that encode proteins involved in actin cytoskeleton reorganisation. This deficiency affects haematopoietic cells. PID results in the defective function of immune cells, such as impaired chemokine-induced motility, receptor signalling, development and maturation. Some of the genes mutated in PIDs are related to small Ras homologous (Rho) guanosine triphosphatase (GTPase), one of the families of the Ras superfamily. Most of these genes act as molecular switches by cycling between active guanosine triphosphate-bound and inactive guanosine diphosphate-bound forms to control multiple cellular functions. They are best studied for their role in promoting cytoskeleton reorganisation, cell adhesion and motility. Currently, only three small Rho GTPases, namely, Rac2, Cdc42 and RhoH, have been identified in PIDs. However, several other Rho small G proteins might also contribute to the deregulation and phenotype observed in PIDs. Their contribution in PIDs may involve their main regulator, Rho guanine nucleotide exchange factors such as DOCK2 and DOCK8, wherein mutations may result in the impairment of small Rho GTPase activation. Thus, this review outlines the potential contribution of several small Rho GTPases to the promotion of PIDs.
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Affiliation(s)
- Ilie Fadzilah Hashim
- Primary Immunodeficiency Diseases Group, Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas, Penang, 13200, Malaysia.
| | - Ana Masara Ahmad Mokhtar
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Gelugor, Penang, 11800, Malaysia.
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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.
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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.
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10
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Ahmad Mokhtar AM, Hashim IF, Mohd Zaini Makhtar M, Salikin NH, Amin-Nordin S. The Role of RhoH in TCR Signalling and Its Involvement in Diseases. Cells 2021; 10:950. [PMID: 33923951 PMCID: PMC8072805 DOI: 10.3390/cells10040950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022] Open
Abstract
As an atypical member of the Rho family small GTPases, RhoH shares less than 50% sequence similarity with other members, and its expression is commonly observed in the haematopoietic lineage. To date, RhoH function was observed in regulating T cell receptor signalling, and less is known in other haematopoietic cells. Its activation may not rely on the standard GDP/GTP cycling of small G proteins and is thought to be constitutively active because critical amino acids involved in GTP hydrolysis are absent. Alternatively, its activation can be regulated by other types of regulation, including lysosomal degradation, somatic mutation and transcriptional repressor, which also results in an altered protein expression. Aberrant protein expression of RhoH has been implicated not only in B cell malignancies but also in immune-related diseases, such as primary immunodeficiencies, systemic lupus erythematosus and psoriasis, wherein its involvement may provide the link between immune-related diseases and cancer. RhoH association with these diseases involves several other players, including its interacting partner, ZAP-70; activation regulators, Vav1 and RhoGDI and other small GTPases, such as RhoA, Rac1 and Cdc42. As such, RhoH and its associated proteins are potential attack points, especially in the treatment of cancer and immune-related diseases.
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Affiliation(s)
- Ana Masara Ahmad Mokhtar
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (M.M.Z.M.); (N.H.S.)
| | - Ilie Fadzilah Hashim
- Primary Immunodeficiency Diseases Group, Regenerative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Kepala Batas 13200, Penang, Malaysia;
| | - Muaz Mohd Zaini Makhtar
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (M.M.Z.M.); (N.H.S.)
| | - Nor Hawani Salikin
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (M.M.Z.M.); (N.H.S.)
| | - Syafinaz Amin-Nordin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
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11
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Lee K, Abraham RS. Next-generation sequencing for inborn errors of immunity. Hum Immunol 2021; 82:871-882. [PMID: 33715910 DOI: 10.1016/j.humimm.2021.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/27/2022]
Abstract
Inborn errors of immunity (IEIs) include several hundred gene defects affecting various components of the immune system. As with other constitutional disorders, next-generation sequencing (NGS) is a powerful tool for the diagnosis of these diseases. While NGS can provide molecular confirmation of disease in a patient with a suspected or classic phenotype, it can also identify new molecular defects of the immune system, expand gene-disease phenotypes, clarify mechanism of disease, pattern of inheritance or identify new gene-disease associations. Multiple clinical specialties are involved in the diagnosis and management of patients with IEI, and most have no formal genetic training or expertise. To effectively utilize NGS tools and data in clinical practice, it is relevant and pragmatic to obtain a modicum of knowledge about genetic terminology, the variety of platforms and tools available for high-throughput genomic analysis, the interpretation and implementation of such data in clinical practice. There is considerable variability not only in the technologies and analytical tools used for NGS but in the bioinformatics approach to variant identification and interpretation. The ability to provide a molecular basis for disease has the potential to alter therapeutic management and longer-term treatment of the disease, including developing personalized approaches with molecularly targeted therapies. This review is intended for the clinical specialist or diagnostic immunologist who works in the area of inborn errors of immunity, and provides an overview of the need for genetic testing in these patients (the "why" aspect), the various technologies and analytical approaches, bioinformatics tools, resources, and challenges (the "how" aspect), and the clinical evidence for identifying which patients might be best served by such testing (the "when" aspect).
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Affiliation(s)
- Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Roshini S Abraham
- Diagnostic Immunology Laboratory, Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA.
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12
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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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13
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Sun J, Yang L, Lu Y, Wang H, Peng X, Dong X, Cheng G, Cao Y, Wu B, Wang X, Zhou W. Screening for primary immunodeficiency diseases by next-generation sequencing in early life. Clin Transl Immunology 2020; 9:e1138. [PMID: 32431812 PMCID: PMC7231820 DOI: 10.1002/cti2.1138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective We aimed to use next-generation sequencing (NGS) for the early diagnosis of primary immunodeficiency diseases (PIDs) and define its effects on medical management for an infant cohort in early life. Methods A single-centre study was conducted from November 2015 to April 2018. Infants less than 3 months old with infections or abnormal white blood cell counts were enrolled in the study. Gene variants were analysed by NGS, and once a mutation was found in a PID-associated gene, the immune functions associated with this mutation were detected. The diagnosis rate of PIDs in the cohort was the main outcome. The patients received corresponding management and follow-up treatments. Results Among 2392 patients who were genetically tested with NGS, 51 infants were diagnosed with PIDs. Seven types of PIDs were detected, and the most common (25/51, 49%) were combined immunodeficiencies with associated or syndromic features. Thirty-five patients (68.6%) were cured or had improved outcomes after being diagnosed with PID. The NGS cost was US$280 per case. Conclusions This study not only highlighted the potential of NGS to rapidly deliver molecular diagnoses of PIDs but also indicated that the prevalence of PIDs is underestimated. With broader use, this approach has the potential to alter clinical strategies.
