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Saheb Sharif-Askari N, Hafezi S, Saheb Sharif-Askari F, Ali Hussain Alsayed H, B. M. Ahmed S, Alsafar HS, Halwani R. Multiple inborn errors of type I IFN immunity in a 33-year-old male with a fatal case of COVID-19. Heliyon 2024; 10:e29338. [PMID: 38665565 PMCID: PMC11043952 DOI: 10.1016/j.heliyon.2024.e29338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The host genetic inborn errors of immunity (IEIs) have been shown to contribute to susceptibility to life-threatening coronavirus disease 2019 (COVID-19), as it had been associated previously with other viral infections. Most genetic association studies have described IEIs as a monogenic defect, while there have been no reports of patients with multiple inherited immune deficiencies. This is a complex case of IEIs predisposing to severe viral infections in an unvaccinated 33-year-old male patient. The patient was admitted with no respiratory symptoms, showed a SARS-CoV-2 PCR positive test on the second day of admission, started developing progressive lung consolidation within three days of hospitalization, and was moved from non-invasive to mechanical ventilation within 12 days of hospitalization. Impaired production of type I IFN was detected in patient PBMCs treated with poly(I:C), at both mRNA and protein levels. Whole exome sequencing revealed three mutations across type I IFN production pathway, which were predicted to be loss-of-function (pLOF). The three mutations were predicted to predispose to severe viral infections: monoallelic R488X TLR3, monoallelic His684Arg TLR3, and biallelic Val363Met IRF3. Functional analysis confirmed that all these mutations dysregulated the type I IFN pathway. Evaluation of TLR3 and IRF3 IFN-β1 luciferase reporter activity showed a hypomorphic suppression of function. TOPO TA cloning was used to ascertain the positioning of both TLR3 variants, indicating that both variants were on the same allele. We have described a unique complex IEI patient with multiple mutations, particularly along type I IFN production pathway.
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Affiliation(s)
- Narjes Saheb Sharif-Askari
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Shirin Hafezi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Fatemeh Saheb Sharif-Askari
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of pharmacy practice and pharmacotherapeutics, College of pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Hawra Ali Hussain Alsayed
- Department of Pharmacy, Rashid Hospital, Dubai Academic Health Corporation, Dubai, United Arab Emirates
| | - Samrein B. M. Ahmed
- Department of Biosciences and Chemistry, College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Rabih Halwani
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Prince Abdullah Ben Khaled Celiac Disease Research Chair, department of pediatrics, Faculty of Medicine, King Saud University, Saudi Arabia
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Shpilman Z, Kidane D. Dysregulation of base excision repair factors associated with low tumor immunogenicity in head and neck cancer: implication for immunotherapy. Ther Adv Med Oncol 2024; 16:17588359241248330. [PMID: 38680291 PMCID: PMC11047243 DOI: 10.1177/17588359241248330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Background Head and neck squamous carcinoma (HNSCC) is caused by different exogenous risk factors including smoking cigarettes, alcohol consumption, and HPV infection. Base excision repair (BER) is the frontline to repair oxidative DNA damage, which is initiated by the DNA N-glycosylase proteins (OGG1) and other BER factors including DNA polymerase β (POLB). Objective Explore whether BER genes' (OGG1, POLB) overexpression in HNSCC alters genomic integrity, immunogenicity, and its role in prognostic value. Design RNA sequencing (RNA-Seq) and clinical information (age, gender, histological grade, survival status, and stage) of 530 patients of HNSCC were retrieved from the Cancer Genome Atlas. Patients' data are categorized HPV positive or negative to analyze the tumor data including the tumor stage, POLB, and OGG1 gene expression. Methods RNA-Seq of HNSCC data retrieved and mutation count and aneuploidy score were compared using an unpaired t-test. The TIMER algorithm was used to calculate the tumor abundance of six infiltrating immune cells (CD4+ T cells, CD8+ T cells, B cells, neutrophils, macrophages, and dendritic cells) based on RNA-Seq expression profile data. The correlation between the POLB, OGG1, and immune cells was calculated by Spearman correlation analysis using TIMER 2.0. Results Our data analysis reveals that BER genes frequently overexpressed in HNSCC tumors and increase mutation count. In addition, OGG1 and POLB overexpression are associated with low infiltration of immune cells, low immune checkpoint gene expression (PD-1, cytotoxic T-lymphocyte antigen 4, program death ligand 1, and program death ligand 2), and innate immune signaling genes. Furthermore, dysregulated BER factors in Human papillomavirus (HPV) positive tumors had better overall survival. Conclusion Our analysis suggests that dysregulation of the BER genes panel might be a potential prognosis marker and/or an attractive target for an immune checkpoint blockade in HNSCC cancers. However, our observation still requires further experimental-based scientific validation studies.
