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Hurley K, Ozaki M, Philippot Q, Galvin L, Crosby D, Kirwan M, Gill DR, Alysandratos KD, Jenkins G, Griese M, Nathan N, Borie R. A roadmap to precision treatments for familial pulmonary fibrosis. EBioMedicine 2024; 104:105135. [PMID: 38718684 PMCID: PMC11096859 DOI: 10.1016/j.ebiom.2024.105135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/19/2024] Open
Abstract
Interstitial lung diseases (ILDs) in adults and children (chILD) are a heterogeneous group of lung disorders leading to inflammation, abnormal tissue repair and scarring of the lung parenchyma often resulting in respiratory failure and death. Inherited factors directly cause, or contribute significantly to the risk of developing ILD, so called familial pulmonary fibrosis (FPF), and monogenic forms may have a poor prognosis and respond poorly to current treatments. Specific, variant-targeted or precision treatments are lacking. Clinical trials of repurposed drugs, anti-fibrotic medications and specific treatments are emerging but for many patients no interventions exist. We convened an expert working group to develop an overarching framework to address the existing research gaps in basic, translational, and clinical research and identified areas for future development of preclinical models, candidate medications and innovative clinical trials. In this Position Paper, we summarise working group discussions, recommendations, and unresolved questions concerning precision treatments for FPF.
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Affiliation(s)
- Killian Hurley
- Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland; Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
| | - Mari Ozaki
- Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland; Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Quentin Philippot
- Université Paris Cité, Inserm, PHERE, Hôpital Bichat, AP-HP, Service de Pneumologie A, Centre Constitutif du Centre de Référence des Maladies Pulmonaires Rares, FHU APOLLO, Paris, France; Physiopathology and Epidemiology of Respiratory Diseases, Inserm U1152, UFR de Médecine, Université Paris Cité, 75018, Paris, France
| | - Liam Galvin
- European Pulmonary Fibrosis Federation, Overijse, Belgium
| | | | - Mary Kirwan
- Department of General Practice, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Deborah R Gill
- UK Respiratory Gene Therapy Consortium, London, United Kingdom; Gene Medicine Research Group, Radcliffe Department of Medicine (NDCLS), University of Oxford, Oxford, United Kingdom
| | - Konstantinos-Dionysios Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, 02118, USA; The Pulmonary Center and Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Gisli Jenkins
- Imperial College London, 4615, National Heart & Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Matthias Griese
- Department of Pediatric Pneumology, German Center for Lung Research (DZL), Dr von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Nadia Nathan
- Sorbonne Université, Pediatric Pulmonology and Reference Center for Rare Lung Diseases RespiRare, Inserm U933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, APHP, Paris, France
| | - Raphael Borie
- Université Paris Cité, Inserm, PHERE, Hôpital Bichat, AP-HP, Service de Pneumologie A, Centre Constitutif du Centre de Référence des Maladies Pulmonaires Rares, FHU APOLLO, Paris, France
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2
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Lenz D, Schlieben LD, Shimura M, Bianzano A, Smirnov D, Kopajtich R, Berutti R, Adam R, Aldrian D, Baric I, Baumann U, Bozbulut NE, Brugger M, Brunet T, Bufler P, Burnytė B, Calvo PL, Crushell E, Dalgiç B, Das AM, Dezsőfi A, Distelmaier F, Fichtner A, Freisinger P, Garbade SF, Gaspar H, Goujon L, Hadzic N, Hartleif S, Hegen B, Hempel M, Henning S, Hoerning A, Houwen R, Hughes J, Iorio R, Iwanicka-Pronicka K, Jankofsky M, Junge N, Kanavaki I, Kansu A, Kaspar S, Kathemann S, Kelly D, Kirsaçlioğlu CT, Knoppke B, Kohl M, Kölbel H, Kölker S, Konstantopoulou V, Krylova T, Kuloğlu Z, Kuster A, Laass MW, Lainka E, Lurz E, Mandel H, Mayerhanser K, Mayr JA, McKiernan P, McClean P, McLin V, Mention K, Müller H, Pasquier L, Pavlov M, Pechatnikova N, Peters B, Petković Ramadža D, Piekutowska-Abramczuk D, Pilic D, Rajwal S, Rock N, Roetig A, Santer R, Schenk W, Semenova N, Sokollik C, Sturm E, Taylor RW, Tschiedel E, Urbonas V, Urreizti R, Vermehren J, Vockley J, Vogel GF, Wagner M, van der Woerd W, Wortmann SB, Zakharova E, Hoffmann GF, Meitinger T, Murayama K, Staufner C, Prokisch H. Genetic landscape of pediatric acute liver failure of indeterminate origin. Hepatology 2024; 79:1075-1087. [PMID: 37976411 PMCID: PMC11020061 DOI: 10.1097/hep.0000000000000684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 09/23/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND AIMS Pediatric acute liver failure (PALF) is a life-threatening condition. In Europe, the main causes are viral infections (12%-16%) and inherited metabolic diseases (14%-28%). Yet, in up to 50% of cases the underlying etiology remains elusive, challenging clinical management, including liver transplantation. We systematically studied indeterminate PALF cases referred for genetic evaluation by whole-exome sequencing (WES), and analyzed phenotypic and biochemical markers, and the diagnostic yield of WES in this condition. APPROACH AND RESULTS With this international, multicenter observational study, patients (0-18 y) with indeterminate PALF were analyzed by WES. Data on the clinical and biochemical phenotype were retrieved and systematically analyzed. RESULTS In total, 260 indeterminate PALF patients from 19 countries were recruited between 2011 and 2022, of whom 59 had recurrent PALF. WES established a genetic diagnosis in 37% of cases (97/260). Diagnostic yield was highest in children with PALF in the first year of life (41%), and in children with recurrent acute liver failure (64%). Thirty-six distinct disease genes were identified. Defects in NBAS (n=20), MPV17 (n=8), and DGUOK (n=7) were the most frequent findings. When categorizing, the most frequent were mitochondrial diseases (45%), disorders of vesicular trafficking (28%), and cytosolic aminoacyl-tRNA synthetase deficiencies (10%). One-third of patients had a fatal outcome. Fifty-six patients received liver transplantation. CONCLUSIONS This study elucidates a large contribution of genetic causes in PALF of indeterminate origin with an increasing spectrum of disease entities. The high proportion of diagnosed cases and potential treatment implications argue for exome or in future rapid genome sequencing in PALF diagnostics.
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Affiliation(s)
- Dominic Lenz
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Lea D. Schlieben
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Masaru Shimura
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
- Department of Metabolism, Chiba Children’s Hospital, Centre for Medical Genetics, Chiba, Japan
| | - Alyssa Bianzano
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Robert Kopajtich
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Riccardo Berutti
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Rüdiger Adam
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, University Children’s Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Denise Aldrian
- Paediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivo Baric
- Department of Paediatrics, University Hospital Centre Zagreb, University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Ulrich Baumann
- Department of Peadiatric Kidney, Liver, and Metabolic Diseases, Division for Paediatric Gastroenterology and Hepatology, Hannover Medical School, Hannover, Germany
| | - Neslihan E. Bozbulut
- Department of Paediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Melanie Brugger
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Philip Bufler
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Birutė Burnytė
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Pier L. Calvo
- Regina Margherita Children’s Hospital, Paediatic Gastroenterology Unit, Torino, Italy
| | - Ellen Crushell
- National Centre for Inherited Metabolic Disorders, Children’s Health Ireland, Dublin, Ireland
| | - Buket Dalgiç
- Department of Paediatric Gastroenterology, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Anibh M. Das
- Hannover Medical School, Clinic for Paediatric Kidney, Liver, and Metabolic Diseases, Hannover, Germany
| | - Antal Dezsőfi
- First Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Felix Distelmaier
- Department of General Paediatrics, Neonatology and Paediatric Cardiology, University Children’s Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander Fichtner
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Peter Freisinger
- Department of Paediatrics, Hospital Reutlingen, Reutlingen, Germany
| | - Sven F. Garbade
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Harald Gaspar
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Louise Goujon
- CLAD Ouest CHU Hôpital Sud, CRMR Déficiences intellectuelles, Service de Génétique Médicale, Rennes, France
| | - Nedim Hadzic
- King’s College Hospital, Paediatric Liver, GI & Nutrition Centre, London, United Kingdom
| | - Steffen Hartleif
- Eberhard Karls University Tuebingen, Paediatric Gastroenterology and Hepatology, Tuebingen, Germany
| | - Bianca Hegen
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
- University Medical Centre Hamburg-Eppendorf, Institute of Human Genetics, Hamburg
| | - Stephan Henning
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andre Hoerning
- Department of Paediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Roderick Houwen
- Paediatric Gastroenterology, UMC Utrecht, Utrecht, The Netherlands
| | - Joanne Hughes
- Children’s Health Ireland, Temple Street Hospital, Dublin, Ireland
| | - Raffaele Iorio
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | | | - Martin Jankofsky
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Norman Junge
- Department of Peadiatric Kidney, Liver, and Metabolic Diseases, Division for Paediatric Gastroenterology and Hepatology, Hannover Medical School, Hannover, Germany
| | - Ino Kanavaki
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Third Department of Paediatrics, Attikon University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Aydan Kansu
- Department of Paediatric Gastroenterology, Ankara University, School of Medicine, Ankara, Turkey
| | - Sonja Kaspar
- Department of Paediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Simone Kathemann
- Department of Paediatrics II, Paediatric Gastroenterology, Hepatology and Liver Transplantation, University Hospital Essen, Essen, Germany
| | - Deidre Kelly
- Birmingham Children’s Hospital NHS Trust, Liver Unit, Birmingham, UK
| | - Ceyda T. Kirsaçlioğlu
- Department of Paediatric Gastroenterology, Ankara University, School of Medicine, Ankara, Turkey
| | - Birgit Knoppke
- University Hospital Regensburg, KUNO University Children’s Hospital, Regensburg, Germany
| | - Martina Kohl
- Department of General Paediatrics, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Heike Kölbel
- Department of Paediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro and Behavioral Sciences, University Duisburg-Essen, Essen, Germany
| | - Stefan Kölker