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Affiliation(s)
- Jinqiao Sun
- Department of Clinical Immunology Children's Hospital of Fudan University Shanghai China
| | - Lin Yang
- Clinical Genetic Center Children's Hospital of Fudan University Shanghai China
| | - Yulan Lu
- Children's Hospital & Institutes of Biomedical Sciences Fudan university Shanghai China.,Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Huijun Wang
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Xiaomin Peng
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Xinran Dong
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Guoqiang Cheng
- Department of Neonatology Children's Hospital of Fudan University Shanghai China
| | - Yun Cao
- Department of Neonatology Children's Hospital of Fudan University Shanghai China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Xiaochuan Wang
- Department of Clinical Immunology Children's Hospital of Fudan University Shanghai China
| | - Wenhao Zhou
- Department of Neonatology Children's Hospital of Fudan University Shanghai China
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14
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Sevim Bayrak C, Itan Y. Identifying disease-causing mutations in genomes of single patients by computational approaches. Hum Genet 2020; 139:769-776. [PMID: 32405658 DOI: 10.1007/s00439-020-02179-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022]
Abstract
Over the last decade next generation sequencing (NGS) has been extensively used to identify new pathogenic mutations and genes causing rare genetic diseases. The efficient analyses of NGS data is not trivial and requires a technically and biologically rigorous pipeline that addresses data quality control, accurate variant filtration to minimize false positives and false negatives, and prioritization of the remaining genes based on disease genomics and physiological knowledge. This review provides a pipeline including all these steps, describes popular software for each step of the analysis, and proposes a general framework for the identification of causal mutations and genes in individual patients of rare genetic diseases.
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Affiliation(s)
- Cigdem Sevim Bayrak
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, US.
| | - Yuval Itan
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, US.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, US
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15
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Cabral-Marques O, Schimke LF, de Oliveira EB, El Khawanky N, Ramos RN, Al-Ramadi BK, Segundo GRS, Ochs HD, Condino-Neto A. Flow Cytometry Contributions for the Diagnosis and Immunopathological Characterization of Primary Immunodeficiency Diseases With Immune Dysregulation. Front Immunol 2019; 10:2742. [PMID: 31849949 PMCID: PMC6889851 DOI: 10.3389/fimmu.2019.02742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/08/2019] [Indexed: 12/24/2022] Open
Abstract
Almost 70 years after establishing the concept of primary immunodeficiency disorders (PIDs), more than 320 monogenic inborn errors of immunity have been identified thanks to the remarkable contribution of high-throughput genetic screening in the last decade. Approximately 40 of these PIDs present with autoimmune or auto-inflammatory symptoms as the primary clinical manifestation instead of infections. These PIDs are now recognized as diseases of immune dysregulation. Loss-of function mutations in genes such as FOXP3, CD25, LRBA, IL-10, IL10RA, and IL10RB, as well as heterozygous gain-of-function mutations in JAK1 and STAT3 have been reported as causative of these disorders. Identifying these syndromes has considerably contributed to expanding our knowledge on the mechanisms of immune regulation and tolerance. Although whole exome and whole genome sequencing have been extremely useful in identifying novel causative genes underlying new phenotypes, these approaches are time-consuming and expensive. Patients with monogenic syndromes associated with autoimmunity require faster diagnostic tools to delineate therapeutic strategies and avoid organ damage. Since these PIDs present with severe life-threatening phenotypes, the need for a precise diagnosis in order to initiate appropriate patient management is necessary. More traditional approaches such as flow cytometry are therefore a valid option. Here, we review the application of flow cytometry and discuss the relevance of this powerful technique in diagnosing patients with PIDs presenting with immune dysregulation. In addition, flow cytometry represents a fast, robust, and sensitive approach that efficiently uncovers new immunopathological mechanisms underlying monogenic PIDs.
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Affiliation(s)
- Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lena F Schimke
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | | | - Nadia El Khawanky
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg im Breisgau, Germany.,Precision Medicine Theme, The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Rodrigo Nalio Ramos
- INSERM U932, SiRIC Translational Immunotherapy Team, Institut Curie, Paris Sciences et Lettres Research University, Paris, France
| | - Basel K Al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | | | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, United States
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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16
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Li J, Li J, Li J, Yao H, Liu F, Gusella JF, Shi X, Chen X. A rare case of acquired immunodeficiency associated with myelodysplastic syndrome. Mol Genet Genomic Med 2019; 7:e923. [PMID: 31503426 PMCID: PMC6825869 DOI: 10.1002/mgg3.923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Pediatric myelodysplastic syndromes (MDS) display clonal genomic instability that can lead to acquisition of other hematological disorders, usually by loss of heterozygosity. Immunodeficiency caused by uniparental disomy (UPD) has not previously been reported. METHODS We investigated a 13-year-old boy who suffered from recurrent infections and pancytopenia for 1 year. Both the comet assay and chromosome breakage analysis were normal, but the bone marrow showed evidence of dysplasia characteristic of MDS. With his normal sister as donor, he underwent failed hematopoietic stem cell transplantation (HSCT) with reduced intensity conditioning (RIC) followed by successful HSCT with myeloablative conditioning (MAC). We used single nucleotide polymorphism (SNP) array, targeted gene panel, and whole exome sequencing to investigate the etiology of his disease. RESULTS The molecular analyses revealed multiple regions of homozygosity, one region encompassing a homozygous missense variant of recombination activating gene 1 (RAG1) which was previously associated with severe immunodeficiency in infancy. This RAG1 mutation was heterozygous in the proband's fingernail DNA, but was changed to homozygous in the proband's marrow by somatic acquisition of UPD event. No other pathogenic driver mutation for MDS-related genes was identified. CONCLUSION The hematological phenotype, somatic genomic instability, and response to HSCT MAC but not HSCT RIC deduced to a diagnosis of MDS type refractory cytopenia of children in this patient. His immunodeficiency was secondary to MDS due to somatic acquisition of homozygosity for known pathogenic RAG1 mutation.
