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Justiz-Vaillant AA, Gopaul D, Akpaka PE, Soodeen S, Arozarena Fundora R. Severe Combined Immunodeficiency-Classification, Microbiology Association and Treatment. Microorganisms 2023; 11:1589. [PMID: 37375091 DOI: 10.3390/microorganisms11061589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Severe combined immunodeficiency (SCID) is a primary inherited immunodeficiency disease that presents before the age of three months and can be fatal. It is usually due to opportunistic infections caused by bacteria, viruses, fungi, and protozoa resulting in a decrease in number and impairment in the function of T and B cells. Autosomal, X-linked, and sporadic forms exist. Evidence of recurrent opportunistic infections and lymphopenia very early in life should prompt immunological investigation and suspicion of this rare disorder. Adequate stem cell transplantation is the treatment of choice. This review aimed to provide a comprehensive approach to the microorganisms associated with severe combined immunodeficiency (SCID) and its management. We describe SCID as a syndrome and summarize the different microorganisms that affect children and how they can be investigated and treated.
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Affiliation(s)
- Angel A Justiz-Vaillant
- Department of Paraclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Darren Gopaul
- Department of Internal Medicine, Port of Spain General Hospital, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Patrick Eberechi Akpaka
- Department of Paraclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
- Eric Williams Medical Sciences Complex, North Central Regional Health Authority, Champs Fleurs, Trinidad and Tobago
| | - Sachin Soodeen
- Department of Paraclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Rodolfo Arozarena Fundora
- Eric Williams Medical Sciences Complex, North Central Regional Health Authority, Champs Fleurs, Trinidad and Tobago
- Department of Clinical and Surgical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
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2
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Ott N, Faletti L, Heeg M, Andreani V, Grimbacher B. JAKs and STATs from a Clinical Perspective: Loss-of-Function Mutations, Gain-of-Function Mutations, and Their Multidimensional Consequences. J Clin Immunol 2023:10.1007/s10875-023-01483-x. [PMID: 37140667 DOI: 10.1007/s10875-023-01483-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/01/2023] [Indexed: 05/05/2023]
Abstract
The JAK/STAT signaling pathway plays a key role in cytokine signaling and is involved in development, immunity, and tumorigenesis for nearly any cell. At first glance, the JAK/STAT signaling pathway appears to be straightforward. However, on closer examination, the factors influencing the JAK/STAT signaling activity, such as cytokine diversity, receptor profile, overlapping JAK and STAT specificity among non-redundant functions of the JAK/STAT complexes, positive regulators (e.g., cooperating transcription factors), and negative regulators (e.g., SOCS, PIAS, PTP), demonstrate the complexity of the pathway's architecture, which can be quickly disturbed by mutations. The JAK/STAT signaling pathway has been, and still is, subject of basic research and offers an enormous potential for the development of new methods of personalized medicine and thus the translation of basic molecular research into clinical practice beyond the use of JAK inhibitors. Gain-of-function and loss-of-function mutations in the three immunologically particularly relevant signal transducers STAT1, STAT3, and STAT6 as well as JAK1 and JAK3 present themselves through individual phenotypic clinical pictures. The established, traditional paradigm of loss-of-function mutations leading to immunodeficiency and gain-of-function mutation leading to autoimmunity breaks down and a more differentiated picture of disease patterns evolve. This review is intended to provide an overview of these specific syndromes from a clinical perspective and to summarize current findings on pathomechanism, symptoms, immunological features, and therapeutic options of STAT1, STAT3, STAT6, JAK1, and JAK3 loss-of-function and gain-of-function diseases.