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | | | - Tatiana Krylova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Zarife Kuloğlu
- Department of Paediatric Gastroenterology, Ankara University, School of Medicine, Ankara, Turkey
| | - Alice Kuster
- Department of Neurometabolism, University Hospital of Nantes, Nantes, France
| | - Martin W. Laass
- Department of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Elke Lainka
- Department of Paediatrics II, Paediatric Gastroenterology, Hepatology and Liver Transplantation, University Hospital Essen, Essen, Germany
| | - Eberhard Lurz
- Department of Paediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Hanna Mandel
- Department of Paediatrics, Rambam Medical Centre, Meyer Children’s Hospital, Metabolic Unit, Haifa, Israel
| | - Katharina Mayerhanser
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Johannes A. Mayr
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Patrick McKiernan
- University of Pittsburgh and Children’s Hospital of Pittsburgh of UPMC, Pittsburgh Liver Research Centre, Pittsburgh, Pennsylvania, USA
| | | | - Valerie McLin
- Department of Paediatrics, Gynecology, and Obstetrics, Division of Paediatric Subspecialities, Swiss Paediatric Liver Centre, Paediatric Gastroenterology, Hepatology and Nutrition Unit, University of Geneva, Geneva, Switzerland
| | - Karine Mention
- Jeanne de Flandres Hospital, Reference Centre for Inherited Metabolic Diseases, Lille, France
| | - Hanna Müller
- Department of Paediatrics, Division of Neonatology and Paediatric Intensive Care, University Hospital Marburg, Marburg, Germany
| | - Laurent Pasquier
- CLAD Ouest CHU Hôpital Sud, CRMR Déficiences intellectuelles, Service de Génétique Médicale, Rennes, France
| | - Martin Pavlov
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
| | - Natalia Pechatnikova
- Healthcare Department Morozov Children’s City Clinical Hospital, Moscow City, Moscow
| | - Bianca Peters
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Danijela Petković Ramadža
- Department of Paediatrics, University Hospital Centre Zagreb, University of Zagreb, School of Medicine, Zagreb, Croatia
| | | | - Denisa Pilic
- Department of Paediatrics II, Paediatric Gastroenterology, Hepatology and Liver Transplantation, University Hospital Essen, Essen, Germany
| | - Sanjay Rajwal
- Department of Paediatrics, Gynecology, and Obstetrics, Division of Paediatric Subspecialities, Swiss Paediatric Liver Centre, Paediatric Gastroenterology, Hepatology and Nutrition Unit, University of Geneva, Geneva, Switzerland
| | - Nathalie Rock
- Department of Paediatrics, Gynecology, and Obstetrics, Division of Paediatric Subspecialities, Swiss Paediatric Liver Centre, Paediatric Gastroenterology, Hepatology and Nutrition Unit, University of Geneva, Geneva, Switzerland
| | - Agnès Roetig
- Laboratory of Genetics of Mitochondrial Diseases, Imagine Institute, University Paris Cité, INSERM UMR, Paris, France
| | - René Santer
- Department of Paediatrics, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Wilfried Schenk
- Department of Paediatrics, University Hospital Augsburg, Augsburg, Germany
| | - Natalia Semenova
- Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Christiane Sokollik
- Department of Paediatrics, Division of Paediatric Gastroenterology, Hepatology and Nutrition, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ekkehard Sturm
- Eberhard Karls University Tuebingen, Paediatric Gastroenterology and Hepatology, Tuebingen, Germany
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eva Tschiedel
- Department of Paediatrics I, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Vaidotas Urbonas
- Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Roser Urreizti
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, IRSJD, Esplugues de Llobregat, Barcelona, Spain and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)- Instituto de Salud Carlos III, Spain
| | - Jan Vermehren
- University Hospital Regensburg, KUNO University Children’s Hospital, Regensburg, Germany
| | - Jerry Vockley
- University of Pittsburgh and Children’s Hospital of Pittsburgh of UPMC, Pittsburgh Liver Research Centre, Pittsburgh, Pennsylvania, USA
| | - Georg-Friedrich Vogel
- Paediatrics I, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Cell Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matias Wagner
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Saskia B. Wortmann
- University Children’s Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Georg F. Hoffmann
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Thomas Meitinger
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Kei Murayama
- Department of Metabolism, Chiba Children’s Hospital, Centre for Medical Genetics, Chiba, Japan
| | - Christian Staufner
- Heidelberg University, Medical Faculty, University Hospital Heidelberg, Center for Child and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Centre, Helmholtz Munich, Munich Germany
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Sheen K, Myung S, Lee DM, Yu S, Choi Y, Kim T, Kim J, Ji SG, Kim MS, Kim W, Lee Y, Kim MS, Park YC. RNA-Seq of an LPS-Induced Inflammation Model Reveals Transcriptional Profile Patterns of Inflammatory Processes. Life (Basel) 2024; 14:558. [PMID: 38792580 PMCID: PMC11121855 DOI: 10.3390/life14050558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/10/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
The LPS-induced inflammation model is widely used for studying inflammatory processes due to its cost-effectiveness, reproducibility, and faithful representation of key hallmarks. While researchers often validate this model using clinical cytokine markers, a comprehensive understanding of gene regulatory mechanisms requires extending investigation beyond these hallmarks. Our study leveraged multiple whole-blood bulk RNA-seq datasets to rigorously compare the transcriptional profiles of the well-established LPS-induced inflammation model with those of several human diseases characterized by systemic inflammation. Beyond conventional inflammation-associated systems, we explored additional systems indirectly associated with inflammatory responses (i.e., ISR, RAAS, and UPR) using a customized core inflammatory gene list. Our cross-condition-validation approach spanned four distinct conditions: systemic lupus erythematosus (SLE) patients, dengue infection, candidemia infection, and staphylococcus aureus exposure. This analysis approach, utilizing the core gene list aimed to assess the model's suitability for understanding the gene regulatory mechanisms underlying inflammatory processes triggered by diverse factors. Our analysis resulted in elevated expressions of innate immune-associated genes, coinciding with suppressed expressions of adaptive immune-associated genes. Also, upregulation of genes associated with cellular stresses and mitochondrial innate immune responses underscored oxidative stress as a central driver of the corresponding inflammatory processes in both the LPS-induced and other inflammatory contexts.
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Affiliation(s)
- Kisung Sheen
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Seokho Myung
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Medicine, Kyung Hee University College of Medicine, Seoul 02453, Republic of Korea
| | - Dong-Min Lee
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Acupuncture & Moxibustion, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea
| | - Sanghyeon Yu
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Yueun Choi
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Taeyoon Kim
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Jihan Kim
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Medicine, Kyung Hee University College of Medicine, Seoul 02453, Republic of Korea
| | - Sang-Gu Ji
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Myung-Seo Kim
- Department of Orthopaedic Surgery, Shoulder & Elbow Clinic, Kyung Hee University School of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea;
| | - Wonnam Kim
- Division of Pharmacology, School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea;
| | - Yoonsung Lee
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
| | - Man S. Kim
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea; (K.S.); (S.M.); (D.-M.L.); (S.Y.); (Y.C.); (T.K.); (J.K.); (S.-G.J.); (Y.L.)
| | - Yeon-Cheol Park
- Department of Acupuncture & Moxibustion, Kyung Hee University College of Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea
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von Hardenberg S, Klefenz I, Steinemann D, Di Donato N, Baumann U, Auber B, Klemann C. Current genetic diagnostics in inborn errors of immunity. Front Pediatr 2024; 12:1279112. [PMID: 38659694 PMCID: PMC11039790 DOI: 10.3389/fped.2024.1279112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
New technologies in genetic diagnostics have revolutionized the understanding and management of rare diseases. This review highlights the significant advances and latest developments in genetic diagnostics in inborn errors of immunity (IEI), which encompass a diverse group of disorders characterized by defects in the immune system, leading to increased susceptibility to infections, autoimmunity, autoinflammatory diseases, allergies, and malignancies. Various diagnostic approaches, including targeted gene sequencing panels, whole exome sequencing, whole genome sequencing, RNA sequencing, or proteomics, have enabled the identification of causative genetic variants of rare diseases. These technologies not only facilitated the accurate diagnosis of IEI but also provided valuable insights into the underlying molecular mechanisms. Emerging technologies, currently mainly used in research, such as optical genome mapping, single cell sequencing or the application of artificial intelligence will allow even more insights in the aetiology of hereditary immune defects in the near future. The integration of genetic diagnostics into clinical practice significantly impacts patient care. Genetic testing enables early diagnosis, facilitating timely interventions and personalized treatment strategies. Additionally, establishing a genetic diagnosis is necessary for genetic counselling and prognostic assessments. Identifying specific genetic variants associated with inborn errors of immunity also paved the way for the development of targeted therapies and novel therapeutic approaches. This review emphasizes the challenges related with genetic diagnosis of rare diseases and provides future directions, specifically focusing on IEI. Despite the tremendous progress achieved over the last years, several obstacles remain or have become even more important due to the increasing amount of genetic data produced for each patient. This includes, first and foremost, the interpretation of variants of unknown significance (VUS) in known IEI genes and of variants in genes of unknown significance (GUS). Although genetic diagnostics have significantly contributed to the understanding and management of IEI and other rare diseases, further research, exchange between experts from different clinical disciplines, data integration and the establishment of comprehensive guidelines are crucial to tackle the remaining challenges and maximize the potential of genetic diagnostics in the field of rare diseases, such as IEI.