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Affiliation(s)
- Zackary Shpilman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Department of Physiology and Biophysics, College of Medicine, Howard University, Washington, DC, USA
| | - Dawit Kidane
- Department of Physiology and Biophysics, College of Medicine, Howard University, 520 W Street, Northwestern Washington, DC 20059, USA
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Borna S, Meffre E, Bacchetta R. FOXP3 deficiency, from the mechanisms of the disease to curative strategies. Immunol Rev 2024; 322:244-258. [PMID: 37994657 DOI: 10.1111/imr.13289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
FOXP3 gene is a key transcription factor driving immune tolerance and its deficiency causes immune dysregulation, polyendocrinopathy, enteropathy X-linked syndrome (IPEX), a prototypic primary immune regulatory disorder (PIRD) with defective regulatory T (Treg) cells. Although life-threatening, the increased awareness and early diagnosis have contributed to improved control of the disease. IPEX currently comprises a broad spectrum of clinical autoimmune manifestations from severe early onset organ involvement to moderate, recurrent manifestations. This review focuses on the mechanistic advancements that, since the IPEX discovery in early 2000, have informed the role of the human FOXP3+ Treg cells in controlling peripheral tolerance and shaping the overall immune landscape of IPEX patients and carrier mothers, contributing to defining new treatments.
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Affiliation(s)
- Simon Borna
- Department of Pediatrics, Division of Hematology, Oncology Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Eric Meffre
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, USA
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Hematology, Oncology Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, California, USA
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Mansour R, El-Hassan R, El-Orfali Y, Saidu A, Al-Kalamouni H, Chen Q, Benamar M, Dbaibo G, Hanna-Wakim R, Chatila TA, Massaad MJ. The opposing effects of two gene defects in STX11 and SLP76 on the disease in a patient with an inborn error of immunity. J Allergy Clin Immunol 2023; 152:1597-1606. [PMID: 37595757 DOI: 10.1016/j.jaci.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Inborn errors of immunity are mostly monogenic. However, disease phenotype and outcome may be modified by the coexistence of a second gene defect. OBJECTIVE We sought to identify the genetic basis of the disease in a patient who experienced bleeding episodes, pancytopenia, hepatosplenomegaly, and recurrent pneumonia that resulted in death. METHODS Genetic analysis was done using next-generation sequencing. Protein expression and phosphorylation were determined by immunoblotting. T-cell proliferation and F-actin levels were studied by flow cytometry. RESULTS The patient harbored 2 homozygous deletions in STX11 (c.369_370del, c.374_376del; p.V124fs60∗) previously associated with familial hemophagocytic lymphohistiocytosis and a novel homozygous missense variant in SLP76 (c.767C>T; p.T256I) that resulted in an approximately 85% decrease in SLP76 levels and absent T-cell proliferation. The patient's heterozygous family members showed an approximately 50% decrease in SLP76 levels but normal immune function. SLP76-deficient J14 Jurkat cells did not express SLP76 and had decreased extracellular signal-regulated kinase signaling, basal F-actin levels, and polymerization following T-cell receptor stimulation. Reconstitution of J14 cells with T256I mutant SLP76 resulted in low protein expression and abnormal extracellular signal-regulated kinase phosphorylation and F-actin polymerization after T-cell receptor activation compared with normal expression and J14 function when wild-type SLP76 was introduced. CONCLUSIONS The hypomorphic mutation in SLP76 tones down the hyperinflammation due to STX11 deletion, resulting in a combined immunodeficiency that overshadows the hemophagocytic lymphohistiocytosis phenotype. To our knowledge, this study represents the first report of the opposing effects of 2 gene defects on the disease in a patient with an inborn error of immunity.
