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Orellana H, Yan J, Paul A, Tokita M, Ding Y, Ghosh R, Lewis KL, Davis J, Jamal L, Jodarski C, Similuk M, Saucier N, Zhu Z, Wang Y, Wu S, Ruggieri J, Su HC, Uzel G, Nahas S, Cooper M, Walkiewicz MA. Case report: Deep sequencing and long-read genome sequencing refine prior genetic analyses in families with apparent gonadal mosaicism in PIK3CD-related activated PI3K delta syndrome. Front Immunol 2024; 15:1451212. [PMID: 39253077 PMCID: PMC11381395 DOI: 10.3389/fimmu.2024.1451212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 07/29/2024] [Indexed: 09/11/2024] Open
Abstract
Gonadal and gonosomal mosaicism describe phenomena in which a seemingly healthy individual carries a genetic variant in a subset of their gonadal tissue or gonadal and somatic tissue(s), respectively, with risk of transmitting the variant to their offspring. In families with one or more affected offspring, occurrence of the same apparently de novo variants can be an indicator of mosaicism in either parent. Panel-based deep sequencing has the capacity to detect low-level mosaic variants with coverage exceeding the typical limit of detection provided by current, readily available sequencing techniques. In this study, we report three families with more than one affected offspring with either confirmed or apparent parental gonosomal or gonadal mosaicism for PIK3CD pathogenic variants. Data from targeted deep sequencing was suggestive of low-level maternal gonosomal mosaicism in Family 1. Through this approach we did not detect pathogenic variants in PIK3CD from parental samples in Family 2 and Family 3. We conclude that mosaicism was likely confined to the maternal gonads in Family 2. Subsequent long-read genome sequencing in Family 3 showed that the paternal chromosome harbored the pathogenic variant in PIK3CD in both affected children, consistent with paternal gonadal mosaicism. Detection of parental mosaic variants enables accurate risk assessment, informs reproductive decision-making, and provides helpful context to inform clinical management in families with PIK3CD pathogenic variants.
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Affiliation(s)
- Halyn Orellana
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jia Yan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alex Paul
- Department of Pediatrics, Division of Rheumatology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Mari Tokita
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yan Ding
- Infinity-Biologix LLC (D/B/A SAMPLED), Piscataway, NJ, United States
| | - Rajarshi Ghosh
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Katie L Lewis
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Joie Davis
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Leila Jamal
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Colleen Jodarski
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Morgan Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Nermina Saucier
- Department of Pediatrics, Division of Rheumatology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Zhanyang Zhu
- Infinity-Biologix LLC (D/B/A SAMPLED), Piscataway, NJ, United States
| | - Yihe Wang
- Infinity-Biologix LLC (D/B/A SAMPLED), Piscataway, NJ, United States
| | - Sitao Wu
- Infinity-Biologix LLC (D/B/A SAMPLED), Piscataway, NJ, United States
| | - Jason Ruggieri
- Infinity-Biologix LLC (D/B/A SAMPLED), Piscataway, NJ, United States
| | - Helen C Su
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Gulbu Uzel
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Shareef Nahas
- Infinity-Biologix LLC (D/B/A SAMPLED), Piscataway, NJ, United States
| | - Megan Cooper
- Department of Pediatrics, Division of Rheumatology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Magdalena A Walkiewicz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Aluri J, Cooper MA. Somatic mosaicism in inborn errors of immunity: Current knowledge, challenges, and future perspectives. Semin Immunol 2023; 67:101761. [PMID: 37062181 PMCID: PMC11321052 DOI: 10.1016/j.smim.2023.101761] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
Inborn errors of immunity (IEI) are a diverse group of monogenic disorders of the immune system due to germline variants in genes important for the immune response. Over the past decade there has been increasing recognition that acquired somatic variants present in a subset of cells can also lead to immune disorders or 'phenocopies' of IEI. Discovery of somatic mosaicism causing IEI has largely arisen from investigation of seemingly sporadic cases of IEI with predominant symptoms of autoinflammation and/or autoimmunity in which germline disease-causing variants are not detected. Disease-causing somatic mosaicism has been identified in genes that also cause germline IEI, such as FAS, and in genes without significant corresponding germline disease, such as UBA1 and TLR8. There are challenges in detecting low-level somatic variants, and it is likely that the extent of the somatic mosaicism causing IEI is largely uncharted. Here we review the field of somatic mosaicism leading to IEI and discuss challenges and methods for somatic variant detection, including diagnostic approaches for molecular diagnoses of patients.
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Affiliation(s)
- Jahnavi Aluri
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA.
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3
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Aluri J, Cooper MA. Genetic Mosaicism as a Cause of Inborn Errors of Immunity. J Clin Immunol 2021; 41:718-728. [PMID: 33864184 PMCID: PMC8068627 DOI: 10.1007/s10875-021-01037-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Inborn errors of immunity (IEIs) are a heterogeneous group of disorders due to genetic defects in the immune response that have a broad clinical spectrum. Diagnosis of the precise genetic cause of IEI has led to improved care and treatment of patients; however, genetic diagnosis using standard approaches is only successful in ~40% of patients and is particularly challenging in “sporadic” cases without a family history. Standard genetic testing for IEI evaluates for germline changes in genes encoding proteins important for the immune response. It is now clear that IEI can also arise from de novo mutations leading to genetic variants present in germ cells and/or somatic cells. In particular, somatic mosaicism, i.e., post-zygotic genetic changes in DNA sequence, is emerging as a significant contributor to IEI. Testing for somatic mosaicism can be challenging, and both older sequencing techniques such as Sanger sequencing and newer next-generation sequencing may not be sensitive enough to detect variants depending on the platform and analysis tools used. Investigation of multiple tissue samples and specifically targeting sequence technologies to detect low frequency variants is important for detection of variants. This review examines the role and functional consequences of genetic mosaicism in IEI. We emphasize the need to refine the current exome and genome analysis pipeline to efficiently identify mosaic variants and recommend considering somatic mosaicism in disease discovery and in the first-tier of genetic analysis.