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Affiliation(s)
| | - Isabel Klefenz
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Nataliya Di Donato
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ulrich Baumann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Christian Klemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
- Department of Pediatric Immunology, Rheumatology and Infectiology, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
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5
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Ricci S, Sarli WM, Lodi L, Canessa C, Lippi F, Dini D, Ferrari M, Pisano L, Sieni E, Indolfi G, Resti M, Azzari C. HLH as an additional warning sign of inborn errors of immunity beyond familial-HLH in children: a systematic review. Front Immunol 2024; 15:1282804. [PMID: 38415256 PMCID: PMC10896843 DOI: 10.3389/fimmu.2024.1282804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
Background Hemophagocytic Lymphohistiocytosis (HLH) is a rare and life-threatening condition characterized by a severe impairment of the immune homeostasis. While Familial-HLH (FHL) is a known cause, the involvement of other Inborn Errors of Immunity (IEI) in pediatric-HLH remains understudied. Objective This systematic review aimed to assess the clinical features, triggers, laboratory data, treatment, and outcomes of pediatric HLH patients with IEI other than FHL (IEInotFHL), emphasizing the importance of accurate identification and management. Methods A systematic search for studies meeting inclusion criteria was conducted in PubMed, EMBASE, MEDLINE, and Cochrane Central. Quality assessment was performed through JBI criteria. Results A comprehensive search yielded 108 records meeting inclusion criteria, involving 178 patients. We identified 46 different IEI according to IUIS 2022 Classification. Combined immunodeficiencies, immune dysregulation disorders, and phagocyte defects were the IEI most frequently associated with HLH. In 75% of cases, HLH preceded the IEI diagnosis, often with an unrecognized history of severe infections. Triggers reflected the specific infection susceptibilities within IEI groups. Liver and central nervous system involvement were less common than in FHL cases. Treatment approaches and outcomes varied, with limited long-term follow-up data, limiting the assessment of therapeutic efficacy across IEI groups. Conclusion A comprehensive evaluation encompassing immunological, infectious, and genetic aspects is essential in pediatric-HLH. Relying solely on FHL or EBV susceptibility disorders tests is insufficient, as diverse other IEI can contribute to HLH. Early recognition of HLH as a potential warning sign can guide timely diagnostic investigations and facilitate tailored therapeutic interventions for improved outcomes. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=371425, PROSPERO, CRD42022371425.
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Affiliation(s)
- Silvia Ricci
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Walter Maria Sarli
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Lorenzo Lodi
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Clementina Canessa
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Francesca Lippi
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Donata Dini
- Department of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Marta Ferrari
- Department of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Laura Pisano
- Department of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Elena Sieni
- Pediatric Hematology-Oncology Department, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Giuseppe Indolfi
- Department of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
- Department Neurofarba, University of Florence, Florence, Italy
| | - Massimo Resti
- Department of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Chiara Azzari
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital IRCCS, Florence, Italy
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6
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Yu JE. New primary immunodeficiencies 2023 update. Curr Opin Pediatr 2024; 36:112-123. [PMID: 38001560 DOI: 10.1097/mop.0000000000001315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
PURPOSE OF REVIEW Primary immunodeficiency diseases (PIDs), also called inborn errors of immunity (IEI), are genetic disorders characterized by increased susceptibility to infection and/or aberrant regulation of immunological pathways. This review summarizes and highlights the new IEI disorders in the International Union of Immunological Societies (IUIS) 2022 report and current trends among new PIDs. RECENT FINDINGS Since the 2019 IUIS report and the 2021 IUIS interim update, the IUIS IEI classification now includes 485 validated IEIs. Increasing utilization of genetic testing and advances in the strategic evaluation of genetic variants has continued to drive the identification of, not only novel IEI disorders, but additional genetic etiologies for known IEI disorders and phenotypes. SUMMARY The recognition of new IEIs continues to advance at a rapid pace, which is due in part to increased performance and application of genetic modalities as well as expansion of the underlying science that is applied to convincingly establish causality. These disorders, as a whole, continue to emphasize the specificity of immunity, complexity of immune mechanisms, and the fine balance that defines immune homeostasis.
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Affiliation(s)
- Joyce E Yu
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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7
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Liu H, Han Z, Chen L, Zhang J, Zhang Z, Chen Y, Liu F, Wang K, Liu J, Sai N, Zhou X, Zhou C, Hu S, Wen Q, Ma L. ZNFX1 promotes AMPK-mediated autophagy against Mycobacterium tuberculosis by stabilizing Prkaa2 mRNA. JCI Insight 2024; 9:e171850. [PMID: 38016036 PMCID: PMC10906457 DOI: 10.1172/jci.insight.171850] [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: 04/27/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Tuberculosis has the highest mortality rate worldwide for a chronic infectious disease caused by a single pathogen. RNA-binding proteins (RBPs) are involved in autophagy - a key defense mechanism against Mycobacterium tuberculosis (M. tuberculosis) infection - by modulating RNA stability and forming intricate regulatory networks. However, the functions of host RBPs during M. tuberculosis infection remain relatively unexplored. Zinc finger NFX1-type containing 1 (ZNFX1), a conserved RBP critically involved in immune deficiency diseases and mycobacterial infections, is significantly upregulated in M. tuberculosis-infected macrophages. Here, we aimed to explore the immunoregulatory functions of ZNFX1 during M. tuberculosis infection. We observed that Znfx1 knockout markedly compromised the multifaceted immune responses mediated by macrophages. This compromise resulted in reduced phagocytosis, suppressed macrophage activation, increased M. tuberculosis burden, progressive lung tissue injury, and chronic inflammation in M. tuberculosis-infected mice. Mechanistic investigations revealed that the absence of ZNFX1 inhibited autophagy, consequently mediating immune suppression. ZNFX1 critically maintained AMPK-regulated autophagic flux by stabilizing protein kinase AMP-activated catalytic subunit alpha 2 mRNA, which encodes a key catalytic α subunit of AMPK, through its zinc finger region. This process contributed to M. tuberculosis growth suppression. These findings reveal a function of ZNFX1 in establishing anti-M. tuberculosis immune responses, enhancing our understanding of the roles of RBPs in tuberculosis immunity and providing a promising approach to bolster antituberculosis immunotherapy.
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Frémond ML, Berteloot L, Hadchouel A. [Lung involvement in autoinflammatory diseases]. Rev Mal Respir 2024; 41:18-28. [PMID: 38040588 DOI: 10.1016/j.rmr.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/31/2023] [Indexed: 12/03/2023]
Abstract
Genetic autoinflammatory diseases are now a recognized and rapidly expanding group. The lung involvement historically associated with autoinflammatory diseases is inflammatory seritis, primarily seen in familial Mediterranean fever and other interleukin-1 mediated diseases. Over the last ten years, pulmonary involvement has been the core presentation of two autoinflammatory diseases associated with constitutive type I interferon activation, i.e. SAVI and COPA syndrome. Most patients with these diseases usually develop early progression to pulmonary fibrosis, which is responsible for high rates of morbidity and mortality. Other rare autoinflammatory diseases are associated with alveolar proteinosis, particularly when related to MARS mutations. Additionally, in adults, VEXAS is frequently associated with pulmonary involvement, albeit without prognosis effect. A molecular approach to autoinflammatory diseases enables not only the definition of biomarkers for diagnosis, but also the identification of targeted treatments. Examples include JAK inhibitors in SAVI and COPA syndrome, even though this therapy does not prevent progression to pulmonary fibrosis. Another illustrative example is the efficacy of methionine supplementation in alveolar proteinosis linked to MARS mutations. Overall, in autoinflammatory diseases the lung is now emerging as a possible affected organ. Continuing discovery of new autoinflammatory diseases is likely to uncover further pathologies involving the lung. Such advances are expected to lead to the development of novel therapeutic perspectives.
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Affiliation(s)
- M-L Frémond
- Unité d'immuno-hématologie et rhumatologie pédiatriques, hôpital Necker-Enfants-Malades, AP-HP, centre université de Paris-Cité, 149, rue de Sèvres, 75015 Paris, France; Institut imagine, laboratoire de neurogénétique et neuroinflammation, université de Paris-Cité, 24, boulevard du Montparnasse, 75015 Paris, France.
| | - L Berteloot
- Service de radiologie pédiatrique, hôpital Necker-Enfants-Malades, AP-HP, centre université de Paris-Cité, 75015 Paris, France
| | - A Hadchouel
- Institut Necker-Enfants-Malades (INEM), Inserm, université Paris-Cité, 75015 Paris, France; Service de pneumologie et allergologie pédiatriques, hôpital Necker-Enfants-Malades, AP-HP, centre université de Paris-Cité, 75015 Paris, France
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9
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Al-Saud B, Alshareef T, Al-Alwan M, Alazami AM. ZNFX1 Deficiency in a Child with Interstitial Pneumonitis and Peripheral Monocytosis. J Clin Immunol 2023; 43:1529-1532. [PMID: 37291413 PMCID: PMC10250176 DOI: 10.1007/s10875-023-01529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/29/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Bandar Al-Saud
- Department of Pediatrics, Division of Allergy & Immunology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Turki Alshareef
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Pediatrics, Division of Nephrology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Monther Al-Alwan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Stem Cell & Tissue Re-engineering Program, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Translational Genomics Department, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia.
