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Chen Y, Li D, Yin J, Xiong J, Xu M, Qi Q, Yang W. Diagnostic yield of next-generation sequencing in suspect primary immunodeficiencies diseases: a systematic review and meta-analysis. Clin Exp Med 2024; 24:131. [PMID: 38890201 PMCID: PMC11189333 DOI: 10.1007/s10238-024-01392-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
To determine the diagnostic yield of Next-generation sequencing (NGS) in suspect Primary Immunodeficiencies Diseases (PIDs). This systematic review was conducted following PRISMA criteria. Searching Pubmed and Web of Science databases, the following keywords were used in the search: ("Next-generation sequencing") OR "whole exome sequencing" OR "whole genome sequencing") AND ("primary immunodeficiency disease" OR "PIDs"). We used STARD items to assess the risk of bias in the included studies. The meta-analysis included 29 studies with 5847 patients, revealing a pooled positive detection rate of 42% (95% CI 0.29-0.54, P < 0.001) for NGS in suspected PID cases. Subgroup analyses based on family history demonstrated a higher detection rate of 58% (95% CI 0.43-0.71) in patients with a family history compared to 33% (95% CI 0.21-0.46) in those without (P < 0.001). Stratification by disease types showed varied detection rates, with Severe Combined Immunodeficiency leading at 58% (P < 0.001). Among 253 PID-related genes, RAG1, ATM, BTK, and others constituted major contributors, with 34 genes not included in the 2022 IUIS gene list. The application of NGS in suspected PID patients can provide significant diagnostic results, especially in patients with a family history. Meanwhile, NGS performs excellently in accurately diagnosing disease types, and early identification of disease types can benefit patients in treatment.
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Affiliation(s)
- Yingying Chen
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Dongrui Li
- The First Clinical College of Guangzhou Medical University, Guangzhou, 510180, China
| | - Jiawen Yin
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Jinglin Xiong
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Min Xu
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Qing Qi
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Wenlin Yang
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
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Shi X, Cao X, Huang M, Zhang P, Yang G, Ren A, Dai X, Chen R, Yang Z, Cai Z, Chen Y, Zhao X, Huang P, Du Z. Identification and Functional Analysis of a de novo IKZF3 Mutation in a Pediatric Patient with Combined Immunodeficiency. J Clin Immunol 2024; 44:117. [PMID: 38758229 DOI: 10.1007/s10875-024-01706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/03/2024] [Indexed: 05/18/2024]
Abstract
AIOLOS, a vital member of the IKAROS protein family, plays a significant role in lymphocyte development and function through DNA binding and protein-protein interactions. Mutations in the IKZF3 gene, which encodes AIOLOS, lead to a rare combined immunodeficiency often linked with infections and malignancy. In this study, we evaluated a 1-year-4-month-old female patient presenting with recurrent infections, diarrhea, and failure to thrive. Laboratory investigations revealed decreased T lymphocyte and immunoglobulin levels. Through whole-exome and Sanger sequencing, we discovered a de novo mutation in IKZF3 (NM_012481; exon 5 c.571G > C, p.Gly191Arg), corresponding to the third DNA-binding zinc finger region of the encoded protein AIOLOS. Notably, the patient with the AIOLOS G191R mutation showed reduced recent thymic emigrants in naïve CD4+T cells compared to healthy counterparts of the same age, while maintaining normal levels of Th1, Th2, Th17, Treg, and Tfh cells. This mutation also resulted in decreased switched memory B cells and lower CD23 and IgM expression. In vitro studies revealed that AIOLOS G191R does not impact the expression of AIOLOS but compromises its stability, DNA binding and pericentromeric targeting. Furthermore, AIOLOS G191R demonstrated a dominant-negative effect over the wild-type protein. This case represents the first reported instance of a mutation in the third DNA-binding zinc finger region of AIOLOS highlighting its pivotal role in immune cell functionality.
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Affiliation(s)
- Xiaoqi Shi
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Xiuli Cao
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Meiying Huang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Pingping Zhang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Guangli Yang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Aiyan Ren
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Xin Dai
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, China
- Department of Hematology, Central People's Hospital of Zhanjiang, Zhanjiang, China
| | - Ran Chen
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhigang Yang
- Zhanjiang Institute of Clinical Medicine, Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, China
- Department of Hematology, Central People's Hospital of Zhanjiang, Zhanjiang, China
| | - Zeyuan Cai
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Yan Chen
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
| | - Xiaodong Zhao
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Pei Huang
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China.