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Affiliation(s)
- Juanjuan Li
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Junhui Li
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Jianguo Li
- Department of RheumatologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Hailan Yao
- Department of Molecular ImmunologyCapital Institute of PediatricsBeijingChina
| | - Fang Liu
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingChina
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
| | - Xiaodong Shi
- Department of HematologyAffiliated Children’s Hospital of Capital Institute of PediatricsBeijingChina
| | - Xiaoli Chen
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijingChina
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17
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Biological Network Approaches and Applications in Rare Disease Studies. Genes (Basel) 2019; 10:genes10100797. [PMID: 31614842 PMCID: PMC6827097 DOI: 10.3390/genes10100797] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/30/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022] Open
Abstract
Network biology has the capability to integrate, represent, interpret, and model complex biological systems by collectively accommodating biological omics data, biological interactions and associations, graph theory, statistical measures, and visualizations. Biological networks have recently been shown to be very useful for studies that decipher biological mechanisms and disease etiologies and for studies that predict therapeutic responses, at both the molecular and system levels. In this review, we briefly summarize the general framework of biological network studies, including data resources, network construction methods, statistical measures, network topological properties, and visualization tools. We also introduce several recent biological network applications and methods for the studies of rare diseases.
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18
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The histone methyltransferase Setd2 is indispensable for V(D)J recombination. Nat Commun 2019; 10:3353. [PMID: 31350389 PMCID: PMC6659703 DOI: 10.1038/s41467-019-11282-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/19/2019] [Indexed: 12/28/2022] Open
Abstract
The diverse repertoire of T cell receptors (TCR) and immunoglobulins is generated through the somatic rearrangement of respective V, D and J gene segments, termed V(D)J recombination, during early T or B cell development. However, epigenetic regulation of V(D)J recombination is still not fully understood. Here we show that the deficiency of Setd2, a histone methyltransferase that catalyzes lysine 36 trimethylation on histone 3 (H3K36me3) in mice, causes a severe developmental block of thymocytes at the CD4−CD8− DN3 stage. While H3K36me3 is normally enriched at the TCRβ locus, Setd2 deficiency reduces TCRβ H3K36me3 and suppresses TCRβ V(D)J rearrangement by impairing RAG1 binding to TCRβ loci and the DNA double-strand break repair. Similarly, Setd2 ablation also impairs immunoglobulin V(D)J rearrangement to induce B cell development block at the pro-B stage. Lastly, SETD2 is frequently mutated in patients with primary immunodeficiency. Our study thus demonstrates that Setd2 is required for optimal V(D)J recombination and normal lymphocyte development. The repertoire of adaptive immune receptor is generated by V(D)J recombination, somatic rearrangements of V, D and J gene segments, in the respective loci. Here the authors show that the deficiency of Setd2, a histone methyl transfer, impairs V(D)J recombination and induces severe developmental blocks in both T and B lineages.
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19
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Identification of candidate disease genes in patients with common variable immunodeficiency. QUANTITATIVE BIOLOGY 2019. [DOI: 10.1007/s40484-019-0174-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Cifaldi C, Brigida I, Barzaghi F, Zoccolillo M, Ferradini V, Petricone D, Cicalese MP, Lazarevic D, Cittaro D, Omrani M, Attardi E, Conti F, Scarselli A, Chiriaco M, Di Cesare S, Licciardi F, Davide M, Ferrua F, Canessa C, Pignata C, Giliani S, Ferrari S, Fousteri G, Barera G, Merli P, Palma P, Cesaro S, Gattorno M, Trizzino A, Moschese V, Chini L, Villa A, Azzari C, Finocchi A, Locatelli F, Rossi P, Sangiuolo F, Aiuti A, Cancrini C, Di Matteo G. Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies. Front Immunol 2019; 10:316. [PMID: 31031743 PMCID: PMC6470723 DOI: 10.3389/fimmu.2019.00316] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Primary Immunodeficiencies (PIDs) are a heterogeneous group of genetic immune disorders. While some PIDs can manifest with more than one phenotype, signs, and symptoms of various PIDs overlap considerably. Recently, novel defects in immune-related genes and additional variants in previously reported genes responsible for PIDs have been successfully identified by Next Generation Sequencing (NGS), allowing the recognition of a broad spectrum of disorders. Objective: To evaluate the strength and weakness of targeted NGS sequencing using custom-made Ion Torrent and Haloplex (Agilent) panels for diagnostics and research purposes. Methods: Five different panels including known and candidate genes were used to screen 105 patients with distinct PID features divided in three main PID categories: T cell defects, Humoral defects and Other PIDs. The Ion Torrent sequencing platform was used in 73 patients. Among these, 18 selected patients without a molecular diagnosis and 32 additional patients were analyzed by Haloplex enrichment technology. Results: The complementary use of the two custom-made targeted sequencing approaches allowed the identification of causative variants in 28.6% (n = 30) of patients. Twenty-two out of 73 (34.6%) patients were diagnosed by Ion Torrent. In this group 20 were included in the SCID/CID category. Eight out of 50 (16%) patients were diagnosed by Haloplex workflow. Ion Torrent method was highly successful for those cases with well-defined phenotypes for immunological and clinical presentation. The Haloplex approach was able to diagnose 4 SCID/CID patients and 4 additional patients with complex and extended phenotypes, embracing all three PID categories in which this approach was more efficient. Both technologies showed good gene coverage. Conclusions: NGS technology represents a powerful approach in the complex field of rare disorders but its different application should be weighted. A relatively small NGS target panel can be successfully applied for a robust diagnostic suspicion, while when the spectrum of clinical phenotypes overlaps more than one PID an in-depth NGS analysis is required, including also whole exome/genome sequencing to identify the causative gene.