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Chinnici A, Beneforti L, Pegoraro F, Trambusti I, Tondo A, Favre C, Coniglio ML, Sieni E. Approaching hemophagocytic lymphohistiocytosis. Front Immunol 2023; 14:1210041. [PMID: 37426667 PMCID: PMC10324660 DOI: 10.3389/fimmu.2023.1210041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
Hemophagocytic Lymphohistiocytosis (HLH) is a rare clinical condition characterized by sustained but ineffective immune system activation, leading to severe and systemic hyperinflammation. It may occur as a genetic or sporadic condition, often triggered by an infection. The multifaceted pathogenesis results in a wide range of non-specific signs and symptoms, hampering early recognition. Despite a great improvement in terms of survival in the last decades, a considerable proportion of patients with HLH still die from progressive disease. Thus, prompt diagnosis and treatment are crucial for survival. Faced with the complexity and the heterogeneity of syndrome, expert consultation is recommended to correctly interpret clinical, functional and genetic findings and address therapeutic decisions. Cytofluorimetric and genetic analysis should be performed in reference laboratories. Genetic analysis is mandatory to confirm familial hemophagocytic lymphohistiocytosis (FHL) and Next Generation Sequencing is increasingly adopted to extend the spectrum of genetic predisposition to HLH, though its results should be critically discussed with specialists. In this review, we critically revise the reported laboratory tools for the diagnosis of HLH, in order to outline a comprehensive and widely available workup that allows to reduce the time between the clinical suspicion of HLH and its final diagnosis.
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Affiliation(s)
- Aurora Chinnici
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Linda Beneforti
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Francesco Pegoraro
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Irene Trambusti
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Annalisa Tondo
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Claudio Favre
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Maria Luisa Coniglio
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
| | - Elena Sieni
- Department of Pediatric Hematology Oncology, Meyer Children’s Hospital IRCCS, Florence, Italy
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11
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von Hardenberg S, Wallaschek H, Du C, Schmidt G, Auber B. A holistic approach to maximise diagnostic output in trio exome sequencing. Front Pediatr 2023; 11:1183891. [PMID: 37274821 PMCID: PMC10238563 DOI: 10.3389/fped.2023.1183891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Rare genetic diseases are a major cause for severe illness in children. Whole exome sequencing (WES) is a powerful tool for identifying genetic causes of rare diseases. For a better and faster assessment of the vast number of variants that are identified in the index patient in WES, parental sequencing can be applied ("trio WES"). Methods We assessed the diagnostic rate of routine trio WES including analysis of copy number variants in 224 pediatric patients during an evaluation period of three years. Results Trio WES provided a diagnosis in 67 (30%) of all 224 analysed children. The turnaround time of trio WES analysis has been reduced significantly from 41 days in 2019 to 23 days in 2021. Copy number variants could be identified to be causative in 10 cases (4.5%), underlying the importance of copy number variant analysis. Variants in three genes which were previously not associated with a clinical condition (GAD1, TMEM222 and ZNFX1) were identified using the matching tool GeneMatcher and were part of the first description of a new syndrome. Discussion Trio WES has proven to have a high diagnostic yield and to shorten the process of identifying the correct diagnosis in paediatric patients. Re-evaluation of all 224 trio WES 1-3 years after initial analysis did not establish new diagnoses. Initiating (trio) WES as a first-tier diagnostics including copy number variant detection should be considered as early as possible, especially for children treated in ICU, if a monogenetic disease is suspected.
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Affiliation(s)
| | | | | | | | - Bernd Auber
- Correspondence: Sandra von Hardenberg Bernd Auber
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12
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Nayir Buyuksahin H, Kiper N. Childhood Interstitial Lung Disease. PEDIATRIC ALLERGY, IMMUNOLOGY, AND PULMONOLOGY 2023; 36:5-15. [PMID: 36695653 DOI: 10.1089/ped.2022.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Childhood interstitial lung disease (chILD) is a heterogeneous group of diseases with various clinical and imaging findings. The incidence and prevalence have increased in recent years, probably due to better comprehension of these rare diseases and increased awareness among physicians. chILDs present with nonspecific pulmonary symptoms, such as tachypnea, hypoxemia, cough, rales, and failure to thrive. Unnecessary invasive procedures can be avoided if specific mutations are detected through genetic examinations or if typical imaging patterns are recognized on computed tomography. Disease knowledge and targeted therapies are improving through international collaboration. Pulmonary involvement in systemic diseases is not uncommon. Pulmonary involvement may be the first finding in connective tissue diseases. This review aims to present a systematic patient-targeted approach to the diagnosis of chILD.
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Affiliation(s)
- Halime Nayir Buyuksahin
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Nural Kiper
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
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13
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Nathan N, Griese M, Michel K, Carlens J, Gilbert C, Emiralioglu N, Torrent-Vernetta A, Marczak H, Willemse B, Delestrain C, Epaud R. Diagnostic workup of childhood interstitial lung disease. Eur Respir Rev 2023; 32:32/167/220188. [PMID: 36813289 PMCID: PMC9945877 DOI: 10.1183/16000617.0188-2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/18/2022] [Indexed: 02/24/2023] Open
Abstract
Childhood interstitial lung diseases (chILDs) are rare and heterogeneous diseases with significant morbidity and mortality. An accurate and quick aetiological diagnosis may contribute to better management and personalised treatment. On behalf of the European Respiratory Society Clinical Research Collaboration for chILD (ERS CRC chILD-EU), this review summarises the roles of the general paediatrician, paediatric pulmonologists and expert centres in the complex diagnostic workup. Each patient's aetiological chILD diagnosis must be reached without prolonged delays in a stepwise approach from medical history, signs, symptoms, clinical tests and imaging, to advanced genetic analysis and specialised procedures including bronchoalveolar lavage and biopsy, if necessary. Finally, as medical progress is fast, the need to revisit a diagnosis of "undefined chILD" is stressed.
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Affiliation(s)
- Nadia Nathan
- AP-HP, Sorbonne Université, Pediatric Pulmonology Department and Reference Center for Rare Lung Disease RespiRare, Armand Trousseau Hospital, Paris, France .,Sorbonne Université, Inserm UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Paris, France
| | - Matthias Griese
- Department of Paediatric Pneumology, Dr von Hauner Children's Hospital, German Centre for Lung Research, University of Munich, Munich, Germany
| | - Katarzyna Michel
- Department of Paediatric Pneumology, Dr von Hauner Children's Hospital, German Centre for Lung Research, University of Munich, Munich, Germany
| | - Julia Carlens
- Clinic for Pediatric Pneumology, Hannover Medical School, Hannover, Germany
| | - Carlee Gilbert
- Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Nagehan Emiralioglu
- Department of Pediatric Pulmonology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Alba Torrent-Vernetta
- Pediatric Allergy and Pulmonology Section, Department of Pediatrics, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Honorata Marczak
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Brigitte Willemse
- Department of Pediatric Pneumology and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Céline Delestrain
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands,Centre Hospitalier Intercommunal de Créteil, Service de Pédiatrie Générale, Créteil, France,Centre des Maladies Respiratoires Rares (RESPIRARE®), CRCM, Créteil, France
| | - Ralph Epaud
- Centre Hospitalier Intercommunal de Créteil, Service de Pédiatrie Générale, Créteil, France,Centre des Maladies Respiratoires Rares (RESPIRARE®), CRCM, Créteil, France,University Paris Est Créteil, INSERM, IMRB, Créteil, France
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14
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Errami A, El Baghdadi J, Ailal F, Benhsaien I, Ouazahrou K, Abel L, Casanova JL, Boisson-Dupuis S, Bustamante J, Bousfiha AA. Mendelian susceptibility to mycobacterial disease: an overview. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-022-00358-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Abstract
Background
Mycobacteria include ubiquitous species of varying virulence. However, environmental and individual-specific factors, particularly host genetics, play a crucial role in the outcome of exposure to mycobacteria. The first molecular evidence of a monogenic predisposition to mycobacteria came from the study of Mendelian susceptibility to mycobacterial disease (MSMD), a rare inborn error of IFN-γ immunity conferring a selective susceptibility to infections even with low virulent mycobacteria, in patients, mostly children, without recognizable immune defects in routine tests. This article provides a global and updated description of the most important molecular, cellular, and clinical features of all known monogenic defects of MSMD.
Results
Over the last 20 years, 19 genes were found to be mutated in MSMD patients (IFNGR1, IFNGR2, IFNG, IL12RB1, IL12RB2, IL23R, IL12B, ISG15, USP18, ZNFX1, TBX21, STAT1, TYK2, IRF8, CYBB, JAK1, RORC, NEMO, and SPPL2A), and the allelic heterogeneity at these loci has led to the definition of 35 different genetic defects. Despite the clinical and genetic heterogeneity, almost all genetic etiologies of MSMD alter the interferon gamma (IFN-γ)-mediated immunity, by impairing or abolishing IFN-γ production or the response to this cytokine or both. It was proven that the human IFN-γ level is a quantitative trait that defines the outcome of mycobacterial infection.