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China.
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China.
| | - Zuochen Du
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou, China.
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, China.
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China.
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Aykut A, Durmaz A, Karaca N, Gulez N, Genel F, Celmeli F, Cogurlu MT, Akcan M, Cicek D, Cipe FE, Kiykim A, Yıldıran A, Unluhizarci K, Kilic SS, Aksu G, Ardeniz O, Kutukculer N. Primary immune regulatory disorders (PIRD): expanding the mutation spectrum in Turkey and identification of sixteen novel variants. Immunol Res 2024:10.1007/s12026-024-09477-6. [PMID: 38644452 DOI: 10.1007/s12026-024-09477-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
Human Inborn Errors of Immunity (IEIs) encompass a clinically and genetically heterogeneous group of disorders, ranging from mild cases to severe, life-threatening types. Among these, Primary Immune Regulatory Disorders (PIRDs) constitute a subset of IEIs characterized by diverse clinical phenotypes, prominently featuring severe atopy, autoimmunity, lymphoproliferation, hyperinflammation, autoinflammation, and susceptibility to malignancies. According to the latest report from the International Union of Immunological Societies (IUIS), PIRDs arise from mutations in various genes including LYST, RAB27A, AP3B1, AP3D1, PRF1, UNC13D, STX11, STXBP2, FAAP24, SLC7A7, RASGRP1, CD70, CTPS1, RLTPR, ITK, MAGT1, PRKCD, TNFRSF9, SH2DIA, XIAP, CD27 (TNFRSF7), FAS (TNFRSF6), FASLG (TNFSF6), CASP10, CASP8, FADD, LRBA, STAT3, AIRE, ITCH, ZAP70, TPP2, JAK1, PEPD, FOXP3, IL2RA, CTLA4, BACH2, IL2RB, DEF6, FERMT1, IL10, IL10RA, IL10RB, NFAT5, TGFB1, and RIPK1 genes. We designed a targeted next-generation sequencing (TNGS) workflow using the Ion AmpliSeq™ Primary Immune Deficiency Research Panel to sequence 264 genes associated with IEIs on the Ion S5™ Sequencer. In this study, we report the identification of 38 disease-causing variants, including 16 novel ones, detected in 40 patients across 15 distinct PIRD genes. The application of next-generation sequencing enabled rapid and precise diagnosis of patients with PIRDs.
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Affiliation(s)
- Ayca Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, Izmir, Turkey.
| | - Asude Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, Izmir, Turkey
| | - Neslihan Karaca
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Nesrin Gulez
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University, Uz Pediatric Diseases and Surgery Training and Research Hospital, Dr. Behcet, Izmir, Turkey
| | - Ferah Genel
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University, Uz Pediatric Diseases and Surgery Training and Research Hospital, Dr. Behcet, Izmir, Turkey
| | - Fatih Celmeli
- Immunology and Allergy Diseases, Saglık Bilimleri University, Antalya Training and Research Hospital Pediatric, Antalya, Turkey
| | - M Tuba Cogurlu
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Saglık Bilimleri University, Kocaeli Derince Training and Research Hospital, Kocaeli, Turkey
| | - Mediha Akcan
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Adnan Menderes University, Aydın, Turkey
| | - Dilek Cicek
- Department of Pediatric Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Funda Erol Cipe
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Ayca Kiykim
- Department of Pediatric Health and Diseases, Cerrahpasa Faculty of Medicine, Pediatric Allergy Immunology, Istanbul, Turkey
| | - Alisan Yıldıran
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Kursad Unluhizarci
- Department of Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Sara Sebnem Kilic
- Department of Pediatric Immunology and Rheumatology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Guzide Aksu
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Omur Ardeniz
- Department of Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Necil Kutukculer
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
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Seitz L, Gaitan D, Berkemeier CM, Berger CT, Recher M. Cluster analysis of flowcytometric immunophenotyping with extended T cell subsets in suspected immunodeficiency. Immun Inflamm Dis 2023; 11:e1106. [PMID: 38156376 PMCID: PMC10698832 DOI: 10.1002/iid3.1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/30/2023] Open
Abstract
BACKGROUND Patients with immunodeficiencies commonly experience diagnostic delays resulting in morbidity. There is an unmet need to identify patients earlier, especially those with high risk for complications. Compared to immunoglobulin quantification and flowcytometric B cell subset analysis, expanded T cell subset analysis is rarely performed in the initial evaluation of patients with suspected immunodeficiency. The simultaneous interpretation of multiple immune variables, including lymphocyte subsets, is challenging. OBJECTIVE To evaluate the diagnostic value of cluster analyses of immune variables in patients with suspected immunodeficiency. METHODS Retrospective analysis of 38 immune system variables, including seven B cell and sixteen T cell subpopulations, in 107 adult patients (73 with immunodeficiency, 34 without) evaluated at a tertiary outpatient immunology clinic. Correlation analyses of individual variables, k-means cluster analysis with evaluation of the classification into "no immunodeficiency" versus "immunodeficiency" and visual analyses of hierarchical heatmaps were performed. RESULTS Binary classification of patients into groups with and without immunodeficiency was correct in 54% of cases with the full data set and increased to 69% and 75% of cases, respectively, when only 16 variables with moderate (p < .05) or 7 variables with strong evidence (p < .01) for a difference between groups were included. In a cluster heatmap with all patients but only moderately differing variables and a heatmap with only immunodeficient patients restricted to T cell variables alone, segregation of most patients with common variable immunodeficiency and combined immunodeficiency was observed. CONCLUSION Cluster analyses of immune variables, including detailed lymphocyte flowcytometry with T cell subpopulations, may support clinical decision making for suspected immunodeficiency in daily practice.