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Affiliation(s)
- Nils Ott
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Laura Faletti
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Heeg
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Division of Biological Sciences, Department of Molecular Biology, University of California, La Jolla, San Diego, CA, USA
| | - Virginia Andreani
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
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3
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Butzmann A, Sridhar K, Jangam D, Song H, Singh A, Kumar J, Chisholm KM, Pinsky B, Huang F, Ohgami RS. Mutations in JAK/STAT and NOTCH1 Genes Are Enriched in Post-Transplant Lymphoproliferative Disorders. Front Oncol 2022; 11:790481. [PMID: 35111674 PMCID: PMC8801788 DOI: 10.3389/fonc.2021.790481] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/13/2021] [Indexed: 12/22/2022] Open
Abstract
Post-transplant lymphoproliferative disorders (PTLD) are diseases occurring in immunocompromised patients after hematopoietic stem cell transplantation (HCT) or solid organ transplantation (SOT). Although PTLD occurs rarely, it may be associated with poor outcomes. In most cases, PTLD is driven by Epstein-Barr virus (EBV) infection. Few studies have investigated the mutational landscape and gene expression profile of PTLD. In our study, we performed targeted deep sequencing and RNA-sequencing (RNA-Seq) on 16 cases of florid follicular hyperplasia (FFH) type PTLD and 15 cases of other PTLD types that include: ten monomorphic (M-PTLD), three polymorphic (P-PTLD), and two classic Hodgkin lymphoma type PTLDs (CHL-PTLD). Our study identified recurrent mutations in JAK3 in five of 15 PTLD cases and one of 16 FFH-PTLD cases, as well as 16 other genes that were mutated in M-PTLD, P-PTLD, CHL-PTLD and FFH-PTLD. Digital image analysis demonstrated significant differences in single cell area, major axis, and diameter when comparing cases of M-PTLD and P-PTLD to FFH-PTLD. No morphometric relationship was identified with regards to a specific genetic mutation. Our findings suggest that immune regulatory pathways play an essential role in PTLD, with the JAK/STAT pathway affected in many PTLDs.
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Affiliation(s)
- Alexandra Butzmann
- Agilent Technologies, Santa Clara, CA, United States
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Alexandra Butzmann,
| | - Kaushik Sridhar
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Diwash Jangam
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Hanbing Song
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Amol Singh
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Jyoti Kumar
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Karen M. Chisholm
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, United States
| | - Benjamin Pinsky
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Franklin Huang
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Robert S. Ohgami
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
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4
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El Hawary R, Meshaal S, Mauracher A, Opitz L, Abd Elaziz D, Lotfy S, Eldash A, Boutros J, Galal N, Pachlopnik Schmid J, Elmarsafy A. Whole-exome sequencing of T - B + severe combined immunodeficiency in Egyptian infants, JAK3 predominance and novel variants. Clin Exp Immunol 2021; 203:448-457. [PMID: 33040328 PMCID: PMC7874839 DOI: 10.1111/cei.13536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022] Open
Abstract
Severe combined immunodeficiency (SCID) is fatal if not treated with immune reconstitution. In Egypt, T- B+ SCID accounts for 38·5% of SCID diagnoses. An accurate genetic diagnosis is essential for choosing appropriate treatment modalities and for offering genetic counseling to the patient's family. The objectives of this study were to describe the clinical, immunological and molecular characteristics of a cohort of twenty Egyptian patients with T- B+ SCID. The initial diagnosis (based on clinical features and flow cytometry) was followed by molecular investigation (whole-exome sequencing). All patients had the classic clinical picture for SCID, including failure to thrive (n = 20), oral candidiasis (n = 17), persistent diarrhea (n = 14), pneumonia (n = 13), napkin dermatitis (n = 10), skin rash (n = 7), otitis media (n = 3) and meningitis (n = 2). The onset of manifestations was at the age of 2·4 ± 1·6 months and diagnosis at the age of 6·7 ± ·5 months, giving a diagnostic delay of 4·3 months. JAK3 gene variants were most frequent (n = 12) with three novel variants identified, followed by IL2Rγ variants (n = 6) with two novel variants. IL7Rα and CD3ε variants were found once, with a novel variant each. T- B+ NK- SCID accounted for approximately 90% of the Egyptian patients with T- B+ SCID. Of these T- B+ NK- SCID cases, 60% were autosomal recessive syndromes caused by JAK3 mutations and 30% were X-linked syndromes. It might be useful to sequence the JAK3 gene (i.e. targeted Sanger sequencing) in all T- B+ SCID patients, especially after X-linked SCID has been ruled out. Hence, no more than 10% of T- B+ SCID patients might require next-generation for a molecular diagnosis.