Conclusion
The study of these monogenic defects contributes to understanding the molecular mechanism of mycobacterial infections in humans and to the development of new diagnostic and therapeutic approaches to improve care and prognosis. These discoveries also bridge the gap between the simple Mendelian inheritance and complex human genetics.
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15
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Planas R, Felber M, Vavassori S, Pachlopnik Schmid J. The hyperinflammatory spectrum: from defects in cytotoxicity to cytokine control. Front Immunol 2023; 14:1163316. [PMID: 37187762 PMCID: PMC10175623 DOI: 10.3389/fimmu.2023.1163316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Cytotoxic lymphocytes kill target cells through polarized release of the content of cytotoxic granules towards the target cell. The importance of this cytotoxic pathway in immune regulation is evidenced by the severe and often fatal condition, known as hemophagocytic lymphohistiocytosis (HLH) that occurs in mice and humans with inborn errors of lymphocyte cytotoxic function. The clinical and preclinical data indicate that the damage seen in severe, virally triggered HLH is due to an overwhelming immune system reaction and not the direct effects of the virus per se. The main HLH-disease mechanism, which links impaired cytotoxicity to excessive release of pro-inflammatory cytokines is a prolongation of the synapse time between the cytotoxic effector cell and the target cell, which prompts the former to secrete larger amounts of cytokines (including interferon gamma) that activate macrophages. We and others have identified novel genetic HLH spectrum disorders. In the present update, we position these newly reported molecular causes, including CD48-haploinsufficiency and ZNFX1-deficiency, within the pathogenic pathways that lead to HLH. These genetic defects have consequences on the cellular level on a gradient model ranging from impaired lymphocyte cytotoxicity to intrinsic activation of macrophages and virally infected cells. Altogether, it is clear that target cells and macrophages may play an independent role and are not passive bystanders in the pathogenesis of HLH. Understanding these processes which lead to immune dysregulation may pave the way to novel ideas for medical intervention in HLH and virally triggered hypercytokinemia.
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Affiliation(s)
- Raquel Planas
- Division of Immunology, University Children’s Hospital Zurich, Zurich, Switzerland
- Department of Cell Biology, Physiology and Immunology, University of Barcelona, Barcelona, Spain
| | - Matthias Felber
- Division of Immunology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Stefano Vavassori
- Division of Immunology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children’s Hospital Zurich, Zurich, Switzerland
- Pediatric Immunology, University of Zurich, Zurich, Switzerland
- *Correspondence: Jana Pachlopnik Schmid,
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Gao X, Michel K, Griese M. Interstitial Lung Disease in Immunocompromised Children. Diagnostics (Basel) 2022; 13:diagnostics13010064. [PMID: 36611354 PMCID: PMC9818431 DOI: 10.3390/diagnostics13010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The range of pulmonary complications beyond infections in pediatric immunocompromised patients is broad but not well characterized. Our goal was to assess the spectrum of disorders with a focus on interstitial lung diseases (ILD) in immunodeficient patients. METHODS We reviewed 217 immunocompromised children attending a specialized pneumology service during a period of 23 years. We assigned molecular diagnoses where possible and categorized the underlying immunological conditions into inborn errors of immunity or secondary immunodeficiencies according to the IUIS and the pulmonary conditions according to the chILD-EU classification system. RESULTS Among a wide array of conditions, opportunistic and chronic infections were the most frequent. ILD had a 40% prevalence. Of these children, 89% had a CT available, and 66% had a lung biopsy, which supported the diagnosis of ILD in 95% of cases. Histology was often lymphocyte predominant with the histo-pattern of granulomatous and lymphocytic interstitial lung disease (GLILD), follicular bronchiolitis or lymphocytic interstitial pneumonitis. Of interest, DIP, PAP and NSIP were also diagnosed. ILD was detected in several immunological disorders not yet associated with ILD. CONCLUSIONS Specialized pneumological expertise is necessary to manage the full spectrum of respiratory complications in pediatric immunocompromised patients.
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Affiliation(s)
| | | | - Matthias Griese
- Correspondence: ; Tel.: +49-89-4400-57870; Fax: +49-89-4400-57872
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17
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In Silico Prediction of Hub Genes Involved in Diabetic Kidney and COVID-19 Related Disease by Differential Gene Expression and Interactome Analysis. Genes (Basel) 2022; 13:genes13122412. [PMID: 36553678 PMCID: PMC9778100 DOI: 10.3390/genes13122412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Diabetic kidney disease (DKD) is a frequently chronic kidney pathology derived from diabetes comorbidity. This condition has irreversible damage and its risk factor increases with SARS-CoV-2 infection. The prognostic outcome for diabetic patients with COVID-19 is dismal, even with intensive medical treatment. However, there is still scarce information on critical genes involved in the pathophysiological impact of COVID-19 on DKD. Herein, we characterize differential expression gene (DEG) profiles and determine hub genes undergoing transcriptional reprogramming in both disease conditions. Out of 995 DEGs, we identified 42 shared with COVID-19 pathways. Enrichment analysis elucidated that they are significantly induced with implications for immune and inflammatory responses. By performing a protein-protein interaction (PPI) network and applying topological methods, we determine the following five hub genes: STAT1, IRF7, ISG15, MX1 and OAS1. Then, by network deconvolution, we determine their co-expressed gene modules. Moreover, we validate the conservancy of their upregulation using the Coronascape database (DB). Finally, tissue-specific regulation of the five predictive hub genes indicates that OAS1 and MX1 expression levels are lower in healthy kidney tissue. Altogether, our results suggest that these genes could play an essential role in developing severe outcomes of COVID-19 in DKD patients.
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18
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Boycott KM, Hartley T, Kernohan KD, Dyment DA, Howley H, Innes AM, Bernier FP, Brudno M. Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery. Am J Hum Genet 2022; 109:1947-1959. [PMID: 36332610 PMCID: PMC9674964 DOI: 10.1016/j.ajhg.2022.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
The past decade has witnessed a rapid evolution in rare disease (RD) research, fueled by the availability of genome-wide (exome and genome) sequencing. In 2011, as this transformative technology was introduced to the research community, the Care4Rare Canada Consortium was launched: initially as FORGE, followed by Care4Rare, and Care4Rare SOLVE. Over what amounted to three eras of diagnosis and discovery, the Care4Rare Consortium used exome sequencing and, more recently, genome and other 'omic technologies to identify the molecular cause of unsolved RDs. We achieved a diagnostic yield of 34% (623/1,806 of participating families), including the discovery of deleterious variants in 121 genes not previously associated with disease, and we continue to study candidate variants in novel genes for 145 families. The Consortium has made significant contributions to RD research, including development of platforms for data collection and sharing and instigating a Canadian network to catalyze functional characterization research of novel genes. The Consortium was instrumental to implementing genome-wide sequencing as a publicly funded test for RD diagnosis in Canada. Despite the successes of the past decade, the challenge of solving all RDs remains enormous, and the work is far from over. We must leverage clinical and 'omic data for secondary use, develop tools and policies to support safe data sharing, continue to explore the utility of new and emerging technologies, and optimize research protocols to delineate complex disease mechanisms. Successful approaches in each of these realms is required to offer diagnostic clarity to all families with RDs.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada,Corresponding author
| | - Taila Hartley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Heather Howley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Francois P. Bernier
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
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19
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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: 5] [Impact Index Per Article: 2.5] [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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20
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Anti-cytokine autoantibodies and inborn errors of immunity. J Immunol Methods 2022; 508:113313. [PMID: 35817172 DOI: 10.1016/j.jim.2022.113313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/06/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
The past quarter of a century has witnessed an inordinate increase in our understanding of primary immunodeficiencies / inborn errors of immunity. These include a significant increase in the number of identified conditions, broadening the phenotypes of existing entities, delineation of classical inborn errors of immunity from those with a narrow phenotype, and a gradual shift from supportive to definitive care in patients afflicted with these diseases. It has also seen the discovery of conditions broadly defined as phenocopies of primary immunodeficiencies, where somatic mutations or autoantibodies mimic a recognised primary immunodeficiency's presentation in the absence of the underlying genetic basis for that disease. This article will provide a review of the anti-cytokine autoantibody-mediated phenocopies of inborn errors of immunity and discuss the therapeutic and laboratory aspects of this group of diseases.
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21
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Ouyang JPT, Zhang WL, Seydoux G. The conserved helicase ZNFX-1 memorializes silenced RNAs in perinuclear condensates. Nat Cell Biol 2022; 24:1129-1140. [PMID: 35739318 PMCID: PMC9276528 DOI: 10.1038/s41556-022-00940-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 05/11/2022] [Indexed: 01/23/2023]
Abstract
RNA-mediated interference (RNAi) is a conserved mechanism that uses small RNAs (sRNAs) to silence gene expression. In the Caenorhabditis elegans germline, transcripts targeted by sRNAs are used as templates for sRNA amplification to propagate silencing into the next generation. Here we show that RNAi leads to heritable changes in the distribution of nascent and mature transcripts that correlate with two parallel sRNA amplification loops. The first loop, dependent on the nuclear Argonaute HRDE-1, targets nascent transcripts and reduces but does not eliminate productive transcription at the locus. The second loop, dependent on the conserved helicase ZNFX-1, targets mature transcripts and concentrates them in perinuclear condensates. ZNFX-1 interacts with sRNA-targeted transcripts that have acquired poly(UG) tails and is required to sustain pUGylation and robust sRNA amplification in the inheriting generation. By maintaining a pool of transcripts for amplification, ZNFX-1 prevents premature extinction of the RNAi response and extends silencing into the next generation.