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Affiliation(s)
- Luca Seitz
- Immunodeficiency Laboratory, Department of BiomedicineUniversity Hospital Basel and University of BaselBaselSwitzerland
- Department of Rheumatology and Immunology, Inselspital, University Hospital BernUniversity of BernBernSwitzerland
| | - Daniel Gaitan
- Immunodeficiency Laboratory, Department of BiomedicineUniversity Hospital Basel and University of BaselBaselSwitzerland
| | - Caroline M. Berkemeier
- Division of Medical Immunology, Laboratory MedicineUniversity Hospital BaselBaselSwitzerland
| | - Christoph T. Berger
- University Center for ImmunologyUniversity Hospital BaselBaselSwitzerland
- Translational Immunology, Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Mike Recher
- Immunodeficiency Laboratory, Department of BiomedicineUniversity Hospital Basel and University of BaselBaselSwitzerland
- University Center for ImmunologyUniversity Hospital BaselBaselSwitzerland
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Bhattad S, Mohite RS, Singh N, Kotecha U, Jhawar P, Ramprakash S, Commondoor R, Jayaram A, Rayabarapu P, Kumar H, Unni J, Cyril G, Kumar S, Pachat D, Jakka S, Makam A, Porta F, Ginigeri C. Profile of 208 patients with inborn errors of immunity at a tertiary care center in South India. Clin Exp Med 2023; 23:5399-5412. [PMID: 37898571 DOI: 10.1007/s10238-023-01225-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023]
Abstract
Primary immune deficiencies or inborn errors of immunity (IEI) are a heterogeneous group of disorders that predispose affected individuals to infections, allergy, autoimmunity, autoinflammation and malignancies. IEIs are increasingly being recognized in the Indian subcontinent. Two hundred and eight patients diagnosed with an IEI during February 2017 to November 2021 at a tertiary care center in South India were included in the study. The clinical features, laboratory findings including microbiologic and genetic data, and treatment and outcome details were analyzed. The diagnosis of IEI was confirmed in a total of 208 patients (198 kindreds) based on relevant immunological tests and/or genetic tests. The male-to-female ratio was 1.8:1. Of the 208 patients, 72 (34.6%) were < 1 yr, 112 (53.8%) were 1-18 years, and 24 (11.5%) were above 18 years. The most common IEI in our cohort was SCID (17.7%) followed by CGD (12.9%) and CVID (9.1%). We also had a significant proportion of patients with DOCK8 deficiency (7.2%), LAD (6.2%) and six patients (2.8%) with autoinflammatory diseases. Autoimmunity was noted in forty-six (22%) patients. Molecular testing was performed in 152 patients by exome sequencing on the NGS platform, and a genetic variant was reported in 132 cases. Twenty-nine children underwent 34 HSCT, and 135 patients remain on supportive therapy such as immunoglobulin replacement and/or antimicrobial prophylaxis. Fifty-nine (28.3%) patients died during the study period, and infections were the predominant cause of mortality. Seven families underwent prenatal testing in the subsequent pregnancy. We describe the profile of 208 patients with IEI, and to the best of our knowledge, this represents the largest data on IEI from the Indian subcontinent reported so far.
