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Alamad B, Elliott K, Knight JC. Cross-population applications of genomics to understand the risk of multifactorial traits involving inflammation and immunity. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e3. [PMID: 38549844 PMCID: PMC10953767 DOI: 10.1017/pcm.2023.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 04/26/2024]
Abstract
The interplay between genetic and environmental factors plays a significant role in interindividual variation in immune and inflammatory responses. The availability of high-throughput low-cost genotyping and next-generation sequencing has revolutionized our ability to identify human genetic variation and understand how this varies within and between populations, and the relationship with disease. In this review, we explore the potential of genomics for patient benefit, specifically in the diagnosis, prognosis and treatment of inflammatory and immune-related diseases. We summarize the knowledge arising from genetic and functional genomic approaches, and the opportunity for personalized medicine. The review covers applications in infectious diseases, rare immunodeficiencies and autoimmune diseases, illustrating advances in diagnosis and understanding risk including use of polygenic risk scores. We further explore the application for patient stratification and drug target prioritization. The review highlights a key challenge to the field arising from the lack of sufficient representation of genetically diverse populations in genomic studies. This currently limits the clinical utility of genetic-based diagnostic and risk-based applications in non-Caucasian populations. We highlight current genome projects, initiatives and biobanks from diverse populations and how this is being used to improve healthcare globally by improving our understanding of genetic susceptibility to diseases and regional pathogens such as malaria and tuberculosis. Future directions and opportunities for personalized medicine and wider application of genomics in health care are described, for the benefit of individual patients and populations worldwide.
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Affiliation(s)
- Bana Alamad
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kate Elliott
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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2
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Dufrasne F. Immune Diseases: Challenges, Hopes and Recent Achievements. Pharmaceuticals (Basel) 2024; 17:97. [PMID: 38256930 PMCID: PMC10821122 DOI: 10.3390/ph17010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Although they have been greatly described for about 50 years, we have gained a much greater understanding of immune diseases since the beginning of this millennium [...].
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Affiliation(s)
- François Dufrasne
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
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3
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Awni AA, Hamed ZO, Abdul-Hassan Abbas A, Abdulamir AS. Effect of NLRP3 inflammasome genes polymorphism on disease susceptibility and response to TNF-α inhibitors in Iraqi patients with rheumatoid arthritis. Heliyon 2023; 9:e16814. [PMID: 37332933 PMCID: PMC10275785 DOI: 10.1016/j.heliyon.2023.e16814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/19/2023] [Accepted: 05/29/2023] [Indexed: 06/20/2023] Open
Abstract
Background Rheumatoid arthritis (RA) is a genetically predisposed, systemic, chronic, inflammatory disease. Immune system dysregulation and inherited susceptibility polymorphisms suggest that this type of variation is functional and may help predict disease susceptibility and develop new therapeutic strategies. Anti-TNF-alpha (TNF-α) drugs are highly effective RA treatments, but not all patients respond the same way. It's important to figure out whether RA risk alleles can identify and predict anti-TNF-α-responsiveness in RA patients. Aims of the study Examine the function of the NLR family pyrin domain containing 3 (NLRP3) and caspase recruitment domain family member 8 (CARD8) genes polymorphisms and their morbid genotypes and alleles in RA patients and apparently healthy controls. In addition, their role in disease susceptibility, severity, and response to anti-TNF-α therapy. Also, examine how single nucleotide polymorphisms (SNPs) affect serum levels of pro-inflammatory cytokines like TNF-α and interleukin (IL)-1β. Materials and methods 100 RA patients (88 females, 12 males) and 100 apparently healthy people (86 females, 14 males) were examined. To measure serum TNF-α and IL-1β, Elabscience sandwich ELISA kits were used. Iraq Biotech, Turkey DNA extraction kit was used to extract genomic DNA from whole blood. CARD8 (rs2043211) and NLRP3 (rs4612666) were genotyped using Agilent, AriaMx, USA, through Tri-Plex SYBR Green-based real-time PCR allelic discrimination assays. Geneious software, version 2019.2.2, used to design primers from published sequences (GenBank accession no. GCA 009914755.1). Primer specificity was determined by NCBI's BLAST. Results Study found that there is association between cytokines serum level and 28-joints disease activity score (DAS-28). The level of TNF-α increases with the higher DAS-28 (r2 = 0.45, P < 0.0001). Also, IL- 1β level increases with higher DAS-28 (r2 = 0.51, P < 0.0001). There were no statistically significant variations between patients with RA and the control group in the distribution of CARD8 SNP rs2043211 and NLRP3 SNP rs4612666 genotypes (P = 0.17 and 0.08 respectively) as well their alleles (P = 0.059 and 0.879 respectively). CARD8 (rs2043211) TT genotype was more frequent in patients with higher DAS-28 (P < 0.0001) and higher TNF-α and IL-1β serum levels (P < 0.0001 for both). Also, NLRP3 (rs4612666) TT genotype was more frequent in patients with higher DAS-28 (P < 0.0001) and higher TNF-α and IL- 1β serum levels (P < 0.0001 for both). Interestingly, this study revealed that CARD8 (rs2043211) and NLRP3 (rs4612666) variant genotypes are associated with lower response to anti-TNF-α drugs. Conclusions Serum TNF-α and IL-1β correlate with DAS-28 and disease activity. Non-responders have elevated TNF-α and IL-1β. CARD8 rs2043211 and NLRP3 rs4612666 variant polymorphisms are associated with high serum TNF-α and IL-1β, active disease course, poor disease outcomes, and low response to anti-TNF-α therapy.