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Affiliation(s)
- R. El Hawary
- Faculty of MedicineClinical Pathology DepartmentCairo UniversityCairoEgypt
| | - S. Meshaal
- Faculty of MedicineClinical Pathology DepartmentCairo UniversityCairoEgypt
| | - A.A. Mauracher
- Division of ImmunologyUniversity Children’s Hospital ZurichZurichSwitzerland
| | - L. Opitz
- ETH ZurichFunctional Genomics Center ZürichUniversity of ZurichZurichSwitzerland
| | - D. Abd Elaziz
- Faculty of MedicinePediatrics DepartmentCairo UniversityCairoEgypt
| | - S. Lotfy
- Faculty of MedicinePediatrics DepartmentCairo UniversityCairoEgypt
| | - A. Eldash
- Faculty of MedicineClinical Pathology DepartmentCairo UniversityCairoEgypt
| | - J. Boutros
- Faculty of MedicinePediatrics DepartmentCairo UniversityCairoEgypt
| | - N. Galal
- Faculty of MedicinePediatrics DepartmentCairo UniversityCairoEgypt
| | | | - A. Elmarsafy
- Faculty of MedicinePediatrics DepartmentCairo UniversityCairoEgypt
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5
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Favoino E, Prete M, Catacchio G, Ruscitti P, Navarini L, Giacomelli R, Perosa F. Working and safety profiles of JAK/STAT signaling inhibitors. Are these small molecules also smart? Autoimmun Rev 2021; 20:102750. [PMID: 33482338 DOI: 10.1016/j.autrev.2021.102750] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Abstract
The Janus kinase (JAK)/signal transducers and activators of transcription (STAT) pathway is an important intracellular route through which many different extracellular soluble molecules, by reaching membrane receptors, can signal the nucleus. The spectrum of soluble molecules that use the JAK/STAT pathway through their corresponding receptors is quite large (almost 50 different molecules), and includes some cytokines involved in the pathogenesis of many immune-mediated diseases. Such diseases, when left untreated, present an evident hyperactivation of JAK/STAT signaling. Therefore, given the pathogenetic role of JAK/STAT, drugs known as JAK inhibitors (JAKi), that target one or more JAKs, have been developed to counteract JAK/STAT signal hyperactivation. As some hematological malignancies present an intrinsic JAK/STAT hyperactivation due to a JAK mutation, some JAKi have also been successfully used in this context. Regulatory agencies for drug administration in different countries have already approved a few JAKi in the setting of either immune-mediated diseases or hematological malignancies. Aim of this review is to describe the physiology of intracellular JAK/STAT pathway signaling and the pathological conditions associated to its dysregulation. Then, the rationale for targeting JAK in rheumatic autoimmune diseases is discussed, along with clinical data from registration studies showing the efficacy of these drugs. Finally, the excellent safety profile of JAKi is discussed in the context of the apparent poor specificity of JAK/STAT pathway signal.