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Affiliation(s)
- Sagar Bhattad
- Pediatric Immunology and Rheumatology, Aster CMI Hospital, Bengaluru, India.
| | - Rachna S Mohite
- Pediatric Immunology and Rheumatology, Aster CMI Hospital, Bengaluru, India
| | - Neha Singh
- Pediatric Immunology and Rheumatology, Aster CMI Hospital, Bengaluru, India
| | | | - Prerna Jhawar
- Department of Fetal Medicine, Rainbow Hospital, Bengaluru, India
| | - Stalin Ramprakash
- Pediatric Hemato-Oncology and BMT Unit, Aster CMI Hospital, Bengaluru, India
| | - Raghuram Commondoor
- Pediatric Hemato-Oncology and BMT Unit, Aster CMI Hospital, Bengaluru, India
| | | | | | - Harish Kumar
- Pediatric Intensive Care Unit, Aster CMI Hospital, Bengaluru, India
| | | | | | | | | | | | | | - Fulvio Porta
- Onco-Hematology and Bone Marrow Transplantation (BMT) Unit, Ospedale Dei Bambini, Brescia, Italy
| | - Chetan Ginigeri
- Pediatric Intensive Care Unit, Aster CMI Hospital, Bengaluru, India
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6
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Peng XP, Al-Ddafari MS, Caballero-Oteyza A, El Mezouar C, Mrovecova P, Dib SE, Massen Z, Smahi MCE, Faiza A, Hassaïne RT, Lefranc G, Aribi M, Grimbacher B. Next generation sequencing (NGS)-based approach to diagnosing Algerian patients with suspected inborn errors of immunity (IEIs). Clin Immunol 2023; 256:109758. [PMID: 37678716 DOI: 10.1016/j.clim.2023.109758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/23/2023] [Accepted: 09/02/2023] [Indexed: 09/09/2023]
Abstract
The advent of next-generation sequencing (NGS) technologies has greatly expanded our understanding of both the clinical spectra and genetic landscape of inborn errors of immunity (IEIs). Endogamous populations may be enriched for unique, ancestry-specific disease-causing variants, a consideration that significantly impacts molecular testing and analysis strategies. Herein, we report on the application of a 2-step NGS-based testing approach beginning with targeted gene panels (TGPs) tailored to specific IEI subtypes and reflexing to whole exome sequencing (WES) if negative for Northwest Algerian patients with suspected IEIs. Our overall diagnostic yield of 57% is comparable to others broadly applying short-read NGS to IEI detection, but data from our localized cohort show some similarities and differences from NGS studies performed on larger regional IEI cohorts. This suggests the importance of tailoring diagnostic strategies to local demographics and needs, but also highlights ongoing concerns inherent to the application of genomics for clinical IEI diagnostics.
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Affiliation(s)
- Xiao P Peng
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
| | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Andres Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
| | - Chahrazed El Mezouar
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Pavla Mrovecova
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Saad Eddin Dib
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Zoheir Massen
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Mohammed Chems-Eddine Smahi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Specialized Mother-Child Hospital of Tlemcen, Department of Neonatology, Faculty of Medicine, University of Tlemcen, Algeria
| | - Alddafari Faiza
- Department of Internal Medicine, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Tlemcen, Algeria
| | | | - Gérard Lefranc
- Institute of Human Genetics, UMR 9002 CNRS-University of Montpellier, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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7
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Yanes T, Sullivan A, Barbaro P, Brion K, Hollway G, Peake J, McNaughton P. Evaluation and pilot testing of a multidisciplinary model of care to mainstream genomic testing for paediatric inborn errors of immunity. Eur J Hum Genet 2023; 31:1125-1132. [PMID: 36864115 PMCID: PMC10545723 DOI: 10.1038/s41431-023-01321-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/01/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Molecular diagnosis of paediatric inborn errors of immunity (IEI) influences management decisions and alters clinical outcomes, through early use of targeted and curative therapies. The increasing demand for genetic services has resulted in growing waitlists and delayed access to vital genomic testing. To address this issue, the Queensland Paediatric Immunology and Allergy Service, Australia, developed and evaluated a mainstreaming model of care to support point-of-care genomic testing for paediatric IEI. Key features of the model of care included a genetic counsellor embedded in the department, state-wide multidisciplinary team meetings, and variant prioritisation meetings to review whole exome sequencing (WES) data. Of the 62 children presented at the MDT, 43 proceeded to WES, of which nine (21%) received a confirmed molecular diagnosis. Changes to treatment and management were reported for all children with a positive result, including curative hematopoietic stem cell transplantation (n = 4). Four children were also referred for further investigations of variants of uncertain significance or additional testing due to ongoing suspicion of genetic cause after negative result. Demonstrating engagement with the model of care, 45% of the patients were from regional areas and on average, 14 healthcare providers attended the state-wide multidisciplinary team meetings. Parents demonstrated understanding of the implications of testing, reported minimal decisional regret post-test, and identified benefits to genomic testing. Overall, our program demonstrated the feasibility of a mainstreaming model of care for paediatric IEI, improved access to genomic testing, facilitated treatment decision-making, and was acceptable to parents and clinicians alike.