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Affiliation(s)
- Cristina Cifaldi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Immacolata Brigida
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Matteo Zoccolillo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Valentina Ferradini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Davide Petricone
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Dejan Lazarevic
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cittaro
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Maryam Omrani
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Attardi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesca Conti
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Alessia Scarselli
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Maria Chiriaco
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Silvia Di Cesare
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesco Licciardi
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Montin Davide
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Clementina Canessa
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Silvia Giliani
- Department of Molecular and Translational Medicine, A. Nocivelli Institute for Molecular Medicine, University of Brescia, Brescia, Italy
| | - Simona Ferrari
- Unit of Medical Genetics, St. Orsola-Malpighi University Hospital, University of Bologna, Bologna, Italy
| | - Georgia Fousteri
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Graziano Barera
- Pediatric Department, San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Merli
- Department of Onco-Hematology and Cell and Gene Therapy, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Paolo Palma
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Simone Cesaro
- Paediatric Hematology-Oncology, “Ospedale della Donna e del Bambino”, Verona, Italy
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Giannina Gaslini, Genoa, Italy
| | - Antonio Trizzino
- Department of Pediatric Hematology and Oncology, “ARNAS Civico Di Cristina Benfratelli” Hospital, Palermo, Italy
| | - Viviana Moschese
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Loredana Chini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Anna Villa
- Milan Unit, National Research Council (CNR) Institute for Genetic and Biomedical Research (IRGB), Milan, Italy
- Humanitas Clinical and Research Institute, Rozzano, Italy
| | - Chiara Azzari
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Andrea Finocchi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, University of Rome La Sapienza, Rome, Italy
| | - Paolo Rossi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Gigliola Di Matteo
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
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21
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Liston A, Humblet-Baron S. Inborn errors of immunity: single mutations unravel mechanisms of immune disease. Immunol Cell Biol 2019; 97:358-359. [PMID: 30942931 DOI: 10.1111/imcb.12247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - Stephanie Humblet-Baron
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
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22
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Application of induced pluripotent stem cells to primary immunodeficiency diseases. Exp Hematol 2019; 71:43-50. [PMID: 30664903 DOI: 10.1016/j.exphem.2019.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/12/2022]
Abstract
Primary immunodeficiency diseases (PIDs) are a heterogeneous group of rare immune disorders with genetic causes. Effective treatments using hematopoietic stem cells or pharmaceutical agents have been around for decades. However, for many patients, these treatment options are ineffective, partly because the rarity of these PIDs complicates the diagnosis and therapy. Induced pluripotent stem cells (iPSCs) offer a potential solution to these problems. The proliferative capacity of iPSCs allows for the preparation of a large, stable supply of hematopoietic cells with the same genome as the patient, allowing for new human cell models that can trace cellular abnormalities during the pathogenesis and lead to new drug discovery. PID models using patient iPSCs have been instrumental in identifying deviations in the development or function of several types of immune cells, revealing new molecular targets for experimental therapies. These models are only in their early stages and for the most part have recapitulated results from existing models using animals or primary cells. However, iPSC-based models are being used to study complex diseases of other organs, including those with multigenic causes, suggesting that advances in differentiation processes will expand iPSC-based models to complex PIDs as well.
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23
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T-cell defects in patients with ARPC1B germline mutations account for combined immunodeficiency. Blood 2018. [PMID: 30254128 DOI: 10.1182/blood-2018-07-863431)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
ARPC1B is a key factor for the assembly and maintenance of the ARP2/3 complex that is involved in actin branching from an existing filament. Germline biallelic mutations in ARPC1B have been recently described in 6 patients with clinical features of combined immunodeficiency (CID), whose neutrophils and platelets but not T lymphocytes were studied. We hypothesized that ARPC1B deficiency may also lead to cytoskeleton and functional defects in T cells. We have identified biallelic mutations in ARPC1B in 6 unrelated patients with early onset disease characterized by severe infections, autoimmune manifestations, and thrombocytopenia. Immunological features included T-cell lymphopenia, low numbers of naïve T cells, and hyper-immunoglobulin E. Alteration in ARPC1B protein structure led to absent/low expression by flow cytometry and confocal microscopy. This molecular defect was associated with the inability of patient-derived T cells to extend an actin-rich lamellipodia upon T-cell receptor (TCR) stimulation and to assemble an immunological synapse. ARPC1B-deficient T cells additionally displayed impaired TCR-mediated proliferation and SDF1-α-directed migration. Gene transfer of ARPC1B in patients' T cells using a lentiviral vector restored both ARPC1B expression and T-cell proliferation in vitro. In 2 of the patients, in vivo somatic reversion restored ARPC1B expression in a fraction of lymphocytes and was associated with a skewed TCR repertoire. In 1 revertant patient, memory CD8+ T cells expressing normal levels of ARPC1B displayed improved T-cell migration. Inherited ARPC1B deficiency therefore alters T-cell cytoskeletal dynamics and functions, contributing to the clinical features of CID.
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24
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T-cell defects in patients with ARPC1B germline mutations account for combined immunodeficiency. Blood 2018; 132:2362-2374. [PMID: 30254128 DOI: 10.1182/blood-2018-07-863431] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/17/2018] [Indexed: 01/19/2023] Open
Abstract
ARPC1B is a key factor for the assembly and maintenance of the ARP2/3 complex that is involved in actin branching from an existing filament. Germline biallelic mutations in ARPC1B have been recently described in 6 patients with clinical features of combined immunodeficiency (CID), whose neutrophils and platelets but not T lymphocytes were studied. We hypothesized that ARPC1B deficiency may also lead to cytoskeleton and functional defects in T cells. We have identified biallelic mutations in ARPC1B in 6 unrelated patients with early onset disease characterized by severe infections, autoimmune manifestations, and thrombocytopenia. Immunological features included T-cell lymphopenia, low numbers of naïve T cells, and hyper-immunoglobulin E. Alteration in ARPC1B protein structure led to absent/low expression by flow cytometry and confocal microscopy. This molecular defect was associated with the inability of patient-derived T cells to extend an actin-rich lamellipodia upon T-cell receptor (TCR) stimulation and to assemble an immunological synapse. ARPC1B-deficient T cells additionally displayed impaired TCR-mediated proliferation and SDF1-α-directed migration. Gene transfer of ARPC1B in patients' T cells using a lentiviral vector restored both ARPC1B expression and T-cell proliferation in vitro. In 2 of the patients, in vivo somatic reversion restored ARPC1B expression in a fraction of lymphocytes and was associated with a skewed TCR repertoire. In 1 revertant patient, memory CD8+ T cells expressing normal levels of ARPC1B displayed improved T-cell migration. Inherited ARPC1B deficiency therefore alters T-cell cytoskeletal dynamics and functions, contributing to the clinical features of CID.