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Affiliation(s)
- Jahnavi Aluri
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, 660 S. Euclid Ave. Box 8208, St. Louis, MO, 63110, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology/Immunology, Washington University in St. Louis, 660 S. Euclid Ave. Box 8208, St. Louis, MO, 63110, USA.
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4
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Thouenon R, Moreno-Corona N, Poggi L, Durandy A, Kracker S. Activated PI3Kinase Delta Syndrome-A Multifaceted Disease. Front Pediatr 2021; 9:652405. [PMID: 34249806 PMCID: PMC8267809 DOI: 10.3389/fped.2021.652405] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
Autosomal dominant gain-of-function mutations in the PIK3CD gene encoding the catalytic subunit p110δ of phosphoinositide 3-kinase-δ (PI3K-δ) or autosomal dominant loss-of-function mutations in the PIK3R1 gene encoding the p85α, p55α and p50α regulatory subunits cause Activated PI3-kinase-δ syndrome (APDS; referred as type 1 APDS and type 2 APDS, respectively). Consequences of these mutations are PI3K-δ hyperactivity. Clinical presentation described for both types of APDS patients is very variable, ranging from mild or asymptomatic features to profound combined immunodeficiency. Massive lymphoproliferation, bronchiectasis, increased susceptibility to bacterial and viral infections and, at a lesser extent, auto-immune manifestations and occurrence of cancer, especially B cell lymphoma, have been described for both types of APDS patients. Here, we review clinical presentation and treatment options as well as fundamental immunological and biological features associated to PI3K-δ increased signaling.
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Affiliation(s)
- Romane Thouenon
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Nidia Moreno-Corona
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Lucie Poggi
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Anne Durandy
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Sven Kracker
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
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Singh A, Joshi V, Jindal AK, Mathew B, Rawat A. An updated review on activated PI3 kinase delta syndrome (APDS). Genes Dis 2019; 7:67-74. [PMID: 32181277 PMCID: PMC7063426 DOI: 10.1016/j.gendis.2019.09.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/21/2019] [Accepted: 09/30/2019] [Indexed: 01/09/2023] Open
Abstract
Activated Phosphoinositide 3-kinase δ syndrome (APDS) is a newly recognised primary immunodeficiency disease. It has currently been a hot topic of clinical research and new data are emerging regarding its pathogenesis, clinical manifestations and treatment. Patients with APDS syndrome have significant autoimmune manifestations and lymphoproliferation. It is important to differentiate APDS from the usual polygenic CVID in view of the availability of targeted therapy like mTOR inhibitors such as Rapamycin and selective PI3Kδ inhibitors. We provide a comprehensive review on this interesting disorder focusing light on its etiology, genetic research and emerging therapy.
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Affiliation(s)
| | | | | | | | - Amit Rawat
- Corresponding author. Paediatric Allergy Immunology Unit, Department of Paediatrics, Advanced Paediatric Centre, Postgraduate Institute of Medical Education & Research, Sector 12, Chandigarh, 160012, India.
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Sharapova SO, Haapaniemi E, Sakovich IS, Rojas J, Gámez-Díaz L, Mareika YE, Guryanova IE, Migas AA, Mikhaleuskaya TM, Grimbacher B, Aleinikova OV. Novel LRBA Mutation and Possible Germinal Mosaicism in a Slavic Family. J Clin Immunol 2018; 38:471-474. [PMID: 29804237 DOI: 10.1007/s10875-018-0515-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/17/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Svetlana O Sharapova
- Research Department, Immunology Laboratory, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, 223053, Borovliani, Minsk Region, Belarus.
| | - Emma Haapaniemi
- Department of Hematology and Regenerative Medicine, Karolinska Institutet, Huddinge, Sweden
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Inga S Sakovich
- Research Department, Immunology Laboratory, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, 223053, Borovliani, Minsk Region, Belarus
| | - Jessica Rojas
- Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Laura Gámez-Díaz
- Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Yuliya E Mareika
- Research Department, Immunology Laboratory, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, 223053, Borovliani, Minsk Region, Belarus
| | - Irina E Guryanova
- Research Department, Immunology Laboratory, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, 223053, Borovliani, Minsk Region, Belarus
| | - Alexandr A Migas
- Research Department, Immunology Laboratory, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, 223053, Borovliani, Minsk Region, Belarus
| | - Taisiya M Mikhaleuskaya
- Research Department, Immunology Laboratory, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, 223053, Borovliani, Minsk Region, Belarus
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Olga V Aleinikova
- Research Department, Immunology Laboratory, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, 223053, Borovliani, Minsk Region, Belarus
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