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Affiliation(s)
- Tatiane Yanes
- Queensland Paediatric Immunology and Allergy Service, Children's Health Queensland, Brisbane, QLD, 4101, Australia.
- The Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, QLD, 4102, Australia.
| | - Anna Sullivan
- Queensland Paediatric Immunology and Allergy Service, Children's Health Queensland, Brisbane, QLD, 4101, Australia
| | - Pasquale Barbaro
- Queensland Paediatric Haematology Service, Queensland Children's Hospital, Brisbane, QLD, 4101, Australia
- Queensland Children's Hospital Laboratory, Pathology Queensland, South Brisbane, QLD, 4101, Australia
| | - Kristian Brion
- Department of Molecular Genetics, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Georgina Hollway
- Department of Molecular Genetics, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Jane Peake
- Queensland Paediatric Immunology and Allergy Service, Children's Health Queensland, Brisbane, QLD, 4101, Australia
- Department of Paediatrics and Child Health, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter McNaughton
- Queensland Paediatric Immunology and Allergy Service, Children's Health Queensland, Brisbane, QLD, 4101, Australia
- Department of Paediatrics and Child Health, The University of Queensland, Brisbane, QLD, 4072, Australia
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8
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Alhumaid S, Al Mutared KM, Al Alawi Z, Sabr Z, Alkhars O, Alabdulqader M, Al Dossary N, ALShakhs FM, Majzoub RA, Alalawi YH, Al Noaim K, Alnaim AA, Al Ghamdi MA, Alahmari AA, Albattat SS, Almubarak YS, Al Abdulmohsen EM, Al Shaikh H, Alobaidan ME, Almusallam HH, Alhassan FM, Alamer MA, Al-Hajji JA, Al-Hajji DA, Alkadi AA, Al Mutair A, Rabaan AA. Severity of SARS-CoV-2 infection in children with inborn errors of immunity (primary immunodeficiencies): a systematic review. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2023; 19:69. [PMID: 37559153 PMCID: PMC10413516 DOI: 10.1186/s13223-023-00831-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/30/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Inborn errors of immunity (IEIs) are considered significant challenges for children with IEIs, their families, and their medical providers. Infections are the most common complication of IEIs and children can acquire coronavirus disease 2019 (COVID-19) even when protective measures are taken. OBJECTIVES To estimate the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children with IEIs and analyse the demographic parameters, clinical characteristics and treatment outcomes in children with IEIs with COVID-19 illness. METHODS For this systematic review, we searched ProQuest, Medline, Embase, PubMed, CINAHL, Wiley online library, Scopus and Nature through the Preferred Reporting Items for Systematic Reviews and Meta Analyses (PRISMA) guideline for studies on the development of COVID-19 in children with IEIs, published from December 1, 2019 to February 28, 2023, with English language restriction. RESULTS Of the 1095 papers that were identified, 116 articles were included in the systematic review (73 case report, 38 cohort 4 case-series and 1 case-control studies). Studies involving 710 children with IEIs with confirmed COVID-19 were analyzed. Among all 710 IEIs pediatric cases who acquired SARS-CoV-2, some children were documented to be admitted to the intensive care unit (ICU) (n = 119, 16.8%), intubated and placed on mechanical ventilation (n = 87, 12.2%), suffered acute respiratory distress syndrome (n = 98, 13.8%) or died (n = 60, 8.4%). Overall, COVID-19 in children with different IEIs patents resulted in no or low severity of disease in more than 76% of all included cases (COVID-19 severity: asymptomatic = 105, mild = 351, or moderate = 88). The majority of children with IEIs received treatment for COVID-19 (n = 579, 81.5%). Multisystem inflammatory syndrome in children (MIS-C) due to COVID-19 in children with IEIs occurred in 103 (14.5%). Fatality in children with IEIs with COVID-19 was reported in any of the included IEIs categories for cellular and humoral immunodeficiencies (n = 19, 18.6%), immune dysregulatory diseases (n = 17, 17.9%), innate immunodeficiencies (n = 5, 10%), bone marrow failure (n = 1, 14.3%), complement deficiencies (n = 1, 9.1%), combined immunodeficiencies with associated or syndromic features (n = 7, 5.5%), phagocytic