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Affiliation(s)
- Elvira Favoino
- Rheumatic and Systemic Autoimmune Diseases Unit, Department of Biomedical Science and Human Oncology (DIMO), University of Bari Medical School, Italy
| | - Marcella Prete
- Internal Medicine, Department of Biomedical Science and Human Oncology (DIMO), University of Bari Medical School, Italy
| | - Giacomo Catacchio
- Rheumatic and Systemic Autoimmune Diseases Unit, Department of Biomedical Science and Human Oncology (DIMO), University of Bari Medical School, Italy
| | - Piero Ruscitti
- Rheumatology Unit, Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Luca Navarini
- Rheumatology and Immunology Unit, Department of Medicine, University of Rome 'Campus Biomedico', Italy
| | - Roberto Giacomelli
- Rheumatology and Immunology Unit, Department of Medicine, University of Rome 'Campus Biomedico', Italy
| | - Federico Perosa
- Rheumatic and Systemic Autoimmune Diseases Unit, Department of Biomedical Science and Human Oncology (DIMO), University of Bari Medical School, Italy.
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6
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Mehawej C, Khayat CD, Hamdan N, Chouery E, Platt CD. A family history of SCID and unrevealing WES: An approach to management and guidance of patients. Clin Immunol 2020; 218:108520. [PMID: 32629161 DOI: 10.1016/j.clim.2020.108520] [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: 04/20/2020] [Revised: 06/12/2020] [Accepted: 06/27/2020] [Indexed: 10/23/2022]
Abstract
Severe Combined Immunodeficiency (SCID) is a genetically heterogeneous group of disorders characterized by severe T cell lymphopenia and defective T and B cell function. Without prompt diagnosis and early intervention, patients with SCID typically die from infection within the first year of life. Advances in molecular genetics have led to rapid and efficient diagnosis of SCID cases, particularly when paired with newborn screening. However, some cases remain unsolved, and this is of particular relevance to families that plan to have more children. Here we report a patient who died from complications of SCID in whom whole exome sequencing failed to reveal a candidate variant. We describe how Sanger sequencing of parents was used to study the genomic regions that were poorly covered by WES, and how immune phenotyping results were used in the setting of genetic counseling.
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Affiliation(s)
- Cybel Mehawej
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon.
| | | | - Nadine Hamdan
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Eliane Chouery
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Craig D Platt
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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7
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Adashek JJ, Kato S, Lippman SM, Kurzrock R. The paradox of cancer genes in non-malignant conditions: implications for precision medicine. Genome Med 2020; 12:16. [PMID: 32066498 PMCID: PMC7027240 DOI: 10.1186/s13073-020-0714-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/30/2020] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing has enabled patient selection for targeted drugs, some of which have shown remarkable efficacy in cancers that have the cognate molecular signatures. Intriguingly, rapidly emerging data indicate that altered genes representing oncogenic drivers can also be found in sporadic non-malignant conditions, some of which have negligible and/or low potential for transformation to cancer. For instance, activating KRAS mutations are discerned in endometriosis and in brain arteriovenous malformations, inactivating TP53 tumor suppressor mutations in rheumatoid arthritis synovium, and AKT, MAPK, and AMPK pathway gene alterations in the brains of Alzheimer's disease patients. Furthermore, these types of alterations may also characterize hereditary conditions that result in diverse disabilities and that are associated with a range of lifetime susceptibility to the development of cancer, varying from near universal to no elevated risk. Very recently, the repurposing of targeted cancer drugs for non-malignant conditions that are associated with these genomic alterations has yielded therapeutic successes. For instance, the phenotypic manifestations of CLOVES syndrome, which is characterized by tissue overgrowth and complex vascular anomalies that result from the activation of PIK3CA mutations, can be ameliorated by the PIK3CA inhibitor alpelisib, which was developed and approved for breast cancer. In this review, we discuss the profound implications of finding molecular alterations in non-malignant conditions that are indistinguishable from those driving cancers, with respect to our understanding of the genomic basis of medicine, the potential confounding effects in early cancer detection that relies on sensitive blood tests for oncogenic mutations, and the possibility of reverse repurposing drugs that are used in oncology in order to ameliorate non-malignant illnesses and/or to prevent the emergence of cancer.
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Affiliation(s)
- Jacob J Adashek
- Department of Internal Medicine, University of South Florida, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Scott M Lippman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA.