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Affiliation(s)
- Abdullah Abbas Awni
- College of Medical Sciences Techniques, The University of Mashreq, Baghdad, Iraq
| | - Zainab Oday Hamed
- Therapeutics and Clinical Pharmacy Department, Baghdad College of Medical Sciences, Baghdad, Iraq
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4
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Xia L, Liu XH, Yuan Y, Lowrie DB, Fan XY, Li T, Hu ZD, Lu SH. An Updated Review on MSMD Research Globally and A Literature Review on the Molecular Findings, Clinical Manifestations, and Treatment Approaches in China. Front Immunol 2022; 13:926781. [PMID: 36569938 PMCID: PMC9774035 DOI: 10.3389/fimmu.2022.926781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/20/2022] [Indexed: 12/13/2022] Open
Abstract
Mendelian susceptibility to mycobacterial disease (MSMD) arises from a group of rare inherited errors of immunity that result in selective susceptibility of otherwise healthy people to clinical disease caused by low virulence strains of mycobacteria, such as Mycobacterium bovis Bacille Calmette-Guérin (BCG) and environmental mycobacteria. Patients have normal resistance to other pathogens and no overt abnormalities in routine immunological and hematological evaluations for primary immunodeficiencies. At least 19 genes and 34 clinical phenotypes have been identified in MSMD. However, there have been no systematic reports on the clinical characteristics and genetic backgrounds of MSMD in China. In this review, on the one hand, we summarize an update findings on molecular defects and immunological mechanisms in the field of MSMD research globally. On the other hand, we undertook a systematic review of PubMed (MEDLINE), the Cochrane Central Register of Controlled Trials (CENTRAL), Web of Science, EMBASE, CNKI, and Wanfang to identify articles published before Jan 23, 2022, to summarize the clinical characteristics, diagnosis, treatment, and prognosis of MSMD in China. All the English and Chinese publications were searched without any restriction on article types.
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Affiliation(s)
- Lu Xia
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xu-Hui Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yuan Yuan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Douglas B. Lowrie
- Shenzhen National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Tao Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhi-Dong Hu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,*Correspondence: Zhi-Dong Hu, ; Shui-Hua Lu,
| | - Shui-Hua Lu
- Shenzhen National Clinical Research Center for Infectious Disease, Shenzhen, China,Department of tuberculosis, The Third People’s Hospital of Shenzhen, Shenzhen, China,*Correspondence: Zhi-Dong Hu, ; Shui-Hua Lu,
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5
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- 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.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - 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.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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6
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Boz V, Zanchi C, Levantino L, Riccio G, Tommasini A. Druggable monogenic immune defects hidden in diverse medical specialties: Focus on overlap syndromes. World J Clin Pediatr 2022; 11:136-150. [PMID: 35433297 PMCID: PMC8985491 DOI: 10.5409/wjcp.v11.i2.136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/03/2021] [Accepted: 01/08/2022] [Indexed: 02/06/2023] Open
Abstract
In the last two decades two new paradigms changed our way of perceiving primary immunodeficiencies: An increasing number of immune defects are more associated with inflammatory or autoimmune features rather than with infections. Some primary immune defects are due to hyperactive pathways that can be targeted by specific inhibitors, providing innovative precision treatments that can change the natural history of diseases. In this article we review some of these “druggable” inborn errors of immunity and describe how they can be suspected and diagnosed in diverse pediatric and adult medicine specialties. Since the availability of precision treatments can dramatically impact the course of these diseases, preventing the development of organ damage, it is crucial to widen the awareness of these conditions and to provide practical hints for a prompt detection and cure.
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Affiliation(s)
- Valentina Boz
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34137, Italy
| | - Chiara Zanchi
- Department of Pediatrics, Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste 34137, Italy
| | - Laura Levantino
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34137, Italy
| | - Guglielmo Riccio
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34137, Italy
| | - Alberto Tommasini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste 34137, Italy
- Department of Pediatrics, Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste 34137, Italy
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7
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Meeths M, Bryceson YT. Genetics and pathophysiology of haemophagocytic lymphohistiocytosis. Acta Paediatr 2021; 110:2903-2911. [PMID: 34192386 DOI: 10.1111/apa.16013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022]
Abstract
Haemophagocytic lymphohistiocytosis (HLH) represents a life-threatening hyperinflammatory syndrome. Familial studies have established autosomal and X-linked recessive causes of HLH, highlighting a pivotal role for lymphocyte cytotoxicity in the control of certain virus infections and immunoregulation. Recently, a more complex etiological framework has emerged, linking HLH predisposition to variants in genes required for metabolism or immunity to intracellular pathogens. We review genetic predisposition to HLH and discuss how molecular insights have provided fundamental knowledge of the immune system as well as detailed pathophysiological understanding of hyperinflammatory diseases, highlighting new treatment strategies.
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Affiliation(s)
- Marie Meeths
- Childhood Cancer Research Unit Department of Women’s and Children’s Health Karolinska Institutet Stockholm Sweden
- Theme of Children’s Health Karolinska University Hospital Stockholm Sweden
| | - Yenan T. Bryceson
- Centre for Hematology and Regenerative Medicine Department of Medicine Karolinska Institute Stockholm Sweden
- Division of Clinical Immunology and Transfusion Medicine Karolinska University Hospital Stockholm Sweden
- Broegelmann Research Laboratory Department of Clinical Sciences University of Bergen Bergen Norway
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8
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Körholz J, Gabrielyan A, Sowerby JM, Boschann F, Chen LS, Paul D, Brandt D, Kleymann J, Kolditz M, Toepfner N, Knöfler R, Jacobsen EM, Wolf C, Conrad K, Röber N, Lee-Kirsch MA, Smith KGC, Mundlos S, Berner R, Dalpke AH, Schuetz C, Rae W. One Gene, Many Facets: Multiple Immune Pathway Dysregulation in SOCS1 Haploinsufficiency. Front Immunol 2021; 12:680334. [PMID: 34421895 PMCID: PMC8375263 DOI: 10.3389/fimmu.2021.680334] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/13/2021] [Indexed: 01/25/2023] Open
Abstract
Background Inborn errors of immunity (IEI) present with a large phenotypic spectrum of disease, which can pose diagnostic and therapeutic challenges. Suppressor of cytokine signaling 1 (SOCS1) is a key negative regulator of cytokine signaling, and has recently been associated with a novel IEI. Of patients described to date, it is apparent that SOCS1 haploinsufficiency has a pleiotropic effect in humans. Objective We sought to investigate whether dysregulation of immune pathways, in addition to STAT1, play a role in the broad clinical manifestations of SOCS1 haploinsufficiency. Methods We assessed impacts of reduced SOCS1 expression across multiple immune cell pathways utilizing patient cells and CRISPR/Cas9 edited primary human T cells. Results SOCS1 haploinsufficiency phenotypes straddled across the International Union of Immunological Societies classifications of IEI. We found that reduced SOCS1 expression led to dysregulation of multiple intracellular pathways in immune cells. STAT1 phosphorylation is enhanced, comparably with STAT1 gain-of-function mutations, and STAT3 phosphorylation is similarly reduced with concurrent reduction of Th17 cells. Furthermore, reduced SOCS1 E3 ligase function was associated with increased FAK1 in immune cells, and increased AKT and p70 ribosomal protein S6 kinase phosphorylation. We also found Toll-like receptor responses are increased in SOCS1 haploinsufficiency patients. Conclusions SOCS1 haploinsufficiency is a pleiotropic monogenic IEI. Dysregulation of multiple immune cell pathways may explain the variable clinical phenotype associated with this new condition. Knowledge of these additional dysregulated immune pathways is important when considering the optimum management for SOCS1 haploinsufficient patients.