diseases (n = 3, 5.5%), autoinflammatory diseases (n = 2, 3%) and predominantly antibody deficiencies (n = 5, 2.5%). Mortality was COVID-19-related in a considerable number of children with IEIs (29/60, 48.3%). The highest ICU admission and fatality rates were observed in cases belonging to cellular and humoral immunodeficiencies (26.5% and 18.6%) and immune dysregulatory diseases (35.8% and 17.9%) groups, especially in children infected with SARS-CoV-2 who suffered severe combined immunodeficiency (28.6% and 23.8%), combined immunodeficiency (25% and 15%), familial hemophagocytic lymphohistiocytosis (40% and 20%), X-linked lymphoproliferative diseases-1 (75% and 75%) and X-linked lymphoproliferative diseases-2 (50% and 50%) compared to the other IEIs cases. CONCLUSION Children with IEIs infected with SARS-CoV-2 may experience higher rates of ICU admission and mortality in comparison with the immunocompetent pediatric populations. Underlying immune defects does seem to be independent risk factors for severe SARS-CoV-2 infection in children with IEIs, a number of children with SCID and CID were reported to have prolonged infections-though the number of patients is small-but especially immune dysregulation diseases (XLP1 and XLP2) and innate immunodeficiencies impairing type I interferon signalling (IFNAR1, IFNAR2 and TBK1).
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Affiliation(s)
- Saad Alhumaid
- School of Pharmacy, University of Tasmania, Hobart, 7000, Australia.
| | - Koblan M Al Mutared
- Administration of Pharmaceutical Care, Ministry of Health, 66255, Najran, Saudi Arabia
| | - Zainab Al Alawi
- Division of Allergy and Immunology, College of Medicine, King Faisal University, 31982, Hofuf, Al-Ahsa, Saudi Arabia
| | - Zainah Sabr
- Division of Allergy and Immunology, Pediatric Department, College of Medicine, King Khalid University, 62529, Abha, Saudi Arabia
| | - Ola Alkhars
- Pediatric Department, King Faisal General Hospital, Ministry of Health, 36361, Hofuf, Al-Ahsa, Saudi Arabia
| | - Muneera Alabdulqader
- Pediatric Nephrology Specialty, Pediatric Department, Medical College, King Faisal University, 31982, Hofuf, Al-Ahsa, Saudi Arabia
| | - Nourah Al Dossary
- General Surgery Department, Alomran General Hospital, Ministry of Health, 36358, Hofuf, Al-Ahsa, Saudi Arabia
| | - Fatemah M ALShakhs
- Respiratory Therapy Department, Prince Saud Bin Jalawi Hospital, Ministry of Health, 36424, Al Mubarraz, Al-Ahsa, Saudi Arabia
| | - Rabab Abbas Majzoub
- Department of Pediatrics, College of Medicine, King Faisal University, 31982, Hofuf, Al-Ahsa, Saudi Arabia
| | - Yousef Hassan Alalawi
- Ear, Nose and Throat Department, Al Jabr Hospital for Eye, Ear, Nose and Throat, Ministry of Health, 36422, Al Mubarraz, Al-Ahsa, Saudi Arabia
| | - Khalid Al Noaim
- Department of Pediatrics, College of Medicine, King Faisal University, 31982, Hofuf, Al-Ahsa, Saudi Arabia
| | - Abdulrahman A Alnaim
- Department of Pediatrics, College of Medicine, King Faisal University, 31982, Hofuf, Al-Ahsa, Saudi Arabia
| | - Mohammed A Al Ghamdi
- Department of Pediatrics, King Fahad Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, 34212, Dammam, Saudi Arabia
| | - Abdulaziz A Alahmari
- Department of Pediatrics, King Fahad Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, 34212, Dammam, Saudi Arabia
| | - Sawsan Sami Albattat
- College of Medicine, King Faisal University, 31982, Hofuf, Al-Ahsa, Saudi Arabia
| | - Yasin S Almubarak
- Regional Medical Supply, Al-Ahsa Health Cluster, Ministry of Health, 36361, Hofuf, Al-Ahsa, Saudi Arabia
| | | | - Hanan Al Shaikh
- Infection Prevention and Control Department, Prince Saud Bin Jalawi Hospital, Ministry of Health, 36424, Al Mubarraz, Al-Ahsa, Saudi Arabia
| | - Mortadah Essa Alobaidan
- Pharmacy Department, King Faisal General Hospital, Ministry of Health, 36361, Hofuf, Al-Ahsa, Saudi Arabia
| | - Hadi Hassan Almusallam
- Pharmacy Department, King Faisal General Hospital, Ministry of Health, 36361, Hofuf, Al-Ahsa, Saudi Arabia
| | - Fatimah Mohammed Alhassan
- Pharmacy Department, King Faisal General Hospital, Ministry of Health, 36361, Hofuf, Al-Ahsa, Saudi Arabia
| | - Mohammed Abdulhadi Alamer
- Pharmacy Department, Prince Saud Bin Jalawi Hospital, Ministry of Health, 36424, Al Mubarraz, Al-Ahsa, Saudi Arabia
| | - Jawad Ali Al-Hajji
- Primary Care Medicine, Al-Ahsa Health Cluster, Ministry of Health, 24231, Hofuf, Al-Ahsa, Saudi Arabia