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Affiliation(s)
- John Paul Tsu Ouyang
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wenyan Lucy Zhang
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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22
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Kannan A, Suomalainen M, Volle R, Bauer M, Amsler M, Trinh HV, Vavassori S, Schmid JP, Vilhena G, Marín-González A, Perez R, Franceschini A, von Mering C, Hemmi S, Greber UF. Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects. Viruses 2022; 14:v14071407. [PMID: 35891387 PMCID: PMC9322957 DOI: 10.3390/v14071407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023] Open
Abstract
Pathogen-associated molecular patterns, including cytoplasmic DNA and double-strand (ds)RNA trigger the induction of interferon (IFN) and antiviral states protecting cells and organisms from pathogens. Here we discovered that the transfection of human airway cell lines or non-transformed fibroblasts with 24mer dsRNA mimicking the cellular micro-RNA (miR)29b-1* gives strong anti-viral effects against human adenovirus type 5 (AdV-C5), influenza A virus X31 (H3N2), and SARS-CoV-2. These anti-viral effects required blunt-end complementary RNA strands and were not elicited by corresponding single-strand RNAs. dsRNA miR-29b-1* but not randomized miR-29b-1* mimics induced IFN-stimulated gene expression, and downregulated cell adhesion and cell cycle genes, as indicated by transcriptomics and IFN-I responsive Mx1-promoter activity assays. The inhibition of AdV-C5 infection with miR-29b-1* mimic depended on the IFN-alpha receptor 2 (IFNAR2) and the RNA-helicase retinoic acid-inducible gene I (RIG-I) but not cytoplasmic RNA sensors MDA5 and ZNFX1 or MyD88/TRIF adaptors. The antiviral effects of miR29b-1* were independent of a central AUAU-motif inducing dsRNA bending, as mimics with disrupted AUAU-motif were anti-viral in normal but not RIG-I knock-out (KO) or IFNAR2-KO cells. The screening of a library of scrambled short dsRNA sequences identified also anti-viral mimics functioning independently of RIG-I and IFNAR2, thus exemplifying the diverse anti-viral mechanisms of short blunt-end dsRNAs.
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Affiliation(s)
- Abhilash Kannan
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Neurimmune AG, Wagistrasse 18, 8952 Schlieren, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Romain Volle
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Marco Amsler
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Hung V. Trinh
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Genezen, 9900 Westpoint Dr, Suite 128, Indianapolis, IN 46256, USA
| | - Stefano Vavassori
- Division of Immunology, University Children’s Hospital Zürich, 8032 Zürich, Switzerland; (S.V.); (J.P.S.)
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children’s Hospital Zürich, 8032 Zürich, Switzerland; (S.V.); (J.P.S.)
- Faculty of Medicine, University of Zürich, 8006 Zürich, Switzerland
| | - Guilherme Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain; (G.V.); (R.P.)
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Alberto Marín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Cantoblanco, E-28049 Madrid, Spain;
| | - Ruben Perez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain; (G.V.); (R.P.)
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Andrea Franceschini
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, 20139 Milano, Italy
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Silvio Hemmi
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; (A.K.); (M.S.); (R.V.); (M.B.); (M.A.); (H.V.T.); (A.F.); (C.v.M.); (S.H.)
- Correspondence:
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23
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Tangye SG, Al-Herz W, Bousfiha A, Cunningham-Rundles C, Franco JL, Holland SM, Klein C, Morio T, Oksenhendler E, Picard C, Puel A, Puck J, Seppänen MRJ, Somech R, Su HC, Sullivan KE, Torgerson TR, Meyts I. Human Inborn Errors of Immunity: 2022 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol 2022; 42:1473-1507. [PMID: 35748970 PMCID: PMC9244088 DOI: 10.1007/s10875-022-01289-3] [Citation(s) in RCA: 336] [Impact Index Per Article: 168.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/02/2022] [Indexed: 12/19/2022]
Abstract
We report the updated classification of inborn errors of immunity, compiled by the International Union of Immunological Societies Expert Committee. This report documents the key clinical and laboratory features of 55 novel monogenic gene defects, and 1 phenocopy due to autoantibodies, that have either been discovered since the previous update (published January 2020) or were characterized earlier but have since been confirmed or expanded in subsequent studies. While variants in additional genes associated with immune diseases have been reported in the literature, this update includes only those that the committee assessed that reached the necessary threshold to represent novel inborn errors of immunity. There are now a total of 485 inborn errors of immunity. These advances in discovering the genetic causes of human immune diseases continue to significantly further our understanding of molecular, cellular, and immunological mechanisms of disease pathogenesis, thereby simultaneously enhancing immunological knowledge and improving patient diagnosis and management. This report is designed to serve as a resource for immunologists and geneticists pursuing the molecular diagnosis of individuals with heritable immunological disorders and for the scientific dissection of cellular and molecular mechanisms underlying monogenic and related human immune diseases.
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Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine & Health, UNSW Sydney, Darlinghurst, NSW, Australia.
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Aziz Bousfiha
- Laboratoire d'Immunologie Clinique, d'Inflammation et d'Allergy LICIA Clinical Immunology Unit, Casablanca Children's Hospital, Ibn Rochd Medical School, King Hassan II University, Casablanca, Morocco
| | | | - Jose Luis Franco
- Grupo de Inmunodeficiencias Primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Steven M Holland
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Klein
- Dr von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, APHP, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Capucine Picard
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, APHP, Paris, France
- Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Université Paris Cité, Paris, France
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, INSERM U1163, Necker Hospital, 75015, Paris, France
- Université Paris Cité, Imagine Institute, 75015, Paris, France
| | - Jennifer Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Mikko R J Seppänen
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center and Rare Diseases Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Raz Somech
- Pediatric Department and Immunology Unit, Sheba Medical Center, Tel Aviv, Israel
| | - Helen C Su
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Isabelle Meyts
- Department of Immunology and Microbiology, Laboratory for Inborn Errors of Immunity, Department of Pediatrics, University Hospitals Leuven and KU Leuven, 3000, Leuven, Belgium
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24
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Han L, Zhao Z, Chen X, Yang K, Tan Z, Huang Z, Zhou L, Dai R. Human umbilical cord mesenchymal stem cells-derived exosomes for treating traumatic pancreatitis in rats. Stem Cell Res Ther 2022; 13:221. [PMID: 35619158 PMCID: PMC9137180 DOI: 10.1186/s13287-022-02893-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/10/2022] [Indexed: 01/30/2023] Open
Abstract
Background The therapeutic and protective effects of human umbilical cord mesenchymal stem cells-exosomes (hucMSC-Exs) on traumatic pancreatitis (TP) remain unknown. Here, we established a rat model of TP and evaluated and compared the therapeutic effects of hUC-MSCs and hucMSC-Exs. Methods HucMSC-Exs were obtained by ultracentrifugation and identified using transmission electron microscopy and western blot analysis. TP rats were treated by tail vein injection of hUC-MSCs and hucMSC-Exs. Their homing in rats was observed by performing fluorescence microscopy. The degree of pancreatic tissue damage was assessed by HE staining, the expression levels of amylase, lipase, and inflammatory cytokines were detected by ELISA, apoptosis was detected by TUNEL assay, and the expression levels of various apoptosis-related proteins were detected by western-blot. The expression levels of apoptosis-related molecular markers were detected by RT-qPCR. Results The colonization of exosomes was observed in pancreatic tissue. Compared to TP group, the histopathological score of pancreas was significantly decreased in the TP + hUC-MSCs group and TP + hucMSC-Exs group (P < 0.05). Compared to TP group, the activity of serum amylase and lipase was significantly decreased (P < 0.05). The expression levels of IL-6 and TNF-α were significantly decreased, while those of IL-10 and TGF-β were significantly increased (P < 0.05). The apoptosis index of the TP group was significantly increased (P < 0.05), whereas that of the TP + hUC-MSCs and TP + hucMSC-Exs groups was significantly decreased (P < 0.05). Compared to TP group, the expression levels of Bax, Bcl-2, and Caspase-3 were significantly decreased in the TP + hUC-MSCs group and TP + hucMSC-Exs group (P < 0.05). Conclusion HucMSC-Exs can colonize injured pancreatic tissue, inhibit the apoptosis of acinar cells, and control the systemic inflammatory response to facilitate the repair of pancreatic tissue.