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Affiliation(s)
- Rana Mansour
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rana El-Hassan
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Youmna El-Orfali
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Adam Saidu
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Habib Al-Kalamouni
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Qian Chen
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Mehdi Benamar
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Ghassan Dbaibo
- Department of Biochemistry, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon; Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon; Research Center of Excellence in Immunity and Infections, American University of Beirut, Beirut, Lebanon
| | - Rima Hanna-Wakim
- Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon; Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Michel J Massaad
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon; Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon; Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon; Research Center of Excellence in Immunity and Infections, American University of Beirut, Beirut, Lebanon.
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Sun X, Liu P. Prognostic biomarker NEIL3 and its association with immune infiltration in renal clear cell carcinoma. Front Oncol 2023; 13:1073941. [PMID: 36816967 PMCID: PMC9932331 DOI: 10.3389/fonc.2023.1073941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Background Kidney renal clear cell carcinoma (KIRC) is a malignant tumor with a high degree of immune infiltration. Identifying immune biomarkers is essential for the treatment of KIRC. Studies have identified the potential of NEIL3 to modulate the immune microenvironment and promote tumor progression. However, the role of NEIL3 in KIRC remains uncertain. This study was to investigate the effect of NEIL3 on the prognosis and immune infiltration of patients with KIRC. Methods TCGA and GEO databases were used to study the expression of NEIL3 in KIRC. Cox regression analysis was used to examine the relationship between the expression of NEIL3 and clinicopathological variables and survival. Furthermore, Gene Set Cancer Analysis (GSCA) was applied to study the impact of NEIL3 methylation on outcomes of KIRC. Through gene ontology (GO) and Gene set enrichment (GSEA) analysis, the biological processes and signal pathways related to NEIL3 expression were identified. In addition, immune infiltration analysis was conducted via CIBERSORT analysis, ssGSEA analysis and TISIDB database. Results NEIL3 was overexpressed in KIRC, and it was significantly related with histologic grade, pathologic stage, T stage, M stage, and vital status of KIRC patients (P < 0.001). The expression of NEIL3 was associated with worse outcomes. Univariate and multivariate Cox analysis showed that NEIL3 may be an indicator of adverse outcomes in KIRC. GSEA analysis revealed that NEIL3 may be involved in signal pathways including cell cycle, DNA replication, mismatch repair, P53 signal pathway, and antigen processing and presentation. In addition, immune infiltration analysis showed a positive correlation between NEIL3 expression and multiple immune cells (activated CD8 T cells, activated dendritic cells, myeloid-derived suppressor cells, follicular helper T cells, and regulatory T cells) and immunoinhibitors (PD1, CTLA4, LAG3, TIGHT, IL10, and CD96). Conclusion NEIL3 is a potential independent biomarker of KIRC, which is relevant to immune infiltration.
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Affiliation(s)
- Xiaomei Sun
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Pengfei Liu
- Department of Medical Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China,*Correspondence: Pengfei Liu,
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Chung HJ, Lee JR, Kim TM, Kim S, Park K, Kim MJ, Jung E, Kim S, Lee EA, Ra JS, Hwang S, Lee JY, Schärer OD, Kim Y, Myung K, Kim H. ZNF212 promotes genomic integrity through direct interaction with TRAIP. Nucleic Acids Res 2023; 51:631-649. [PMID: 36594163 PMCID: PMC9881131 DOI: 10.1093/nar/gkac1226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023] Open
Abstract
TRAIP is a key factor involved in the DNA damage response (DDR), homologous recombination (HR) and DNA interstrand crosslink (ICL) repair. However, the exact functions of TRAIP in these processes in mammalian cells are not fully understood. Here we identify the zinc finger protein 212, ZNF212, as a novel binding partner for TRAIP and find that ZNF212 colocalizes with sites of DNA damage. The recruitment of TRAIP or ZNF212 to sites of DNA damage is mutually interdependent. We show that depletion of ZNF212 causes defects in the DDR and HR-mediated repair in a manner epistatic to TRAIP. In addition, an epistatic analysis of Zfp212, the mouse homolog of human ZNF212, in mouse embryonic stem cells (mESCs), shows that it appears to act upstream of both the Neil3 and Fanconi anemia (FA) pathways of ICLs repair. We find that human ZNF212 interacted directly with NEIL3 and promotes its recruitment to ICL lesions. Collectively, our findings identify ZNF212 as a new factor involved in the DDR, HR-mediated repair and ICL repair though direct interaction with TRAIP.