| | - Duaa Ali Al-Hajji
- Nursing Department, King Faisal General Hospital, Ministry of Health, 36361, Hofuf, Al-Ahsa, Saudi Arabia
| | - Anwar Ahmed Alkadi
- Nursing Department, Prince Saud Bin Jalawi Hospital, Ministry of Health, 36424, Al Mubarraz, Al-Ahsa, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, 36342, Al Mubarraz, Al-Ahsa, Saudi Arabia
- College of Nursing, Princess Norah Bint Abdul Rahman University, 11564, Riyadh, Saudi Arabia
- School of Nursing, University of Wollongong, Wollongong, NSW, 2522, Australia
- Nursing Department, Prince Sultan Military College of Health Sciences, 33048, Dhahran, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia
- Department of Public Health/Nutrition, The University of Haripur, Haripur, 22620, Khyber Pakhtunkhwa, Pakistan
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The link between rheumatic disorders and inborn errors of immunity. EBioMedicine 2023; 90:104501. [PMID: 36870198 PMCID: PMC9996386 DOI: 10.1016/j.ebiom.2023.104501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/11/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Inborn errors of immunity (IEIs) are immunological disorders characterized by variable susceptibility to infections, immune dysregulation and/or malignancies, as a consequence of damaging germline variants in single genes. Though initially identified among patients with unusual, severe or recurrent infections, non-infectious manifestations and especially immune dysregulation in the form of autoimmunity or autoinflammation can be the first or dominant phenotypic aspect of IEIs. An increasing number of IEIs causing autoimmunity or autoinflammation, including rheumatic disease have been reported over the last decade. Despite their rarity, identification of those disorders provided insight into the pathomechanisms of immune dysregulation, which may be relevant for understanding the pathogenesis of systemic rheumatic disorders. In this review, we present novel IEIs primarily causing autoimmunity or autoinflammation along with their pathogenic mechanisms. In addition, we explore the likely pathophysiological and clinical relevance of IEIs in systemic rheumatic disorders.
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Alarcón Garavito GA, Moniz T, Déom N, Redin F, Pichini A, Vindrola-Padros C. The implementation of large-scale genomic screening or diagnostic programmes: A rapid evidence review. Eur J Hum Genet 2023; 31:282-295. [PMID: 36517584 PMCID: PMC9995480 DOI: 10.1038/s41431-022-01259-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Genomic healthcare programmes, both in a research and clinical context, have demonstrated a pivotal opportunity to prevent, diagnose, and treat rare diseases. However, implementation factors could increase overall costs and affect uptake. As well, uncertainties remain regarding effective training, guidelines and legislation. The purpose of this rapid evidence review was to draw together the available global evidence on the implementation of genomic testing programmes, particularly on population-based screening and diagnostic programmes implemented at the national level, to understand the range of factors influencing implementation. This review involved a search of terms related to genomics, implementation and health care. The search was limited to peer-reviewed articles published between 2017-2022 and found in five databases. The review included thirty articles drawing on sixteen countries. A wide range of factors was cited as critical to the successful implementation of genomics programmes. These included having policy frameworks, regulations, guidelines; clinical decision support tools; access to genetic counselling; and education and training for healthcare staff. The high costs of implementing and integrating genomics into healthcare were also often barriers to stakeholders. National genomics programmes are complex and require the generation of evidence and addressing implementation challenges. The findings from this review highlight that there is a strong emphasis on addressing genomic education and engagement among varied stakeholders, including the general public, policymakers, and governments. Articles also emphasised the development of appropriate policies and regulatory frameworks to govern genomic healthcare, with a focus on legislation that regulates the collection, storage, and sharing of personal genomic data.