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Affiliation(s)
- Li Han
- General Surgery Center, General Hospital of Western Theater Command, No. 270, Rongdu Rd, Jinniu District, Chengdu, 610083, Sichuan Province, China.,College of Medicine, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhirong Zhao
- College of Medicine, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xingyun Chen
- Department of Hepatobiliary and Pancreatic Surgery, Integrated Traditional Chinese and Western Medicine Hospital of Liangshan Yi Autonomous Prefecture, Xichang, 615000, Sichuan Province, China
| | - Ke Yang
- Department of Cardiovascular Surgery, General Hospital of Western Theater Command, Chengdu, 610083, Sichuan Province, China
| | - Zhen Tan
- General Surgery Center, General Hospital of Western Theater Command, No. 270, Rongdu Rd, Jinniu District, Chengdu, 610083, Sichuan Province, China
| | - Zhu Huang
- General Surgery Center, General Hospital of Western Theater Command, No. 270, Rongdu Rd, Jinniu District, Chengdu, 610083, Sichuan Province, China
| | - Lichen Zhou
- General Surgery Center, General Hospital of Western Theater Command, No. 270, Rongdu Rd, Jinniu District, Chengdu, 610083, Sichuan Province, China.,College of Clinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Ruiwu Dai
- General Surgery Center, General Hospital of Western Theater Command, No. 270, Rongdu Rd, Jinniu District, Chengdu, 610083, Sichuan Province, China. .,College of Medicine, Southwest Jiaotong University, Chengdu, 610031, China. .,College of Clinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
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25
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Chan CP, Jin DY. Cytoplasmic RNA sensors and their interplay with RNA-binding partners in innate antiviral response: theme and variations. RNA (NEW YORK, N.Y.) 2022; 28:449-477. [PMID: 35031583 PMCID: PMC8925969 DOI: 10.1261/rna.079016.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sensing of pathogen-associated molecular patterns including viral RNA by innate immunity represents the first line of defense against viral infection. In addition to RIG-I-like receptors and NOD-like receptors, several other RNA sensors are known to mediate innate antiviral response in the cytoplasm. Double-stranded RNA-binding protein PACT interacts with prototypic RNA sensor RIG-I to facilitate its recognition of viral RNA and induction of host interferon response, but variations of this theme are seen when the functions of RNA sensors are modulated by other RNA-binding proteins to impinge on antiviral defense, proinflammatory cytokine production and cell death programs. Their discrete and coordinated actions are crucial to protect the host from infection. In this review, we will focus on cytoplasmic RNA sensors with an emphasis on their interplay with RNA-binding partners. Classical sensors such as RIG-I will be briefly reviewed. More attention will be brought to new insights on how RNA-binding partners of RNA sensors modulate innate RNA sensing and how viruses perturb the functions of RNA-binding partners.
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Affiliation(s)
- Chi-Ping Chan
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences and State Key Laboratory of Liver Research, Faculty of Medicine Building, Pokfulam, Hong Kong
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26
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Esposito S, D’Abrosca G, Antolak A, Pedone PV, Isernia C, Malgieri G. Host and Viral Zinc-Finger Proteins in COVID-19. Int J Mol Sci 2022; 23:ijms23073711. [PMID: 35409070 PMCID: PMC8998646 DOI: 10.3390/ijms23073711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
An unprecedented effort to tackle the ongoing COVID-19 pandemic has characterized the activity of the global scientific community over the last two years. Hundreds of published studies have focused on the comprehension of the immune response to the virus and on the definition of the functional role of SARS-CoV-2 proteins. Proteins containing zinc fingers, both belonging to SARS-CoV-2 or to the host, play critical roles in COVID-19 participating in antiviral defenses and regulation of viral life cycle. Differentially expressed zinc finger proteins and their distinct activities could thus be important in determining the severity of the disease and represent important targets for drug development. Therefore, we here review the mechanisms of action of host and viral zinc finger proteins in COVID-19 as a contribution to the comprehension of the disease and also highlight strategies for therapeutic developments.
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Lodi L, Mastrolia MV, Bello F, Rossi GM, Angelotti ML, Crow YJ, Romagnani P, Vaglio A. Type I interferon-related kidney disorders. Kidney Int 2022; 101:1142-1159. [PMID: 35339535 DOI: 10.1016/j.kint.2022.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/04/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Type I interferon (IFN-I) mediates tissue damage in a wide range of kidney disorders, directly affecting the biology and function of several renal cell types including podocytes, mesangial, endothelial and parietal epithelial cells (PECs).Enhanced IFN-I signalling is observed in the context of viral infections, autoimmunity (e.g., systemic lupus erythematosus, SLE), and the type 1 interferonopathies (T1Is), rare monogenic disorders characterised by constitutive activation of the IFN-I pathway. All of these IFN I-related disorders can cause renal dysfunction, and share pathogenic and histopathological features. Collapsing glomerulopathy, a histopathological lesion characterised by podocyte loss, collapse of the vascular tuft and PEC proliferation, is commonly associated with viral infections, has been described in T1Is such as Aicardi-Goutières syndrome and STING-associated vasculopathy with onset in infancy (SAVI), and can also be induced by recombinant IFN-therapy. In all of these conditions, podocytes and PECs seem to be the primary target of IFN I-mediated damage. Additionally, immune-mediated glomerular injury is common to viral infections, SLE, and T1Is such as COPA syndrome and DNASE1L3 deficiency, diseases in which IFN-I apparently promotes immune-mediated kidney injury. Finally, kidney pathology primarily characterised by vascular lesions (e.g., thrombotic microangiopathy, vasculitis) is a hallmark of the T1I ADA2 deficiency as well as of SLE, viral infections and IFN-therapy.Defining the nosology, pathogenic mechanisms and histopathological patterns of IFN I-related kidney disorders has diagnostic and therapeutic implications, especially considering the likely near-term availability of novel drugs targeting the IFN-I pathway.
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Affiliation(s)
- Lorenzo Lodi
- Department of Health Sciences, University of Firenze; Immunology Unit, Department of Pediatrics, Meyer Children's Hospital, Firenze, Italy
| | - Maria V Mastrolia
- Rheumatology Unit, Department of Pediatrics, Meyer Children's Hospital, Firenze, Italy
| | - Federica Bello
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | | | - Maria L Angelotti
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Firenze, Firenze, Italy
| | - Yanick J Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Université de Paris, Paris, France
| | - Paola Romagnani
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Firenze, Firenze, Italy; Nephrology and Dialysis Unit, Department of Pediatrics, Meyer Children's Hospital, Firenze, Italy
| | - Augusto Vaglio
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Firenze, Firenze, Italy; Nephrology and Dialysis Unit, Department of Pediatrics, Meyer Children's Hospital, Firenze, Italy.
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28
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Griese M. Etiologic Classification of Diffuse Parenchymal (Interstitial) Lung Diseases. J Clin Med 2022; 11:jcm11061747. [PMID: 35330072 PMCID: PMC8950114 DOI: 10.3390/jcm11061747] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 12/15/2022] Open
Abstract
Interstitial lung diseases (ILD) or diffuse parenchymal lung diseases (DPLD) comprise a large number of disorders. Disease definition and classification allow advanced and personalized judgements on clinical disease, risks for genetic or environmental transmissions, and precision medicine treatments. Registers collect specific rare entities and use ontologies for a precise description of complex phenotypes. Here we present a brief history of ILD classification systems from adult and pediatric pneumology. We center on an etiologic classification, with four main categories: lung-only (native parenchymal) disorders, systemic disease-related disorders, exposure-related disorders, and vascular disorders. Splitting diseases into molecularly defined entities is key for precision medicine and the identification of novel entities. Lumping diseases targeted by similar diagnostic or therapeutic principles is key for clinical practice and register work, as our experience with the European children’s ILD register (chILD-EU) demonstrates. The etiologic classification favored combines pediatric and adult lung diseases in a single system and considers genomics and other -omics as central steps towards the solution of “idiopathic” lung diseases. Future tasks focus on a systems’ medicine approach integrating all data and bringing precision medicine closer to the patients.
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Affiliation(s)
- Matthias Griese
- Department of Pediatric Pneumology, Dr. von Haunersches Kinderspital, University of Munich, German Center for Lung Research, Lindwurmstr. 4a, D-80337 Munich, Germany
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29
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Noma K, Mizoguchi Y, Tsumura M, Okada S. Mendelian susceptibility to mycobacterial diseases: state-of-the-art. Clin Microbiol Infect 2022; 28:1429-1434. [DOI: 10.1016/j.cmi.2022.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/19/2022] [Accepted: 03/03/2022] [Indexed: 11/27/2022]
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30
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Osmond M, Hartley T, Johnstone B, Andjic S, Girdea M, Gillespie M, Buske O, Dumitriu S, Koltunova V, Ramani A, Boycott KM, Brudno M. PhenomeCentral: 7 years of rare disease matchmaking. Hum Mutat 2022; 43:674-681. [PMID: 35165961 DOI: 10.1002/humu.24348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 11/08/2022]
Abstract
A major challenge in validating genetic causes for patients with rare diseases (RDs) is the difficulty in identifying other RD patients with overlapping phenotypes and variants in the same candidate gene. This process, known as matchmaking, requires robust data sharing solutions in order to be effective. In 2014 we launched PhenomeCentral, a RD data repository capable of collecting computer-readable genotypic and phenotypic data for the purposes of RD matchmaking. Over the past 7 years PhenomeCentral's features have been expanded and its dataset has consistently grown. There are currently 1,615 users registered on PhenomeCentral, which have contributed over 12,000 patient cases. Most of these cases contain detailed phenotypic terms, with a significant portion also providing genomic sequence data or other forms of clinical information. Matchmaking within PhenomeCentral, and with connections to other data repositories in the Matchmaker Exchange, have collectively resulted in over 60,000 matches, which have facilitated multiple gene discoveries. The collection of deep phenotypic and genotypic data has also positioned PhenomeCentral well to support next generation of matchmaking initiatives that utilize genome sequencing data, ensuring that PhenomeCentral will remain a useful tool in solving undiagnosed RD cases in the years to come. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada
| | - Brittney Johnstone
- Cancer Genetics and High Risk Program, Sunnybrook Health Sciences Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sasha Andjic
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Marta Girdea
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Meredith Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada
| | | | - Sergiu Dumitriu
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Veronika Koltunova
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada
| | - Arun Ramani
- Hospital for Sick Children, Toronto, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, ON, Canada
| | - Michael Brudno
- DATA Team and Techna Institute, University Health Network, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, ON, Canada.,Hospital for Sick Children, Toronto, ON, Canada
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31
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Blasi G, Bortoletto E, Gasparotto M, Filippini F, Bai CM, Rosani U, Venier P. A glimpse on metazoan ZNFX1 helicases, ancient players of antiviral innate immunity. FISH & SHELLFISH IMMUNOLOGY 2022; 121:456-466. [PMID: 35063603 DOI: 10.1016/j.fsi.2022.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
The human zinc finger NFX1-type containing 1 (ZNFX1) is an interferon-stimulated protein associated to the outer mitochondrial membrane, able to bind dsRNAs and interact with MAVS proteins, promoting type I IFN response in the early stage of viral infection. An N-terminal Armadillo (ARM)-type fold and a large helicase core (P-loop) and zinc fingers confer RNA-binding and ATPase activities to ZNFX1. We studied the phylogenetic distribution of metazoan ZNFX1s, ZNFX1 gene expression trends and genomic and protein signatures during viral infection of invertebrates. Based on 221 ZNFX1 sequences, we obtained a polyphyletic tree with a taxonomy-consistent branching at the phylum-level only. In metazoan genomes, ZNFX1 genes were found either in single copy, with up to some tens of exons in vertebrates, or in multiple copies, with one or a few exons and one of them sometimes encompassing most of the coding sequence, in invertebrates like sponges, sea urchins and mollusks. Structural analyses of selected ZNFX1 proteins showed high conservation of the helicase region (P-loop), an overall conserved region and domain architecture, an ARM-fold mostly traceable, and the presence of intrinsically disordered regions of varying length and position. The remarkable over-expression of ZNFX1 in bivalve and gastropod mollusks infected with dsDNA viruses underscores the antiviral role of ZNFX1, whereas nothing similar was found in virus-infected nematodes and corals. Whether the functional diversification reported in the C. elegans ZNFX1 occurs in other metazoan proteins remains to be established.