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Affiliation(s)
- Julia Körholz
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Anastasia Gabrielyan
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - John M Sowerby
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Lan-Sun Chen
- Institute of Medical Microbiology and Virology, Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Diana Paul
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - David Brandt
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Janina Kleymann
- Department of Internal Medicine, Pneumology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Martin Kolditz
- Department of Internal Medicine, Pneumology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nicole Toepfner
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Ralf Knöfler
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Christine Wolf
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Karsten Conrad
- Institute of Immunology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nadja Röber
- Institute of Immunology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Mundlos
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Research Group (RG) Development and Disease, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Reinhard Berner
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Catharina Schuetz
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - William Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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9
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Abstract
Epstein-Barr virus (EBV) is associated with 200,000 cancers annually, including B-cell lymphomas in immunosuppressed hosts. Hypomorphic mutations of the de novo pyrimidine synthesis pathway enzyme cytidine 5′ triphosphate synthase 1 (CTPS1) suppress cell-mediated immunity, resulting in fulminant EBV infection and EBV+ central nervous system (CNS) lymphomas. Since CTP is a critical precursor for DNA, RNA, and phospholipid synthesis, this observation raises the question of whether the isozyme CTPS2 or cytidine salvage pathways help meet CTP demand in EBV-infected B cells. Here, we found that EBV upregulated CTPS1 and CTPS2 with distinct kinetics in newly infected B cells. While CRISPR CTPS1 knockout caused DNA damage and proliferation defects in lymphoblastoid cell lines (LCLs), which express the EBV latency III program observed in CNS lymphomas, double CTPS1/2 knockout caused stronger phenotypes. EBNA2, MYC, and noncanonical NF-κB positively regulated CTPS1 expression. CTPS1 depletion impaired EBV lytic DNA synthesis, suggesting that latent EBV may drive pathogenesis with CTPS1 deficiency. Cytidine rescued CTPS1/2 deficiency phenotypes in EBV-transformed LCLs and Burkitt B cells, highlighting CTPS1/2 as a potential therapeutic target for EBV-driven lymphoproliferative disorders. Collectively, our results suggest that CTPS1 and CTPS2 have partially redundant roles in EBV-transformed B cells and provide insights into EBV pathogenesis with CTPS1 deficiency.
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10
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Nehmar R, Fauconnier L, Alves‐Filho J, Togbe D, DeCauwer A, Bahram S, Le Bert M, Ryffel B, Georgel P. Aryl hydrocarbon receptor (Ahr)-dependent Il-22 expression by type 3 innate lymphoid cells control of acute joint inflammation. J Cell Mol Med 2021; 25:4721-4731. [PMID: 33734594 PMCID: PMC8107095 DOI: 10.1111/jcmm.16433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 12/20/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) controls several inflammatory and metabolic pathways involved in various diseases, including the development of arthritis. Here, we investigated the role of AHR activation in IL-22-dependent acute arthritis using the K/BxN serum transfer model. We observed an overall reduction of cytokine expression in Ahr-deficient mice, along with decreased signs of joint inflammation. Conversely, we report worsened arthritis symptoms in Il-22 deficient mice. Pharmacological stimulation of AHR with the agonist VAG539, as well as injection of recombinant IL-22, given prior arthritogenic triggering, attenuated inflammation and reduced joint destruction. The protective effect of VAG539 was abrogated in Il-22 deficient mice. Finally, conditional Ahr depletion of Rorc-expressing cells was sufficient to attenuate arthritis, thereby uncovering a previously unsuspected role of AHR in type 3 innate lymphoid cells during acute arthritis.
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Affiliation(s)
- Ramzi Nehmar
- Laboratoire d’ImmunoRhumatologie MoléculaireInstitut national de la santé et de la recherche médicale (INSERM) UMR_S 1109Institut thématique interdisciplinaire (ITI) de Médecine de Précision de StrasbourgTransplantex NGFaculté de MédecineFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de Strasbourg (FMTS)Université de StrasbourgStrasbourgFrance
| | | | - Jose Alves‐Filho
- Department of PharmacologyRibeirao Preto Medical School, University of Sao PauloRibeirao PretoBrazil
| | | | - Aurore DeCauwer
- Laboratoire d’ImmunoRhumatologie MoléculaireInstitut national de la santé et de la recherche médicale (INSERM) UMR_S 1109Institut thématique interdisciplinaire (ITI) de Médecine de Précision de StrasbourgTransplantex NGFaculté de MédecineFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de Strasbourg (FMTS)Université de StrasbourgStrasbourgFrance
| | - Seiamak Bahram
- Laboratoire d’ImmunoRhumatologie MoléculaireInstitut national de la santé et de la recherche médicale (INSERM) UMR_S 1109Institut thématique interdisciplinaire (ITI) de Médecine de Précision de StrasbourgTransplantex NGFaculté de MédecineFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de Strasbourg (FMTS)Université de StrasbourgStrasbourgFrance
| | - Marc Le Bert
- Laboratory of Experimental and Molecular Immunology and Neurogenetics (INEM)UMR 7355CNRS‐University of OrléansOrleansFrance
| | - Bernhard Ryffel
- Laboratory of Experimental and Molecular Immunology and Neurogenetics (INEM)UMR 7355CNRS‐University of OrléansOrleansFrance
| | - Philippe Georgel
- Laboratoire d’ImmunoRhumatologie MoléculaireInstitut national de la santé et de la recherche médicale (INSERM) UMR_S 1109Institut thématique interdisciplinaire (ITI) de Médecine de Précision de StrasbourgTransplantex NGFaculté de MédecineFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de Strasbourg (FMTS)Université de StrasbourgStrasbourgFrance
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11
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Abstract
Primary immunodeficiency diseases (PIDs) are a rapidly growing, heterogeneous group of genetically determined diseases characterized by defects in the immune system. While individually rare, collectively PIDs affect between 1/1,000 and 1/5,000 people worldwide. The clinical manifestations of PIDs vary from susceptibility to infections to autoimmunity and bone marrow failure. Our understanding of the human immune response has advanced by investigation and discovery of genetic mechanisms of PIDs. Studying patients with isolated genetic variants in proteins that participate in complex signaling pathways has led to an enhanced understanding of host response to infection, and mechanisms of autoimmunity and autoinflammation. Identifying genetic mechanisms of PIDs not only furthers immunological knowledge but also benefits patients by dictating targeted therapies or hematopoietic stem cell transplantation. Here, we highlight several of these areas in the field of primary immunodeficiency, with a focus on the most recent advances.