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8
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Moens L, Hershfield M, Arts K, Aksentijevich I, Meyts I. Human adenosine deaminase 2 deficiency: A multi-faceted inborn error of immunity. Immunol Rev 2019; 287:62-72. [PMID: 30565235 DOI: 10.1111/imr.12722] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/23/2018] [Indexed: 12/15/2022]
Abstract
Human adenosine deaminase 1 deficiency was described in the 1970s to cause severe combined immunodeficiency. The residual adenosine deaminase activity in these patients was attributed to adenosine deaminase 2. Human adenosine deaminase type 2 deficiency (DADA2), due to biallelic deleterious mutations in the ADA2 gene, is the first described monogenic type of small- and medium-size vessel vasculitis. The phenotype of DADA2 also includes lymphoproliferation, cytopenia, and variable degrees of immunodeficiency. The physiological role of ADA2 is still enigmatic hence the pathophysiology of the condition is unclear. Preliminary data showed that in the absence of ADA2, macrophage differentiation is skewed to a pro-inflammatory M1 subset, which is detrimental for endothelial integrity. The inflammatory phenotype responds well to anti-TNF therapy with etanercept and that is the first-line treatment for prevention of severe vascular events including strokes. The classic immunosuppressive drugs are not successful in controlling the disease activity. However, hematopoietic stem cell transplantation (HSCT) has been shown to be a definitive cure in DADA2 patients who present with a severe cytopenia. HSCT can also cure the vascular phenotype and is the treatment modality for patients' refractory to anti-cytokine therapies. In this review, we describe what is currently known about the molecular mechanisms of DADA2. Further research on the pathophysiology of this multifaceted condition is needed to fine-tune and steer future therapeutic strategies.
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Affiliation(s)
- Leen Moens
- Department of Microbiology and Immunology, Laboratory for Childhood Immunology, KU Leuven, Leuven, Belgium
| | - Michael Hershfield
- Department of Medicine, School of Medicine, Duke University, Durham, North Carolina
| | - Katrijn Arts
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland
| | - Isabelle Meyts
- Department of Microbiology and Immunology, Laboratory for Childhood Immunology, KU Leuven, Leuven, Belgium.,Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
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9
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Cirillo E, Cancrini C, Azzari C, Martino S, Martire B, Pession A, Tommasini A, Naviglio S, Finocchi A, Consolini R, Pierani P, D'Alba I, Putti MC, Marzollo A, Giardino G, Prencipe R, Esposito F, Grasso F, Scarselli A, Di Matteo G, Attardi E, Ricci S, Montin D, Specchia F, Barzaghi F, Cicalese MP, Quaremba G, Lougaris V, Giliani S, Locatelli F, Rossi P, Aiuti A, Badolato R, Plebani A, Pignata C. Clinical, Immunological, and Molecular Features of Typical and Atypical Severe Combined Immunodeficiency: Report of the Italian Primary Immunodeficiency Network. Front Immunol 2019; 10:1908. [PMID: 31456805 PMCID: PMC6700292 DOI: 10.3389/fimmu.2019.01908] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/29/2019] [Indexed: 12/22/2022] Open
Abstract
Severe combined immunodeficiencies (SCIDs) are a group of inborn errors of the immune system, usually associated with severe or life-threatening infections. Due to the variability of clinical phenotypes, the diagnostic complexity and the heterogeneity of the genetic basis, they are often difficult to recognize, leading to a significant diagnostic delay (DD). Aim of this study is to define presenting signs and natural history of SCID in a large cohort of patients, prior to hematopoietic stem cell or gene therapies. To this purpose, we conducted a 30-year retro-prospective multicenter study within the Italian Primary Immunodeficiency Network. One hundred eleven patients, diagnosed as typical or atypical SCID according to the European Society for Immune Deficiencies criteria, were included. Patients were subsequently classified based on the genetic alteration, pathogenic mechanism and immunological classification. A positive relationship between the age at onset and the DD was found. SCID patients with later onset were identified only in the last decade of observation. Syndromic SCIDs represented 28% of the cohort. Eight percent of the subjects were diagnosed in Intensive Care Units. Fifty-three percent had an atypical phenotype and most of them exhibited a discordant genotype-immunophenotype. Pre-treatment mortality was higher in atypical and syndromic patients. Our study broadens the knowledge of clinical and laboratory manifestations and genotype/phenotype correlation in patients with SCID and may facilitate the diagnosis of both typical and atypical forms of the disease in countries where newborn screening programs have not yet been implemented.