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25
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Primary immunodeficiency diseases in a tuberculosis endemic region: challenges and opportunities. Genes Immun 2018; 20:447-454. [PMID: 30185814 DOI: 10.1038/s41435-018-0041-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 12/11/2022]
Abstract
While individual primary immunodeficiency diseases (PIDs) are rare, collectively they represent a significant burden of disease. Recent estimates show that about one million people in Africa suffer from a PID. However, data from African PID registries reflect only a small percentage of the estimated prevalence. This disparity is partly due to the lack of PID awareness and the masking of PIDs by the endemic pathogens. Over three million tuberculosis (TB) cases were reported in Africa in 2016, with many of these from southern Africa. Despite concerted efforts to address this high burden of disease, the underlying genetic correlates of susceptibility to TB remain poorly understood. High penetrance mutations in immune system genes can cause PIDs that selectively predispose individuals to TB and other mycobacterial diseases. Additionally, the identification of individuals at a heightened risk of developing TB or of presenting with severe or disseminated TB due to their genetic ancestry is crucial to promote a positive treatment outcome. The screening for and identification of PID mutations in TB-endemic regions by next-generation sequencing (NGS) represents a promising approach to improve the understanding of what constitutes an effective immune response to TB, as well as the range of associated PIDs and phenotypes.
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26
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Teku GN, Vihinen M. Simulation of the Dynamics of Primary Immunodeficiencies in B Cells. Front Immunol 2018; 9:1785. [PMID: 30116248 PMCID: PMC6082931 DOI: 10.3389/fimmu.2018.01785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/19/2018] [Indexed: 12/20/2022] Open
Abstract
Primary immunodeficiencies (PIDs) are a group of over 300 hereditary, heterogeneous, and mainly rare disorders that affect the immune system. Various aspects of immune system and PID proteins and genes have been investigated and facilitate systems biological studies of effects of PIDs on B cell physiology and response. We reconstructed a B cell network model based on data for the core B cell receptor activation and response processes and performed semi-quantitative dynamic simulations for normal and B cell PID failure modes. The results for several knockout simulations correspond to previously reported molecular studies and reveal novel mechanisms for PIDs. The simulations for CD21, CD40, LYN, MS4A1, ORAI1, PLCG2, PTPRC, and STIM1 indicated profound changes to major transcription factor signaling and to the network. Significant effects were observed also in the BCL10, BLNK, BTK, loss-of-function CARD11, IKKB, MALT1, and NEMO, simulations whereas only minor effects were detected for PIDs that are caused by constitutively active proteins (PI3K, gain-of-function CARD11, KRAS, and NFKBIA). This study revealed the underlying dynamics of PID diseases, confirms previous observations, and identifies novel candidates for PID diagnostics and therapy.
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Affiliation(s)
| | - Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, Lund, Sweden
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27
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Requena D, Maffucci P, Bigio B, Shang L, Abhyankar A, Boisson B, Stenson PD, Cooper DN, Cunningham-Rundles C, Casanova JL, Abel L, Itan Y. CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency. Front Immunol 2018; 9:1340. [PMID: 29997612 PMCID: PMC6030251 DOI: 10.3389/fimmu.2018.01340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/29/2018] [Indexed: 11/17/2022] Open
Abstract
High-throughput genomic technologies yield about 20,000 variants in the protein-coding exome of each individual. A commonly used approach to select candidate disease-causing variants is to test whether the associated gene has been previously reported to be disease-causing. In the absence of known disease-causing genes, it can be challenging to associate candidate genes with specific genetic diseases. To facilitate the discovery of novel gene-disease associations, we determined the putative biologically closest known genes and their associated diseases for 13,005 human genes not currently reported to be disease-associated. We used these data to construct the closest disease-causing genes (CDG) server, which can be used to infer the closest genes with an associated disease for a user-defined list of genes or diseases. We demonstrate the utility of the CDG server in five immunodeficiency patient exomes across different diseases and modes of inheritance, where CDG dramatically reduced the number of candidate genes to be evaluated. This resource will be a considerable asset for ascertaining the potential relevance of genetic variants found in patient exomes to specific diseases of interest. The CDG database and online server are freely available to non-commercial users at: http://lab.rockefeller.edu/casanova/CDG.
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Affiliation(s)
- David Requena
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States
| | - Patrick Maffucci
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Medicine, Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States
| | - Lei Shang
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States
| | | | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases (Necker Branch), INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Charlotte Cunningham-Rundles
- Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Medicine, Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases (Necker Branch), INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.,Howard Hughes Medical Institute, New York, NY, United States.,Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases (Necker Branch), INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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28
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Carey B, Lambourne J, Porter S, Hodgson T. Chronic mucocutaneous candidiasis due to gain-of-function mutation in STAT1. Oral Dis 2018; 25:684-692. [PMID: 29702748 DOI: 10.1111/odi.12881] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/06/2018] [Accepted: 02/20/2018] [Indexed: 12/26/2022]
Abstract
Chronic mucocutaneous candidiasis (CMC) is a heterogenous group of primary immunodeficiency diseases characterised by susceptibility to chronic or recurrent superficial Candida infection of skin, nails and mucous membranes. Gain-of-function mutations in the STAT1 gene (STAT1-GOF) are the most common genetic aetiology for CMC, and mutation analysis should be considered. These mutations lead to defective responses in Type 1 and Type 17 helper T cells (Th1 and Th17), which, depending on the mutation, also predispose to infection with Staphylococci, Mycobacteria and Herpesviridae. We describe the clinical and genetic findings for three patients with CMC due to gain-of-function mutations in the STAT1 gene.