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Affiliation(s)
- Erica G Schmitt
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine in St. Louis, Missouri 63110, USA; ,
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University School of Medicine in St. Louis, Missouri 63110, USA; ,
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12
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Freeze HH. XMEN: welcome to the glycosphere. J Clin Invest 2020; 130:80-82. [PMID: 31815737 DOI: 10.1172/jci134240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
XMEN (X-linked immunodeficiency with magnesium defect, EBV infection, and neoplasia) is a complex primary immunological deficiency caused by mutations in MAGT1, a putative magnesium transporter. In this issue of the JCI, Ravell et al. greatly expand the clinical picture. The authors investigated patients' mutations and symptoms and reported distinguishing immunophenotypes. They also showed that MAGT1 is required for N-glycosylation of key T cell and NK cell receptors that can account for some of the clinical features. Notably, transfection of the affected lymphocytes with MAGT1 mRNA restored both N-glycosylation and receptor function. Now we can add XMEN to the ever-growing family of congenital disorders of glycosylation (CDG).
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13
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van der Made CI, Hoischen A, Netea MG, van de Veerdonk FL. Primary immunodeficiencies in cytosolic pattern-recognition receptor pathways: Toward host-directed treatment strategies. Immunol Rev 2020; 297:247-272. [PMID: 32640080 DOI: 10.1111/imr.12898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022]
Abstract
In the last decade, the paradigm of primary immunodeficiencies (PIDs) as rare recessive familial diseases that lead to broad, severe, and early-onset immunological defects has shifted toward collectively more common, but sporadic autosomal dominantly inherited isolated defects in the immune response. Patients with PIDs constitute a formidable area of research to study the genetics and the molecular mechanisms of complex immunological pathways. A significant subset of PIDs affect the innate immune response, which is a crucial initial host defense mechanism equipped with pattern-recognition receptors. These receptors recognize pathogen- and damage-associated molecular patterns in both the extracellular and intracellular space. In this review, we will focus on primary immunodeficiencies caused by genetic defects in cytosolic pattern-recognition receptor pathways. We discuss these PIDs organized according to their mutational mechanisms and consequences for the innate host response. The advanced understanding of these pathways obtained by the study of PIDs creates the opportunity for the development of new host-directed treatment strategies.
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Affiliation(s)
- Caspar I van der Made
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud Institute of Molecular Life Sciences (RIMLS), Radboud Institute of Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud Institute of Molecular Life Sciences (RIMLS), Radboud Institute of Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud Institute of Molecular Life Sciences (RIMLS), Radboud Institute of Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud Institute of Molecular Life Sciences (RIMLS), Radboud Institute of Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
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14
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Thaventhiran JED, Lango Allen H, Burren OS, Rae W, Greene D, Staples E, Zhang Z, Farmery JHR, Simeoni I, Rivers E, Maimaris J, Penkett CJ, Stephens J, Deevi SVV, Sanchis-Juan A, Gleadall NS, Thomas MJ, Sargur RB, Gordins P, Baxendale HE, Brown M, Tuijnenburg P, Worth A, Hanson S, Linger RJ, Buckland MS, Rayner-Matthews PJ, Gilmour KC, Samarghitean C, Seneviratne SL, Sansom DM, Lynch AG, Megy K, Ellinghaus E, Ellinghaus D, Jorgensen SF, Karlsen TH, Stirrups KE, Cutler AJ, Kumararatne DS, Chandra A, Edgar JDM, Herwadkar A, Cooper N, Grigoriadou S, Huissoon AP, Goddard S, Jolles S, Schuetz C, Boschann F, Lyons PA, Hurles ME, Savic S, Burns SO, Kuijpers TW, Turro E, Ouwehand WH, Thrasher AJ, Smith KGC. Whole-genome sequencing of a sporadic primary immunodeficiency cohort. Nature 2020; 583:90-95. [PMID: 32499645 PMCID: PMC7334047 DOI: 10.1038/s41586-020-2265-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies1-3. Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed4) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of-and interplay between-novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans.
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Affiliation(s)
- James E D Thaventhiran
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
- Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK.