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Affiliation(s)
- Emilia Cirillo
- Pediatric Section, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Caterina Cancrini
- Department of System of Medicine University of Rome Tor Vergata, Rome, Italy.,Unit of Immune and Infectious Disease, University Department of Pediatrics DPUO, Children's Hospital Bambino Gesù, Rome, Italy
| | - Chiara Azzari
- Pediatric Immunology Unit, Anna Meyer Hospital, University of Florence, Florence, Italy
| | - Silvana Martino
- Department of Public Health and Pediatrics, Regina Margherita Children Hospital, University of Turin, Turin, Italy
| | - Baldassarre Martire
- Paediatric Hematology Oncology Unit, Policlinico-Giovanni XXII Hospital, University of Bari, Bari, Italy
| | - Andrea Pession
- Department of Pediatrics, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Alberto Tommasini
- Pediatric Hematology Oncology, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Samuele Naviglio
- Pediatric Hematology Oncology, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Andrea Finocchi
- Department of System of Medicine University of Rome Tor Vergata, Rome, Italy.,Unit of Immune and Infectious Disease, University Department of Pediatrics DPUO, Children's Hospital Bambino Gesù, Rome, Italy
| | - Rita Consolini
- Section of Pediatrics Immunology and Rheumatology, Department of Pediatrics, University of Pisa, Pisa, Italy
| | - Paolo Pierani
- Division of Pediatric Hematology and Oncology, Ospedale G. Salesi, Ancona, Italy
| | - Irene D'Alba
- Division of Pediatric Hematology and Oncology, Ospedale G. Salesi, Ancona, Italy
| | - Maria Caterina Putti
- Department of Child's and Woman's Health, Pediatric Oncology and Hematology, University of Padova, Padova, Italy
| | - Antonio Marzollo
- Department of Child's and Woman's Health, Pediatric Oncology and Hematology, University of Padova, Padova, Italy
| | - Giuliana Giardino
- Pediatric Section, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Rosaria Prencipe
- Pediatric Section, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Federica Esposito
- Pediatric Section, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Fiorentino Grasso
- Pediatric Section, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Alessia Scarselli
- Department of System of Medicine University of Rome Tor Vergata, Rome, Italy.,Unit of Immune and Infectious Disease, University Department of Pediatrics DPUO, Children's Hospital Bambino Gesù, Rome, Italy
| | - Gigliola Di Matteo
- Department of System of Medicine University of Rome Tor Vergata, Rome, Italy.,Unit of Immune and Infectious Disease, University Department of Pediatrics DPUO, Children's Hospital Bambino Gesù, Rome, Italy
| | - Enrico Attardi
- Department of System of Medicine University of Rome Tor Vergata, Rome, Italy
| | - Silvia Ricci
- Pediatric Immunology Unit, Anna Meyer Hospital, University of Florence, Florence, Italy
| | - Davide Montin
- Department of Public Health and Pediatrics, Regina Margherita Children Hospital, University of Turin, Turin, Italy
| | - Fernando Specchia
- Department of Pediatrics, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Federica Barzaghi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Pia Cicalese
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Quaremba
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Vassilios Lougaris
- Department of Clinical and Experimental Sciences, Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, University of Brescia, Brescia, Italy
| | - Silvia Giliani
- A. Nocivelli Institute for Molecular Medicine, Department of Molecular and Translational Medicine, University of Brescia, and ASST Spedali Civili, Brescia, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Paolo Rossi