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Affiliation(s)
- Barbara Carey
- Oral Medicine Unit, UCLH NHS Foundation Trust, Eastman Dental Hospital, UCL Eastman Dental Institute, London, UK
| | - Jonathan Lambourne
- Department of Microbiology and Infectious Diseases, Barts Health NHS Trust, London, UK
| | - Stephen Porter
- Oral Medicine Unit, UCLH NHS Foundation Trust, Eastman Dental Hospital, UCL Eastman Dental Institute, London, UK
| | - Tim Hodgson
- Oral Medicine Unit, UCLH NHS Foundation Trust, Eastman Dental Hospital, UCL Eastman Dental Institute, London, UK
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29
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Abstract
Proper regulation of the immune system is required for protection against pathogens and preventing autoimmune disorders. Inborn errors of the immune system due to inherited or de novo germline mutations can lead to the loss of protective immunity, aberrant immune homeostasis, and the development of autoimmune disease, or combinations of these. Forward genetic screens involving clinical material from patients with primary immunodeficiencies (PIDs) can vary in severity from life-threatening disease affecting multiple cell types and organs to relatively mild disease with susceptibility to a limited range of pathogens or mild autoimmune conditions. As central mediators of innate and adaptive immune responses, T cells are critical orchestrators and effectors of the immune response. As such, several PIDs result from loss of or altered T cell function. PID-associated functional defects range from complete absence of T cell development to uncontrolled effector cell activation. Furthermore, the gene products of known PID causal genes are involved in diverse molecular pathways ranging from T cell receptor signaling to regulators of protein glycosylation. Identification of the molecular and biochemical cause of PIDs can not only guide the course of treatment for patients, but also inform our understanding of the basic biology behind T cell function. In this chapter, we review PIDs with known genetic causes that intrinsically affect T cell function with particular focus on perturbations of biochemical pathways.
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Affiliation(s)
- William A Comrie
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States; Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, United States
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States; Clinical Genomics Program, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, United States.
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30
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Bigley V, Cytlak U, Collin M. Human dendritic cell immunodeficiencies. Semin Cell Dev Biol 2018; 86:50-61. [PMID: 29452225 DOI: 10.1016/j.semcdb.2018.02.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/28/2017] [Accepted: 02/10/2018] [Indexed: 12/21/2022]
Abstract
The critical functions of dendritic cells (DCs) in immunity and tolerance have been demonstrated in many animal models but their non-redundant roles in humans are more difficult to probe. Human primary immunodeficiency (PID), resulting from single gene mutations, may result in DC deficiency or dysfunction. This relatively recent recognition illuminates the in vivo role of human DCs and the pathophysiology of the associated clinical syndromes. In this review, the development and function of DCs as established in murine models and human in vitro systems, discussed. This forms the basis of predicting the effects of DC deficiency in vivo and understanding the consequences of specific mutations on DC development and function. DC deficiency syndromes are associated with heterozygous GATA2 mutation, bi-allelic and heterozygous IRF8 mutation and heterozygous IKZF1 mutation. The intricate involvement of DCs in the balance between immunity and tolerance is leading to increased recognition of their involvement in a number of other immunodeficiencies and autoimmune conditions. Owing to the precise control of transcription factor gene expression by super-enhancer elements, phenotypic anomalies are relatively commonly caused by heterozygous mutations.
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Affiliation(s)
- Venetia Bigley
- Human DC Lab, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK; Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Urszula Cytlak
- Human DC Lab, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew Collin
- Human DC Lab, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK; Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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31
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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.
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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.
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32
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Abstract
Purpose of review Dendritic cells are specialized antigen-presenting cells which link innate and adaptive immunity, through recognition and presentation of antigen to T cells. Although the importance of dendritic cells has been demonstrated in many animal models, their contribution to human immunity remains relatively unexplored in vivo. Given their central role in infection, autoimmunity, and malignancy, dendritic cell deficiency or dysfunction would be expected to have clinical consequences. Recent findings Human dendritic cell deficiency disorders, related to GATA binding protein 2 (GATA2) and interferon regulatory factor 8 (IRF8) mutations, have highlighted the importance of dendritic cells and monocytes in primary immunodeficiency diseases and begun to shed light on their nonredundant roles in host defense and immune regulation in vivo. The contribution of dendritic cell and monocyte dysfunction to the pathogenesis of primary immunodeficiency disease phenotypes is becoming increasingly apparent. However, dendritic cell analysis is not yet a routine part of primary immunodeficiency disease workup. Summary Widespread uptake of dendritic cell/monocyte screening in clinical practice will facilitate the discovery of novel dendritic cell and monocyte disorders as well as advancing our understanding of human dendritic cell biology in health and disease.
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Schwerd T, Twigg SRF, Aschenbrenner D, Manrique S, Miller KA, Taylor IB, Capitani M, McGowan SJ, Sweeney E, Weber A, Chen L, Bowness P, Riordan A, Cant A, Freeman AF, Milner JD, Holland SM, Frede N, Müller M, Schmidt-Arras D, Grimbacher B, Wall SA, Jones EY, Wilkie AOM, Uhlig HH. A biallelic mutation in IL6ST encoding the GP130 co-receptor causes immunodeficiency and craniosynostosis. J Exp Med 2017; 214:2547-2562. [PMID: 28747427 PMCID: PMC5584118 DOI: 10.1084/jem.20161810] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 05/10/2017] [Accepted: 06/21/2017] [Indexed: 12/18/2022] Open
Abstract
Multiple cytokines, including interleukin 6 (IL-6), IL-11, IL-27, oncostatin M (OSM), and leukemia inhibitory factor (LIF), signal via the common GP130 cytokine receptor subunit. In this study, we describe a patient with a homozygous mutation of IL6ST (encoding GP130 p.N404Y) who presented with recurrent infections, eczema, bronchiectasis, high IgE, eosinophilia, defective B cell memory, and an impaired acute-phase response, as well as skeletal abnormalities including craniosynostosis. The p.N404Y missense substitution is associated with loss of IL-6, IL-11, IL-27, and OSM signaling but a largely intact LIF response. This study identifies a novel immunodeficiency with phenotypic similarities to STAT3 hyper-IgE syndrome caused by loss of function of GP130.