| | - Hana Lango Allen
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Oliver S Burren
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - William Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Daniel Greene
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Emily Staples
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Zinan Zhang
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James H R Farmery
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Ilenia Simeoni
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Elizabeth Rivers
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jesmeen Maimaris
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Christopher J Penkett
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Jonathan Stephens
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Sri V V Deevi
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Alba Sanchis-Juan
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Nicholas S Gleadall
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Moira J Thomas
- Department of Immunology, Queen Elizabeth University Hospital, Glasgow, UK
- Gartnavel General Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Ravishankar B Sargur
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Pavels Gordins
- East Yorkshire Regional Adult Immunology and Allergy Unit, Hull Royal Infirmary, Hull and East Yorkshire Hospitals NHS Trust, Hull, UK
| | - Helen E Baxendale
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Matthew Brown
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Paul Tuijnenburg
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Austen Worth
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Steven Hanson
- Institute of Immunity and Transplantation, University College London, London, UK
- Department of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Rachel J Linger
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthew S Buckland
- Institute of Immunity and Transplantation, University College London, London, UK
- Department of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Paula J Rayner-Matthews
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Kimberly C Gilmour
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Crina Samarghitean
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Suranjith L Seneviratne
- Institute of Immunity and Transplantation, University College London, London, UK
- Department of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - David M Sansom
- Institute of Immunity and Transplantation, University College London, London, UK
- Department of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Karyn Megy
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - David Ellinghaus
- Department of Transplantation, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Silje F Jorgensen
- Section of Clinical Immunology and Infectious Diseases, Department of Rheumatology, Dermatology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Tom H Karlsen
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Kathleen E Stirrups
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Antony J Cutler
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Dinakantha S Kumararatne
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - J David M Edgar
- St James's Hospital, Dublin, Ireland
- Trinity College Dublin, Dublin, Ireland
| | | | - Nichola Cooper
- Department of Medicine, Imperial College London, London, UK
| | | | - Aarnoud P Huissoon
- West Midlands Immunodeficiency Centre, University Hospitals Birmingham, Birmingham, UK
- Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Sarah Goddard
- University Hospitals of North Midlands NHS Trust, Stoke-on-Trent, UK
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, UK
| | - Catharina Schuetz
- Department of Pediatric Immunology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Matthew E Hurles
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sinisa Savic
- Department of Clinical Immunology and Allergy, St James's University Hospital, Leeds, UK
- The NIHR Leeds Biomedical Research Centre, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK
| | - Siobhan O Burns
- Institute of Immunity and Transplantation, University College London, London, UK
- Department of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam University Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
- Department of Blood Cell Research, Sanquin, Amsterdam, The Netherlands
| | - Ernest Turro
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Adrian J Thrasher
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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15
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Lye JJ, Williams A, Baralle D. Exploring the RNA Gap for Improving Diagnostic Yield in Primary Immunodeficiencies. Front Genet 2019; 10:1204. [PMID: 31921280 PMCID: PMC6917654 DOI: 10.3389/fgene.2019.01204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Challenges in diagnosing primary immunodeficiency are numerous and diverse, with current whole-exome and whole-genome sequencing approaches only able to reach a molecular diagnosis in 25–60% of cases. We assess these problems and discuss how RNA-focused analysis has expanded and improved in recent years and may now be utilized to gain an unparalleled insight into cellular immunology. We review how investigation into RNA biology can give information regarding the differential expression, monoallelic expression, and alternative splicing—which have important roles in immune regulation and function. We show how this information can inform bioinformatic analysis pipelines and aid in the variant filtering process, expediting the identification of causal variants—especially those affecting splicing—and enhance overall diagnostic ability. We also demonstrate the challenges, which remain in the design of this type of investigation, regarding technological limitation and biological considerations and suggest potential directions for the clinical applications.
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Affiliation(s)
- Jed J Lye
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom
| | - Anthony Williams
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom.,Wessex Investigational Sciences Hub Laboratory (WISH Lab), Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom.,Faculty of Medicine, Highfield Campus, University of Southampton, Southampton, United Kingdom
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16
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Moens L, Hershfield M, Arts K, Aksentijevich I, Meyts I. Human adenosine deaminase 2 deficiency: A multi-faceted inborn error of immunity. Immunol Rev 2019; 287:62-72. [PMID: 30565235 DOI: 10.1111/imr.12722] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/23/2018] [Indexed: 12/15/2022]
Abstract
Human adenosine deaminase 1 deficiency was described in the 1970s to cause severe combined immunodeficiency. The residual adenosine deaminase activity in these patients was attributed to adenosine deaminase 2. Human adenosine deaminase type 2 deficiency (DADA2), due to biallelic deleterious mutations in the ADA2 gene, is the first described monogenic type of small- and medium-size vessel vasculitis. The phenotype of DADA2 also includes lymphoproliferation, cytopenia, and variable degrees of immunodeficiency. The physiological role of ADA2 is still enigmatic hence the pathophysiology of the condition is unclear. Preliminary data showed that in the absence of ADA2, macrophage differentiation is skewed to a pro-inflammatory M1 subset, which is detrimental for endothelial integrity. The inflammatory phenotype responds well to anti-TNF therapy with etanercept and that is the first-line treatment for prevention of severe vascular events including strokes. The classic immunosuppressive drugs are not successful in controlling the disease activity. However, hematopoietic stem cell transplantation (HSCT) has been shown to be a definitive cure in DADA2 patients who present with a severe cytopenia. HSCT can also cure the vascular phenotype and is the treatment modality for patients' refractory to anti-cytokine therapies. In this review, we describe what is currently known about the molecular mechanisms of DADA2. Further research on the pathophysiology of this multifaceted condition is needed to fine-tune and steer future therapeutic strategies.
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Affiliation(s)
- Leen Moens
- Department of Microbiology and Immunology, Laboratory for Childhood Immunology, KU Leuven, Leuven, Belgium
| | - Michael Hershfield
- Department of Medicine, School of Medicine, Duke University, Durham, North Carolina
| | - Katrijn Arts
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland
| | - Isabelle Meyts
- Department of Microbiology and Immunology, Laboratory for Childhood Immunology, KU Leuven, Leuven, Belgium.,Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
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17
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Lenardo MJ, Holland SM. Introduction: Continuing insights into the healthy and diseased immune system through human genetic investigation. Immunol Rev 2019; 287:5-8. [PMID: 30565248 DOI: 10.1111/imr.12730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 11/23/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Michael J Lenardo
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Steven M Holland
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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18
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Abdel-Motal UM, Al-Shaibi A, Elawad M, Lo B. Zero tolerance! A perspective on monogenic disorders with defective regulatory T cells and IBD-like disease. Immunol Rev 2019; 287:236-240. [PMID: 30565246 DOI: 10.1111/imr.12717] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/12/2018] [Indexed: 12/27/2022]
Abstract
Recently, several studies have investigated a number of rare monogenic autoimmune disorders, in which the causative genetic defects were identified and found to affect the development or function of regulatory T cells (Tregs). The studies of these disorders have facilitated a deeper understanding of the mechanisms involved in immune regulation and tolerance. Furthermore, these studies have highlighted the importance of Tregs in maintaining homeostasis at the mucosal interface between the host and microbiome. Here, we offer our perspective on these monogenic autoimmune disorders, highlighting their overlapping clinical features with inflammatory bowel disease.