- Department of System of Medicine University of Rome Tor Vergata, Rome, Italy.,Unit of Immune and Infectious Disease, University Department of Pediatrics DPUO, Children's Hospital Bambino Gesù, Rome, Italy
| | - Alessandro Aiuti
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaele Badolato
- Department of Clinical and Experimental Sciences, Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, University of Brescia, Brescia, Italy
| | - Alessandro Plebani
- Department of Clinical and Experimental Sciences, Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, University of Brescia, Brescia, Italy
| | - Claudio Pignata
- Pediatric Section, Department of Translational Medical Sciences, Federico II University, Naples, Italy
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10
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Cifaldi C, Brigida I, Barzaghi F, Zoccolillo M, Ferradini V, Petricone D, Cicalese MP, Lazarevic D, Cittaro D, Omrani M, Attardi E, Conti F, Scarselli A, Chiriaco M, Di Cesare S, Licciardi F, Davide M, Ferrua F, Canessa C, Pignata C, Giliani S, Ferrari S, Fousteri G, Barera G, Merli P, Palma P, Cesaro S, Gattorno M, Trizzino A, Moschese V, Chini L, Villa A, Azzari C, Finocchi A, Locatelli F, Rossi P, Sangiuolo F, Aiuti A, Cancrini C, Di Matteo G. Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies. Front Immunol 2019; 10:316. [PMID: 31031743 PMCID: PMC6470723 DOI: 10.3389/fimmu.2019.00316] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Primary Immunodeficiencies (PIDs) are a heterogeneous group of genetic immune disorders. While some PIDs can manifest with more than one phenotype, signs, and symptoms of various PIDs overlap considerably. Recently, novel defects in immune-related genes and additional variants in previously reported genes responsible for PIDs have been successfully identified by Next Generation Sequencing (NGS), allowing the recognition of a broad spectrum of disorders. Objective: To evaluate the strength and weakness of targeted NGS sequencing using custom-made Ion Torrent and Haloplex (Agilent) panels for diagnostics and research purposes. Methods: Five different panels including known and candidate genes were used to screen 105 patients with distinct PID features divided in three main PID categories: T cell defects, Humoral defects and Other PIDs. The Ion Torrent sequencing platform was used in 73 patients. Among these, 18 selected patients without a molecular diagnosis and 32 additional patients were analyzed by Haloplex enrichment technology. Results: The complementary use of the two custom-made targeted sequencing approaches allowed the identification of causative variants in 28.6% (n = 30) of patients. Twenty-two out of 73 (34.6%) patients were diagnosed by Ion Torrent. In this group 20 were included in the SCID/CID category. Eight out of 50 (16%) patients were diagnosed by Haloplex workflow. Ion Torrent method was highly successful for those cases with well-defined phenotypes for immunological and clinical presentation. The Haloplex approach was able to diagnose 4 SCID/CID patients and 4 additional patients with complex and extended phenotypes, embracing all three PID categories in which this approach was more efficient. Both technologies showed good gene coverage. Conclusions: NGS technology represents a powerful approach in the complex field of rare disorders but its different application should be weighted. A relatively small NGS target panel can be successfully applied for a robust diagnostic suspicion, while when the spectrum of clinical phenotypes overlaps more than one PID an in-depth NGS analysis is required, including also whole exome/genome sequencing to identify the causative gene.