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Affiliation(s)
- Tobias Schwerd
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, England, UK.,Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Dominik Aschenbrenner
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Santiago Manrique
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England, UK
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Indira B Taylor
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Melania Capitani
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women's National Health Service Foundation Trust, Liverpool, England, UK
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's National Health Service Foundation Trust, Liverpool, England, UK
| | - Liye Chen
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, England, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, England, UK
| | - Andrew Riordan
- Department of Paediatric Infectious Diseases and Immunology, Alder Hey Children's National Health Service Foundation Trust, Liverpool, England, UK
| | - Andrew Cant
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, England, UK
| | - Alexandra F Freeman
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Natalie Frede
- Center for Chronic Immunodeficiency, Universitätsklinikum Freiburg, Freiburg, Germany
| | - Miryam Müller
- Inflammation and Cancer Lab, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dirk Schmidt-Arras
- Inflammation and Cancer Lab, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency, Universitätsklinikum Freiburg, Freiburg, Germany.,Institute of Immunology and Transplantation, Royal Free Hospital, University College London, London, England, UK
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England, UK .,Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals National Health Service Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, England, UK .,Department of Paediatrics, University of Oxford, Oxford, England, UK
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Teku GN, Vihinen M. Simulation of the dynamics of primary immunodeficiencies in CD4+ T-cells. PLoS One 2017; 12:e0176500. [PMID: 28448599 PMCID: PMC5407609 DOI: 10.1371/journal.pone.0176500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Primary immunodeficiencies (PIDs) form a large and heterogeneous group of mainly rare disorders that affect the immune system. T-cell deficiencies account for about one-tenth of PIDs, most of them being monogenic. Apart from genetic and clinical information, lots of other data are available for PID proteins and genes, including functions and interactions. Thus, it is possible to perform systems biology studies on the effects of PIDs on T-cell physiology and response. To achieve this, we reconstructed a T-cell network model based on literature mining and TPPIN, a previously published core T-cell network, and performed semi-quantitative dynamic network simulations on both normal and T-cell PID failure modes. The results for several loss-of-function PID simulations correspond to results of previously reported molecular studies. The simulations for TCR PTPRC, LCK, ZAP70 and ITK indicate profound changes to numerous proteins in the network. Significant effects were observed also in the BCL10, CARD11, MALT1, NEMO, IKKB and MAP3K14 simulations. No major effects were observed for PIDs that are caused by constitutively active proteins. The T-cell model facilitates the understanding of the underlying dynamics of PID disease processes. The approach confirms previous knowledge about T-cell signaling network and indicates several new important proteins that may be of interest when developing novel diagnosis and therapies to treat immunological defects.
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Affiliation(s)
- Gabriel N. Teku
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- * E-mail:
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Stray-Pedersen A, Sorte HS, Samarakoon P, Gambin T, Chinn IK, Coban Akdemir ZH, Erichsen HC, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OK, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR, Wiszniewski W, Fevang B, Aukrust P, Tjønnfjord GE, Gedde-Dahl T, Hjorth-Hansen H, Dybedal I, Nordøy I, Jørgensen SF, Abrahamsen TG, Øverland T, Bechensteen AG, Skogen V, Osnes LTN, Kulseth MA, Prescott TE, Rustad CF, Heimdal KR, Belmont JW, Rider NL, Chinen J, Cao TN, Smith EA, Caldirola MS, Bezrodnik L, Lugo Reyes SO, Espinosa Rosales FJ, Guerrero-Cursaru ND, Pedroza LA, Poli CM, Franco JL, Trujillo Vargas CM, Aldave Becerra JC, Wright N, Issekutz TB, Issekutz AC, Abbott J, Caldwell JW, Bayer DK, Chan AY, Aiuti A, Cancrini C, Holmberg E, West C, Burstedt M, Karaca E, Yesil G, Artac H, Bayram Y, Atik MM, Eldomery MK, Ehlayel MS, Jolles S, Flatø B, Bertuch AA, Hanson IC, Zhang VW, Wong LJ, Hu J, Walkiewicz M, Yang Y, Eng CM, Boerwinkle E, Gibbs RA, Shearer WT, Lyle R, Orange JS, Lupski JR. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol 2017; 139:232-245. [PMID: 27577878 PMCID: PMC5222743 DOI: 10.1016/j.jaci.2016.05.042] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/10/2016] [Accepted: 05/13/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions. OBJECTIVE We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs. METHODS Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping. RESULTS A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays. CONCLUSION This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.
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Affiliation(s)
- Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Norwegian National Unit for Newborn Screening, Oslo University Hospital, Oslo, Norway; Department of Pediatrics, Oslo University Hospital, Oslo, Norway.
| | - Hanne Sørmo Sorte
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tomasz Gambin
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Ivan K Chinn
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Zeynep H Coban Akdemir
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | | | - Lisa R Forbes
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Shen Gu
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Bo Yuan
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Shalini N Jhangiani
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Donna M Muzny
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Sarah K Nicholas
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Lenora M Noroski
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Filiz O Seeborg
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carla M Davis
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Debra L Canter
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Emily M Mace
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Timothy J Vece
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carl E Allen
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Harshal A Abhyankar
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Philip M Boone
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine R Beck
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Wojciech Wiszniewski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Børre Fevang
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Geir E Tjønnfjord
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Henrik Hjorth-Hansen
- Department of Hematology, St Olavs Hospital, Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Dybedal
- Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Ingvild Nordøy
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Silje F Jørgensen
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tore G Abrahamsen
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Vegard Skogen
- Department of Infectious Diseases, Medical Clinic, University Hospital of North-Norway, Tromsø, Norway
| | - Liv T N Osnes
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Mari Ann Kulseth
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trine E Prescott
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ketil R Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Nicholas L Rider
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Javier Chinen
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Tram N Cao
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Eric A Smith
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Tex
| | - Maria Soledad Caldirola
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Liliana Bezrodnik
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Saul Oswaldo Lugo Reyes
- Immunodeficiencies Research Unit, National Institute of Pediatrics, Coyoacan, Mexico City, Mexico
| | | | | | | | - Cecilia M Poli
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Hospital Roberto del Rio, Universidad de Chile, Santiago, Chile
| | - Jose L Franco
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Claudia M Trujillo Vargas
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Nicola Wright
- Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Thomas B Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Andrew C Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Jordan Abbott
- Department of Pediatrics, National Jewish Health, Denver, Colo
| | - Jason W Caldwell
- Section of Pulmonary, Critical Care, Allergic and Immunological Diseases, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston-Salem, NC
| | - Diana K Bayer
- Department of Pediatrics, Division of Pediatric Allergy/Immunology and Pulmonology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Alice Y Chan
- Department of Pediatrics, University of California, San Francisco, Calif
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), and Vita-Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- University Department of Pediatrics, DPUO, Bambino Gesù Children's Hospital, and Tor Vergata University, Rome, Italy
| | - Eva Holmberg
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Christina West
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Magnus Burstedt
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Ender Karaca
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Gözde Yesil
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul, Turkey
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Selcuk University Medical Faculty, Alaeddin Keykubat Kampusu, Konya, Turkey
| | - Yavuz Bayram
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mehmed Musa Atik
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad K Eldomery
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad S Ehlayel
- Department of Pediatrics, Section of Pediatric Allergy and Immunology, Hamad Medical Corporation, Doha, Department of Paediatrics, Weill Cornell Medical College, Ar-Rayyan, Qatar
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Alison A Bertuch
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex
| | - I Celine Hanson
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Victor W Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Eric Boerwinkle
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Human Genetics Center, University of Texas School of Public Health, Houston, Tex
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - William T Shearer
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jordan S Orange
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex.