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Affiliation(s)
- Ussama M Abdel-Motal
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
| | - Ahmad Al-Shaibi
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha, Qatar
| | - Bernice Lo
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
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19
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Human DEF6 deficiency underlies an immunodeficiency syndrome with systemic autoimmunity and aberrant CTLA-4 homeostasis. Nat Commun 2019; 10:3106. [PMID: 31308374 PMCID: PMC6629652 DOI: 10.1038/s41467-019-10812-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 05/29/2019] [Indexed: 12/15/2022] Open
Abstract
Immune responses need to be controlled tightly to prevent autoimmune diseases, yet underlying molecular mechanisms remain partially understood. Here, we identify biallelic mutations in three patients from two unrelated families in differentially expressed in FDCP6 homolog (DEF6) as the molecular cause of an inborn error of immunity with systemic autoimmunity. Patient T cells exhibit impaired regulation of CTLA-4 surface trafficking associated with reduced functional CTLA-4 availability, which is replicated in DEF6-knockout Jurkat cells. Mechanistically, we identify the small GTPase RAB11 as an interactor of the guanine nucleotide exchange factor DEF6, and find disrupted binding of mutant DEF6 to RAB11 as well as reduced RAB11+CTLA-4+ vesicles in DEF6-mutated cells. One of the patients has been treated with CTLA-4-Ig and achieved sustained remission. Collectively, we uncover DEF6 as player in immune homeostasis ensuring availability of the checkpoint protein CTLA-4 at T-cell surface, identifying a potential target for autoimmune and/or cancer therapy. CTLA-4 is critical for balancing protective immunity with self-tolerance. Here the authors identify homozygous DEF6 mutations in patients with severe autoimmunity, one of which received and responds to CTLA-4-Ig, and show that DEF6 is crucial for CTLA-4 cell surface trafficking and immune regulatory function.
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20
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, Houston, TX.,Center for Human Immunobiology, Texas Children's Hospital, Houston, TX
| | - Jordan S Orange
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY.,New York Presbyterian Morgan Stanley Children's Hospital, New York, NY
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21
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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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22
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Noll KE, Ferris MT, Heise MT. The Collaborative Cross: A Systems Genetics Resource for Studying Host-Pathogen Interactions. Cell Host Microbe 2019; 25:484-498. [PMID: 30974083 PMCID: PMC6494101 DOI: 10.1016/j.chom.2019.03.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Host genetic variation has a major impact on infectious disease susceptibility. The study of pathogen resistance genes, largely aided by mouse models, has significantly advanced our understanding of infectious disease pathogenesis. The Collaborative Cross (CC), a newly developed multi-parental mouse genetic reference population, serves as a tractable model system to study how pathogens interact with genetically diverse populations. In this review, we summarize progress utilizing the CC as a platform to develop improved models of pathogen-induced disease and to map polymorphic host response loci associated with variation in susceptibility to pathogens.
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Affiliation(s)
- Kelsey E Noll
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martin T Ferris
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Mark T Heise
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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23
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Cunningham-Rundles C. Common variable immune deficiency: Dissection of the variable. Immunol Rev 2019; 287:145-161. [PMID: 30565247 PMCID: PMC6435035 DOI: 10.1111/imr.12728] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/16/2018] [Indexed: 12/28/2022]
Abstract
Starting about 60 years ago, a number of reports appeared that outlined the severe clinical course of a few adult subjects with profound hypogammaglobinemia. Puzzled by the lack of family history and adult onset of symptoms in most, the name "acquired" hypogammaglobinemia was given, but later altered to the current name common variable immune deficiency. Pathology reports remarked on the loss of lymph node architecture and paucity of plasma cells in lymphoid tissues in these subjects. While characterized by reduced serum IgG and IgA and often IgM, and thus classified among the B-cell defects, an increasing number of cellular defects in these patients have been recognized over time. In the early years, severe respiratory tract infections commonly led to a shortened life span, but the wide spread availability of immune globulin concentrates for the last 25 years has improved survival. However, chronic non-infectious inflammatory and autoimmune conditions have now emerged as challenging clinical problems; these require further immunologic understanding and additional therapeutic measures. Recent study of this phenotypic syndrome have provided an increasingly fertile ground for the identification of autosomal recessive and now more commonly, autosomal dominant gene defects which lead to the loss of B-cell development in this syndrome.
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24
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Rae W, Ward D, Mattocks C, Pengelly RJ, Eren E, Patel SV, Faust SN, Hunt D, Williams AP. Clinical efficacy of a next-generation sequencing gene panel for primary immunodeficiency diagnostics. Clin Genet 2018; 93:647-655. [PMID: 29077208 DOI: 10.1111/cge.13163] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/18/2017] [Accepted: 10/23/2017] [Indexed: 01/04/2023]
Abstract
Primary immunodeficiencies (PIDs) are rare monogenic inborn errors of immunity that result in impairment of functions of the human immune system. PIDs have a broad phenotype with increased morbidity and mortality, and treatment choices are often complex. With increased accessibility of next-generation sequencing (NGS), the rate of discovery of genetic causes for PID has increased exponentially. Identification of an underlying monogenic diagnosis provides important clinical benefits for patients with the potential to alter treatments, facilitate genetic counselling, and pre-implantation diagnostics. We investigated a NGS PID panel of 242 genes within clinical care across a range of PID phenotypes. We also evaluated Phenomizer to predict causal genes from human phenotype ontology (HPO) terms. Twenty-seven participants were recruited, and a total of 15 reportable variants were identified in 48% (13/27) of the participants. The panel results had implications for treatment in 37% (10/27) of participants. Phenomizer identified the genes harbouring variants from HPO terms in 33% (9/27) of participants. This study shows the clinical efficacy that genetic testing has in the care of PID. However, it also highlights some of the disadvantages of gene panels in the rapidly moving field of PID genomics and current challenges in HPO term assignment for PID.