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Affiliation(s)
- Giulia Blasi
- Department of Biology, University of Padova, 35121, Padova, Italy
| | | | | | | | - Chang-Ming Bai
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Yellow Sea Fisheries Research Institute, CAFS, Qingdao, 266237, China
| | - Umberto Rosani
- Department of Biology, University of Padova, 35121, Padova, Italy.
| | - Paola Venier
- Department of Biology, University of Padova, 35121, Padova, Italy.
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Hsu AP, Holland SM. Host genetics of innate immune system in infection. Curr Opin Immunol 2022; 74:140-149. [DOI: 10.1016/j.coi.2021.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023]
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33
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Guillemin A, Kumar A, Wencker M, Ricci EP. Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins. Front Immunol 2022; 12:796012. [PMID: 35087521 PMCID: PMC8787094 DOI: 10.3389/fimmu.2021.796012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.
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Affiliation(s)
- Anissa Guillemin
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
| | - Anuj Kumar
- CRCL, Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Lyon, France
| | - Mélanie Wencker
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, ENS de Lyon, CNRS, UMR 5308, INSERM, Lyon, France
| | - Emiliano P. Ricci
- LBMC, Laboratoire de Biologie et Modelisation de la Cellule, Université de Lyon, ENS de Lyon, Universite Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1293, Lyon, France
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34
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Outcome of over 1500 matches through the Matchmaker Exchange for rare disease gene discovery: The 2-year experience of Care4Rare Canada. Genet Med 2021; 24:100-108. [PMID: 34906465 DOI: 10.1016/j.gim.2021.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/15/2021] [Accepted: 08/23/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Matchmaking has emerged as a useful strategy for building evidence toward causality of novel disease genes in patients with undiagnosed rare diseases. The Matchmaker Exchange (MME) is a collaborative initiative that facilitates international data sharing for matchmaking purposes; however, data on user experience is limited. METHODS Patients enrolled as part of the Finding of Rare Disease Genes in Canada (FORGE) and Care4Rare Canada research programs had their exome sequencing data reanalyzed by a multidisciplinary research team over a 2-year period. Compelling variants in genes not previously associated with a human phenotype were submitted through the MME node PhenomeCentral, and outcomes were collected. RESULTS In this study, 194 novel candidate genes were submitted to the MME, resulting in 1514 matches, and 15% of the genes submitted resulted in collaborations. Most submissions resulted in at least 1 match, and most matches were with GeneMatcher (82%), where additional email exchange was required to evaluate the match because of the lack of phenotypic or inheritance information. CONCLUSION Matchmaking through the MME is an effective way to investigate novel candidate genes; however, it is a labor-intensive process. Engagement from the community to contribute phenotypic, genotypic, and inheritance data will ensure that matchmaking continues to be a useful approach in the future.
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35
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Alawbathani S, Westenberger A, Ordonez-Herrera N, Al-Hilali M, Al Hebby H, Alabbas F, Alhashem AM, Elyamany G, Megarbane A, Kose M, Alhashmi N, Al Sukaiti N, Al-Raqad M, Al-Tawalbeh S, Abu Adas Blanco O, Alkhattabi F, Sng D, Al-Ali R, Khan S, Tawamie H, Tripolszki K, Karageorgou V, Trunzo R, Al Mutairi F, Reversade B, Bauer P, Bertoli-Avella AM. Biallelic ZNFX1 variants are associated with a spectrum of immuno-hematological abnormalities. Clin Genet 2021; 101:247-254. [PMID: 34708404 DOI: 10.1111/cge.14081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/08/2021] [Accepted: 10/23/2021] [Indexed: 12/27/2022]
Abstract
Biallelic changes in the ZNFX1 gene have been recently reported to cause severe familial immunodeficiency. Through a search of our bio/databank with information from genetic testing of >55 000 individuals, we identified nine additional patients from seven families with six novel homozygous ZNFX1 variants. Consistent with the previously described phenotype, our patients suffered from monocytosis, thrombocytopenia, hepatosplenomegaly, recurrent infections, and lymphadenopathy. The two most severely affected probands also had renal involvement and clinical presentations compatible with hemophagocytic lymphohistiocytosis. The disease was less lethal among our patients than previously reported. We identified two missense changes, two variants predicted to result in complete protein loss through nonsense-mediated decay, and two frameshift changes that likely introduce a truncation. Our findings (i) independently confirm the role of ZNFX1 in primary genetic immunodeficiency, (ii) expand the genetic and clinical spectrum of ZNFX1-related disease, and (iii) illustrate the utility of large, well-curated, and continually updated genotype-phenotype databases in resolving molecular diagnoses of patients with initially negative genetic testing findings.
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Affiliation(s)
- Salem Alawbathani
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Ana Westenberger
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | | | - Mariam Al-Hilali
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Homoud Al Hebby
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Fahad Alabbas
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal M Alhashem
- Division of Pediatric Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ghaleb Elyamany
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - André Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.,Division of Medical Genetics, Institut Jerome Lejeune, Paris, France
| | - Melis Kose
- Department of Pediatrics, Division of Inborn Errors of Metabolism, Izmir Katip Çelebi University Medical Faculty, Izmir, Turkey.,Ege University Medical Faculty, Department of Pediatrics, Division of Genetics, Izmir, Turkey
| | - Nadia Alhashmi
- Clinical and Biochemical Genetics Department, Child Health Department, Royal Hospital, Muscat, Oman
| | - Nashat Al Sukaiti
- Allergy and Clinical Immunology Department, Child Health Department, Royal Hospital, Muscat, Oman
| | | | - Samah Al-Tawalbeh
- Queen Rania Al-Abdulla Children Hospital, King Hussein Medical Center, Amman, Jordan
| | | | - Fadiah Alkhattabi
- College of Medicine at Alfaisal University, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Danielle Sng
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore
| | - Ruslan Al-Ali
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Suliman Khan
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Hasan Tawamie
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | | | | | - Roberta Trunzo
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Fuad Al Mutairi
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Genetics & Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore
| | - Peter Bauer
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
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Seth N, Tuano KS, Chinen J. Inborn errors of immunity: Recent progress. J Allergy Clin Immunol 2021; 148:1442-1450. [PMID: 34688776 DOI: 10.1016/j.jaci.2021.10.010] [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: 10/08/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022]
Abstract
Recent advances in the field of inborn errors of immunity (IEIs) have been wide in scope, including progress in mechanisms of disease, diagnosis, and management. New gene defects affecting the immune response continue to be reported, as many as 26 in the year 2020. It was noted that the presentation of IEIs might not include recurrent infections in 9% of cases, and that current diagnostic methods can identify molecular causes in 92% of patients with severe combined immunodeficiency. Progress in immunopathogenesis explained mechanisms leading to symptoms of autosomal-recessive hyper-IgE syndrome. There was an emphasis on research in primary antibody deficiencies. The benefit of antibiotic prophylaxis to reduce the frequency of infections was demonstrated in these patients. The regimen of rituximab and azathioprine or mycophenolate was proven effective for chronic granulocytic interstitial pneumonia. The efficacy and adverse events of hematopoietic stem cell transplant in different IEI conditions were reported, as well as different strategies to improve outcomes, supporting its use in immunodeficiency and immunodysregulatory syndromes. The recent pandemic of coronavirus disease 2019 affected patients with IEIs, in particular those with deficiency in the interferon-mediated activation of the immune response. Initial data suggest that coronavirus disease 2019 vaccines might elicit anti-coronavirus disease 2019-neutralizing antibody responses in some patients with IEI conditions.
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Affiliation(s)
- Neha Seth
- Division of Immunology, Allergy and Retrovirology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, The Woodlands, Tex
| | - Karen S Tuano
- Division of Immunology, Allergy and Retrovirology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, The Woodlands, Tex
| | - Javier Chinen
- Division of Immunology, Allergy and Retrovirology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, The Woodlands, Tex.
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