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Affiliation(s)
| | - Thomas Moniz
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK
| | - Noémie Déom
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK
| | - Federico Redin
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK
| | | | - Cecilia Vindrola-Padros
- Rapid Research Evaluation and Appraisal Lab (RREAL), University College London, 43-45 Foley Street, W1W 7TY, London, UK.
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11
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Clinical, immunological, molecular and therapeutic findings in monogenic immune dysregulation diseases: Middle East and North Africa registry. Clin Immunol 2022; 244:109131. [PMID: 36179983 DOI: 10.1016/j.clim.2022.109131] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022]
Abstract
Monogenic immune dysregulation diseases (MIDD) are caused by defective immunotolerance. This study was designed to increase knowledge on the prevalence and spectrum of MIDDs, genetic patterns, and outcomes in Middle East and North Africa (MENA). MIDD patients from 11 MENA countries (Iran, Turkey, Kuwait, Oman, Algeria, Egypt, United Arab Emirates, Tunisia, Jordan, Qatar, and Azerbaijan) were retrospectively evaluated. 343 MIDD patients (58% males and 42% female) at a median (IQR) age of 101 (42-192) months were enrolled. The most common defective genes were LRBA (23.9%), LYST (8.2%), and RAB27A (7.9%). The most prevalent initial and overall manifestations were infections (32.2% and 75.1%), autoimmunity (18.6% and 41%), and organomegaly (13.3% and 53.8%), respectively. Treatments included immunoglobulin replacement therapy (53%), hematopoietic stem cell transplantation (HSCT) (14.3%), immunosuppressives (36.7%), and surgery (3.5%). Twenty-nine (59.2%) patients survived HSCT. Along with infectious complications, autoimmunity and organomegaly may be the initial or predominant manifestations of MIDD.
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12
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Characterization of Novel Pathogenic Variants Leading to Caspase-8 Cleavage-Resistant RIPK1-Induced Autoinflammatory Syndrome. J Clin Immunol 2022; 42:1421-1432. [PMID: 35716229 PMCID: PMC9674708 DOI: 10.1007/s10875-022-01298-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Pathogenic RIPK1 variants have been described as the cause of two different inborn errors of immunity. Biallelic loss-of-function variants cause the recessively inherited RIPK1 deficiency, while monoallelic variants impairing the caspase-8-mediated RIPK1 cleavage provoke a novel autoinflammatory disease (AID) called cleavage-resistant RIPK1-induced autoinflammatory (CRIA) syndrome. The aim of this study was to characterize the pathogenicity of two novel RIPK1 variants located at the cleavage site of caspase-8 detected in patients with dominantly-inherited, early-onset undefined AID. RIPK1 genotyping was performed by Sanger and next-generation sequencing. Clinical and analytical data were collected from medical charts, and in silico and in vitro assays were performed to evaluate the functional consequences. Genetic analyses identified two novel heterozygous RIPK1 variants at the caspase-8 cleavage site (p.Leu321Arg and p.Asp324Gly), which displayed a perfect intrafamilial phenotype-genotype segregation following a dominant inheritance pattern. Structural analyses suggested that these variants disrupt the normal RIPK1 structure, probably making it less accessible to and/or less cleavable by caspase-8. In vitro experiments confirmed that the p.Leu321Arg and p.Asp324Gly RIPK1 variants were resistant to caspase-8-mediated cleavage and induced a constitutive activation of necroptotic pathway in a similar manner that previously characterized RIPK1 variants causing CRIA syndrome. All these results strongly supported the pathogenicity of the two novel RIPK1 variants and the diagnosis of CRIA syndrome in all enrolled patients. Moreover, the evidences here collected expand the phenotypic and genetic diversity of this recently described AID, and provide interesting data about effectiveness of treatments that may benefit future patients.
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