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Affiliation(s)
- W Rae
- Department of Immunology, University Hospital Southampton NHSFT, Southampton, UK.,Southampton National Institute for Health Research Clinical Research Facility, University Hospital Southampton NHSFT, Southampton, UK
| | - D Ward
- Wessex Investigational Sciences Hub Laboratory, University Hospital Southampton NHSFT, Southampton, UK
| | - C Mattocks
- Wessex Investigational Sciences Hub Laboratory, University Hospital Southampton NHSFT, Southampton, UK
| | - R J Pengelly
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - E Eren
- Department of Immunology, University Hospital Southampton NHSFT, Southampton, UK
| | - S V Patel
- Paediatric Immunology and Infectious Disease, Children's Hospital Southampton, Southampton, UK
| | - S N Faust
- Southampton National Institute for Health Research Clinical Research Facility, University Hospital Southampton NHSFT, Southampton, UK.,Faculty of Medicine, University of Southampton, Southampton, UK.,Paediatric Immunology and Infectious Disease, Children's Hospital Southampton, Southampton, UK
| | - D Hunt
- Wessex Clinical Genetics Service, University Hospital Southampton NHSFT, Southampton, UK
| | - A P Williams
- Department of Immunology, University Hospital Southampton NHSFT, Southampton, UK.,Wessex Investigational Sciences Hub Laboratory, University Hospital Southampton NHSFT, Southampton, UK.,Faculty of Medicine, University of Southampton, Southampton, UK
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25
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Carpier JM, Lucas CL. Epstein-Barr Virus Susceptibility in Activated PI3Kδ Syndrome (APDS) Immunodeficiency. Front Immunol 2018; 8:2005. [PMID: 29387064 PMCID: PMC5776011 DOI: 10.3389/fimmu.2017.02005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 12/26/2017] [Indexed: 12/18/2022] Open
Abstract
Activated PI3Kδ Syndrome (APDS) is an inherited immune disorder caused by heterozygous, gain-of-function mutations in the genes encoding the phosphoinositide 3-kinase delta (PI3Kδ) subunits p110δ or p85δ. This recently described primary immunodeficiency disease (PID) is characterized by recurrent sinopulmonary infections, lymphoproliferation, and susceptibility to herpesviruses, with Epstein–Barr virus (EBV) infection being most notable. A broad range of PIDs having disparate, molecularly defined genetic etiology can cause susceptibility to EBV, lymphoproliferative disease, and lymphoma. Historically, PID patients with loss-of-function mutations causing defective cell-mediated cytotoxicity or antigen receptor signaling were found to be highly susceptible to pathological EBV infection. By contrast, the gain of function in PI3K signaling observed in APDS patients paradoxically renders these patients susceptible to EBV, though the underlying mechanisms are incompletely understood. At a cellular level, APDS patients exhibit deranged B lymphocyte development and defects in class switch recombination, which generally lead to defective immunoglobulin production. Moreover, APDS patients also demonstrate an abnormal skewing of T cells toward terminal effectors with short telomeres and senescence markers. Here, we review APDS with a particular focus on how the altered lymphocyte biology in these patients may confer EBV susceptibility.
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Affiliation(s)
- Jean-Marie Carpier
- Immunobiology Department, Yale University School of Medicine, New Haven, CT, United States
| | - Carrie L Lucas
- Immunobiology Department, Yale University School of Medicine, New Haven, CT, United States
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26
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Sic H, Speletas M, Cornacchione V, Seidl M, Beibel M, Linghu B, Yang F, Sevdali E, Germenis AE, Oakeley EJ, Vangrevelinghe E, Sailer AW, Traggiai E, Gram H, Eibel H. An Activating Janus Kinase-3 Mutation Is Associated with Cytotoxic T Lymphocyte Antigen-4-Dependent Immune Dysregulation Syndrome. Front Immunol 2017; 8:1824. [PMID: 29375547 PMCID: PMC5770691 DOI: 10.3389/fimmu.2017.01824] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/04/2017] [Indexed: 11/13/2022] Open
Abstract
Heterozygous mutations in the cytotoxic T lymphocyte antigen-4 (CTLA-4) are associated with lymphadenopathy, autoimmunity, immune dysregulation, and hypogammaglobulinemia in about 70% of the carriers. So far, the incomplete penetrance of CTLA-4 haploinsufficiency has been attributed to unknown genetic modifiers, epigenetic changes, or environmental effects. We sought to identify potential genetic modifiers in a family with differential clinical penetrance of CTLA-4 haploinsufficiency. Here, we report on a rare heterozygous gain-of-function mutation in Janus kinase-3 (JAK3) (p.R840C), which is associated with the clinical manifestation of CTLA-4 haploinsufficiency in a patient carrying a novel loss-of-function mutation in CTLA-4 (p.Y139C). While the asymptomatic parents carry either the CTLA-4 mutation or the JAK3 variant, their son has inherited both heterozygous mutations and suffers from hypogammaglobulinemia combined with autoimmunity and lymphoid hyperplasia. Although the patient's lymph node and spleen contained many hyperplastic germinal centers with follicular helper T (TFH) cells and immunoglobulin (Ig) G-positive B cells, plasma cell, and memory B cell development was impaired. CXCR5+PD-1+TIGIT+ TFH cells contributed to a large part of circulating T cells, but they produced only very low amounts of interleukin (IL)-4, IL-10, and IL-21 required for the development of memory B cells and plasma cells. We, therefore, suggest that the combination of the loss-of-function mutation in CTLA-4 with the gain-of-function mutation in JAK3 directs the differentiation of CD4 T cells into dysfunctional TFH cells supporting the development of lymphadenopathy, hypogammaglobulinemia, and immunodeficiency. Thus, the combination of rare genetic heterozygous variants that remain clinically unnoticed individually may lead to T cell hyperactivity, impaired memory B cell, and plasma cell development resulting finally in combined immunodeficiency.