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex.
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Meyts I, Bosch B, Bolze A, Boisson B, Itan Y, Belkadi A, Pedergnana V, Moens L, Picard C, Cobat A, Bossuyt X, Abel L, Casanova JL. Exome and genome sequencing for inborn errors of immunity. J Allergy Clin Immunol 2016; 138:957-969. [PMID: 27720020 PMCID: PMC5074686 DOI: 10.1016/j.jaci.2016.08.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/03/2023]
Abstract
The advent of next-generation sequencing (NGS) in 2010 has transformed medicine, particularly the growing field of inborn errors of immunity. NGS has facilitated the discovery of novel disease-causing genes and the genetic diagnosis of patients with monogenic inborn errors of immunity. Whole-exome sequencing (WES) is presently the most cost-effective approach for research and diagnostics, although whole-genome sequencing offers several advantages. The scientific or diagnostic challenge consists in selecting 1 or 2 candidate variants among thousands of NGS calls. Variant- and gene-level computational methods, as well as immunologic hypotheses, can help narrow down this genome-wide search. The key to success is a well-informed genetic hypothesis on 3 key aspects: mode of inheritance, clinical penetrance, and genetic heterogeneity of the condition. This determines the search strategy and selection criteria for candidate alleles. Subsequent functional validation of the disease-causing effect of the candidate variant is critical. Even the most up-to-date dry lab cannot clinch this validation without a seasoned wet lab. The multifariousness of variations entails an experimental rigor even greater than traditional Sanger sequencing-based approaches in order not to assign a condition to an irrelevant variant. Finding the needle in the haystack takes patience, prudence, and discernment.
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Affiliation(s)
- Isabelle Meyts
- Department of Immunology and Microbiology, Childhood Immunology, Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium.
| | - Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Alexandre Bolze
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Helix, San Carlos, Calif
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Leen Moens
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Paris Descartes University-Sorbonne Paris Cité, Paris, France; Study Center for Immunodeficiency, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Xavier Bossuyt
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY; Pediatric Hematology and Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
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Fang M, Abolhassani H, Lim CK, Zhang J, Hammarström L. Next Generation Sequencing Data Analysis in Primary Immunodeficiency Disorders - Future Directions. J Clin Immunol 2016; 36 Suppl 1:68-75. [PMID: 26993986 DOI: 10.1007/s10875-016-0260-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 02/28/2016] [Indexed: 12/16/2022]
Abstract
Primary immunodeficiency diseases (PIDs) comprise a group of highly heterogeneous immune system diseases and around 300 forms of PID have been described to date. Next Generation Sequencing (NGS) has recently become an increasingly used approach for gene identification and molecular diagnosis of human diseases. Herein we summarize the practical considerations for the interpretation of NGS data and the techniques for searching disease-related PID genes, and suggest future directions for research in this field.
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Affiliation(s)
- Mingyan Fang
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, -141 86, Stockholm, SE, Sweden.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Hassan Abolhassani
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, -141 86, Stockholm, SE, Sweden.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Che Kang Lim
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, -141 86, Stockholm, SE, Sweden.,Department of Clinical Research, Singapore General Hospital, Singapore, 169856, Singapore
| | | | - Lennart Hammarström
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, -141 86, Stockholm, SE, Sweden.
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Fodil N, Langlais D, Gros P. Primary Immunodeficiencies and Inflammatory Disease: A Growing Genetic Intersection. Trends Immunol 2016; 37:126-140. [PMID: 26791050 DOI: 10.1016/j.it.2015.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 02/08/2023]
Abstract
Recent advances in genome analysis have provided important insights into the genetic architecture of infectious and inflammatory diseases. The combined analysis of loci detected by genome-wide association studies (GWAS) in 22 inflammatory diseases has revealed a shared genetic core and associated biochemical pathways that play a central role in pathological inflammation. Parallel whole-exome sequencing studies have identified 265 genes mutated in primary immunodeficiencies (PID). Here, we examine the overlap between these two data sets, and find that it consists of genes essential for protection against infections and in which persistent activation causes pathological inflammation. Based on this intersection, we propose that, although strong or inactivating mutations (rare variants) in these genes may cause severe disease (PIDs), their more subtle modulation potentially by common regulatory/coding variants may contribute to chronic inflammation.
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Affiliation(s)
- Nassima Fodil
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - David Langlais
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - Philippe Gros
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada.
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The human gene damage index as a gene-level approach to prioritizing exome variants. Proc Natl Acad Sci U S A 2015; 112:13615-20. [PMID: 26483451 DOI: 10.1073/pnas.1518646112] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The protein-coding exome of a patient with a monogenic disease contains about 20,000 variants, only one or two of which are disease causing. We found that 58% of rare variants in the protein-coding exome of the general population are located in only 2% of the genes. Prompted by this observation, we aimed to develop a gene-level approach for predicting whether a given human protein-coding gene is likely to harbor disease-causing mutations. To this end, we derived the gene damage index (GDI): a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population. We found that the GDI was correlated with selective evolutionary pressure, protein complexity, coding sequence length, and the number of paralogs. We compared GDI with the leading gene-level approaches, genic intolerance, and de novo excess, and demonstrated that GDI performed best for the detection of false positives (i.e., removing exome variants in genes irrelevant to disease), whereas genic intolerance and de novo excess performed better for the detection of true positives (i.e., assessing de novo mutations in genes likely to be disease causing). The GDI server, data, and software are freely available to noncommercial users from lab.rockefeller.edu/casanova/GDI.
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