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Affiliation(s)
- Cristina Cifaldi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Immacolata Brigida
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Matteo Zoccolillo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Valentina Ferradini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Davide Petricone
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Dejan Lazarevic
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cittaro
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Maryam Omrani
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Attardi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesca Conti
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Alessia Scarselli
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Maria Chiriaco
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Silvia Di Cesare
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesco Licciardi
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Montin Davide
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Clementina Canessa
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Silvia Giliani
- Department of Molecular and Translational Medicine, A. Nocivelli Institute for Molecular Medicine, University of Brescia, Brescia, Italy
| | - Simona Ferrari
- Unit of Medical Genetics, St. Orsola-Malpighi University Hospital, University of Bologna, Bologna, Italy
| | - Georgia Fousteri
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Graziano Barera
- Pediatric Department, San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Merli
- Department of Onco-Hematology and Cell and Gene Therapy, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Paolo Palma
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Simone Cesaro
- Paediatric Hematology-Oncology, “Ospedale della Donna e del Bambino”, Verona, Italy
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Giannina Gaslini, Genoa, Italy
| | - Antonio Trizzino
- Department of Pediatric Hematology and Oncology, “ARNAS Civico Di Cristina Benfratelli” Hospital, Palermo, Italy
| | - Viviana Moschese
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Loredana Chini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Anna Villa
- Milan Unit, National Research Council (CNR) Institute for Genetic and Biomedical Research (IRGB), Milan, Italy
- Humanitas Clinical and Research Institute, Rozzano, Italy
| | - Chiara Azzari
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Andrea Finocchi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, University of Rome La Sapienza, Rome, Italy
| | - Paolo Rossi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Gigliola Di Matteo
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
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11
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Di Matteo G, Chiriaco M, Scarselli A, Cifaldi C, Livadiotti S, Di Cesare S, Ferradini V, Aiuti A, Rossi P, Finocchi A, Cancrini C. JAK3 mutations in Italian patients affected by SCID: New molecular aspects of a long-known gene. Mol Genet Genomic Med 2018; 6:713-721. [PMID: 30032486 PMCID: PMC6160700 DOI: 10.1002/mgg3.391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/20/2018] [Accepted: 02/27/2018] [Indexed: 01/01/2023] Open
Abstract
Background Mutations in the Janus Kinase 3 (JAK3) gene cause an autosomal recessive form of severe combined immunodeficiency (SCID) usually characterized by the absence of both T and NK cells, but preserved numbers of B lymphocytes (T‐B+NK‐SCID). The detection of larger (>100 bp) genomic duplications or deletions can be more difficult to be detected by PCR‐based methods or standard NGS protocols, and a broad range of mutation detection techniques are necessary. Methods We report four unrelated Italian patients (two females and two males) with SCID phenotype. Protein expression, functional studies, molecular analysis by standard methods and NGS, and transcripts studies were performed to obtain a definitive diagnosis. Results Here, we describe four JAK3‐deficient patients from four unrelated families. The first patient is homozygous for the known c.1951 C>T mutation causing the amino acidic change p.R651W. The other two patients, originating from the same small Italian town, resulted compound heterozygotes for the same g.15410_16542del deletion and two different novel mutations, g.13319_13321delTTC and c.933T>G (p.F292V), respectively. The fourth patient was compound heterozygous for the novel mutations p.V599G and p.W709R. Defective STAT5 phosphorylation after IL2 or IL15 stimulation corroborated the mutation pathogenicity. Concerning g.15410_16542del mutation, probably due to an unequal homologous recombination between Alu elements of JAK3 gene, microsatellites analysis revealed that both unrelated Pt2 and Pt3 and their carrier family members shared the same haplotype. These data support the hypothesis of a founder effect for the g.15410_16542del mutation that might have inherited in both unrelated families from the same ancient progenitor. Conclusion Different molecular techniques are still required to obtain a definitive diagnosis of AR‐SCID particularly in all cases in which a monoallelic mutation is found by standard mutation scanning methods.
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Affiliation(s)
- Gigliola Di Matteo
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Maria Chiriaco
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Alessia Scarselli
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Cristina Cifaldi
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | | | - Silvia Di Cesare
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Valentina Ferradini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Pediatric Immunohematology Unit, San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Paolo Rossi
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Andrea Finocchi
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Caterina Cancrini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.,Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
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