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Affiliation(s)
- Heiko Sic
- Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Matthaios Speletas
- Department of Immunology and Histocompatibility, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, Greece
| | | | - Maximillian Seidl
- Institute for Surgical Pathology, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Martin Beibel
- Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Bolan Linghu
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States
| | - Fan Yang
- Novartis Institutes for Biomedical Research, Cambridge, MA, United States
| | - Eirini Sevdali
- Department of Immunology and Histocompatibility, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, Greece
| | - Anastasios E Germenis
- Department of Immunology and Histocompatibility, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, Greece
| | | | | | | | | | - Hermann Gram
- Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Hermann Eibel
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
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27
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Rae W, Ward D, Mattocks CJ, Gao Y, Pengelly RJ, Patel SV, Ennis S, Faust SN, Williams AP. Autoimmunity/inflammation in a monogenic primary immunodeficiency cohort. Clin Transl Immunology 2017; 6:e155. [PMID: 28983403 PMCID: PMC5628267 DOI: 10.1038/cti.2017.38] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/09/2017] [Accepted: 07/21/2017] [Indexed: 12/13/2022] Open
Abstract
Primary immunodeficiencies (PIDs) are rare inborn errors of immunity that have a heterogeneous phenotype that can include severe susceptibility to life-threatening infections from multiple pathogens, unique sensitivity to a single pathogen, autoimmune/inflammatory (AI/I) disease, allergies and/or malignancy. We present a diverse cohort of monogenic PID patients with and without AI/I diseases who underwent clinical, genetic and immunological phenotyping. Novel pathogenic variants were identified in IKBKG, CTLA4, NFKB1, GATA2, CD40LG and TAZ as well as previously reported pathogenic variants in STAT3, PIK3CD, STAT1, NFKB2 and STXBP2. AI/I manifestations were frequently encountered in PIDs, including at presentation. Autoimmunity/inflammation was multisystem in those effected, and regulatory T cell (Treg) percentages were significantly decreased compared with those without AI/I manifestations. Prednisolone was used as the first-line immunosuppressive agent in all cases, however steroid monotherapy failed long-term control of autoimmunity/inflammation in the majority of cases and additional immunosuppression was required. Patients with multisystem autoimmunity/inflammation should be investigated for an underlying PID, and in those with PID early assessment of Tregs may help to assess the risk of autoimmunity/inflammation.
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Affiliation(s)
- William Rae
- Department of Immunology, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,Southampton NIHR Wellcome Trust Clinical Research Facility, University of Southampton, University Hospital Southampton, Southampton, UK
| | - Daniel Ward
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.,Wessex Investigational Sciences Hub Laboratory, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Christopher J Mattocks
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.,Wessex Investigational Sciences Hub Laboratory, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Yifang Gao
- Wessex Investigational Sciences Hub Laboratory, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,NIHR Cancer Research UK Experimental Cancer Medicine Centre, Southampton, UK
| | - Reuben J Pengelly
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sanjay V Patel
- Department of Paediatric Immunology and Infectious Diseases, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Saul N Faust
- Southampton NIHR Wellcome Trust Clinical Research Facility, University of Southampton, University Hospital Southampton, Southampton, UK.,Department of Paediatric Immunology and Infectious Diseases, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,Faculty of Medicine, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Anthony P Williams
- Department of Immunology, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,Wessex Investigational Sciences Hub Laboratory, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,NIHR Cancer Research UK Experimental Cancer Medicine Centre, Southampton, UK
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28
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Uhlig HH, Muise AM. Clinical Genomics in Inflammatory Bowel Disease. Trends Genet 2017; 33:629-641. [PMID: 28755896 DOI: 10.1016/j.tig.2017.06.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 12/19/2022]
Abstract
Genomic technologies inform the complex genetic basis of polygenic inflammatory bowel disease (IBD) as well as Mendelian disease-associated IBD. Aiming to diagnose patients that present with extreme phenotypes due to monogenic forms of IBD, genomics has progressed from 'orphan disease' research towards an integrated standard of clinical care. Advances in diagnostic clinical genomics are increasingly complemented by pathway-specific therapies that aim to correct the consequences of genetic defects. This highlights the exceptional potential for personalized precision medicine. IBD is nevertheless a challenging example for genomic medicine because the overall fraction of patients with Mendelian defects is low, the number of potential candidate genes is high, and interventional evidence is still emerging. We discuss requirements and prospects of explanatory and predictive clinical genomics in IBD.
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Affiliation(s)
- Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, UK; Department of Paediatrics, University of Oxford, UK.
| | - Aleixo M Muise
- Program in Cell Biology, Research Institute, Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; SickKids Inflammatory Bowel Disease Centre and Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
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29
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Langlais D, Fodil N, Gros P. Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies. Annu Rev Immunol 2017; 35:1-30. [DOI: 10.1146/annurev-immunol-051116-052442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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30
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Iwata A, Durai V, Tussiwand R, Briseño CG, Wu X, Grajales-Reyes GE, Egawa T, Murphy TL, Murphy KM. Quality of TCR signaling determined by differential affinities of enhancers for the composite BATF-IRF4 transcription factor complex. Nat Immunol 2017; 18:563-572. [PMID: 28346410 PMCID: PMC5401770 DOI: 10.1038/ni.3714] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/23/2017] [Indexed: 12/13/2022]
Abstract
Variable strengths of T cell receptor (TCR) signaling can produce divergent outcomes, but the mechanism remains obscure. The abundance of the transcription factor IRF4 increases with TCR signal strength, but how this would induce distinct types of responses is unclear. We compared TH2 gene expression with BATF/IRF4 enhancer occupancy at varying strengths of TCR stimulation. BATF/IRF4-dependent genes clustered into distinct TCR-sensitivities. Enhancers exhibited a spectrum of occupancy by BATF/IRF4 ternary complex that correlated with TCR-sensitivity of gene expression. DNA sequences immediately flanking the previously defined AICE motif controlled the affinity for BATF/IRF4 for direct binding to DNA. ChIP-exo analysis allowed identification of a novel high-affinity AICE2 motif at a human SNP of CTLA4 associated with resistance to autoimmunity. Thus, the affinity of different enhancers for the BATF-IRF4 complex may underlie divergent signaling outcomes in response to various strengths of TCR signaling.
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Affiliation(s)
- Arifumi Iwata
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Roxane Tussiwand
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Carlos G Briseño
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Xiaodi Wu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Gary E Grajales-Reyes
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA.,Howard Hughes Medical Institute, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
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31
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Lenardo MJ. Clinical Genomics - Molecular Pathogenesis Revealed. N Engl J Med 2016; 375:2117-2119. [PMID: 27959769 PMCID: PMC11090046 DOI: 10.1056/nejmp1611419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Michael J Lenardo
- From the Molecular Development of the Immune System Section, Laboratory of Immunology and Clinical Genomics Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD
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32
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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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33
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Precision treatment with sirolimus in a case of activated phosphoinositide 3-kinase δ syndrome. Clin Immunol 2016; 171:38-40. [DOI: 10.1016/j.clim.2016.07.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 12/30/2022]
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34
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Indications to Epigenetic Dysfunction in the Pathogenesis of Common Variable Immunodeficiency. Arch Immunol Ther Exp (Warsz) 2016; 65:101-110. [DOI: 10.1007/s00005-016-0414-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/10/2016] [Indexed: 12/12/2022]
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