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Affiliation(s)
| | | | | | | | | | - Myung-Jin Kim
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Eunyoung Jung
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea,Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Yonghwan Kim
- Correspondence may also be addressed to Yonghwan Kim. Tel: +82 2 710 9552;
| | - Kyungjae Myung
- Correspondence may also be addressed to Kyungjae Myung. Tel: +82 52 217 5323; Fax: +82 52 217 5519;
| | - Hongtae Kim
- To whom correspondence should be addressed. Tel: +82 52 217 5404; Fax: +82 52 217 5519;
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Vlachogiannis NI, Ntouros PA, Pappa M, Verrou KM, Arida A, Souliotis VL, Sfikakis PP. Deregulated DNA damage response network in Behcet's disease. Clin Immunol 2023; 246:109189. [PMID: 36400336 DOI: 10.1016/j.clim.2022.109189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Behcet's disease (BD) is a chronic, relapsing systemic vasculitis of unknown etiology. Since the DNA repair enzyme NEIL1 has been identified as one of the two genetic risk factors for BD by whole exome study, we examined the potential involvement of the DNA damage response (DDR) network in BD. Peripheral blood mononuclear cells from 26 patients and 26 age-/sex-matched healthy controls were studied. Endogenous DNA damage levels were increased in active BD patients compared to controls or patients in remission. In parallel, BD patients had defective nucleotide excision repair capacity. RNA-sequencing revealed reduced expression of NEIL1 that negatively correlated with DNA damage accumulation. On the other hand, expression of genes involved in senescence and senescence-associated secretory phenotype positively correlated with individual endogenous DNA damage levels. We conclude that deregulated DDR contributes to the proinflammatory environment in BD.
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Affiliation(s)
- Nikolaos I Vlachogiannis
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece.
| | - Panagiotis A Ntouros
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Maria Pappa
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Kleio-Maria Verrou
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece; Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Aikaterini Arida
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Vassilis L Souliotis
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece; Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Petros P Sfikakis
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, Athens, Greece; Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece.
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Chen L, Huan X, Gao XD, Yu WH, Xiao GH, Li TF, Wang ZY, Zhang YC. Biological Functions of the DNA Glycosylase NEIL3 and Its Role in Disease Progression Including Cancer. Cancers (Basel) 2022; 14. [PMID: 36497204 DOI: 10.3390/cancers14235722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
The accumulation of oxidative DNA base damage can severely disrupt the integrity of the genome and is strongly associated with the development of cancer. DNA glycosylase is the critical enzyme that initiates the base excision repair (BER) pathway, recognizing and excising damaged bases. The Nei endonuclease VIII-like 3 (NEIL3) is an emerging DNA glycosylase essential in maintaining genome stability. With an in-depth study of the structure and function of NEIL3, we found that it has properties related to the process of base damage repair. For example, it not only prefers the base damage of single-stranded DNA (ssDNA), G-quadruplex and DNA interstrand crosslinks (ICLs), but also participates in the maintenance of replication fork stability and telomere integrity. In addition, NEIL3 is strongly associated with the progression of cancers and cardiovascular and neurological diseases, is incredibly significantly overexpressed in cancers, and may become an independent prognostic marker for cancer patients. Interestingly, circNEIL3, a circular RNA of exon-encoded origin by NEIL3, also promotes the development of multiple cancers. In this review, we have summarized the structure and the characteristics of NEIL3 to repair base damage. We have focused on NEIL3 and circNEIL3 in cancer development, progression and prognosis.
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Li N, Xu Y, Chen H, Chen L, Zhang Y, Yu T, Yao R, Chen J, Fu Q, Zhou J, Wang J. NEIL3 contributes to the Fanconi anemia/BRCA pathway by promoting the downstream double-strand break repair step. Cell Rep 2022; 41:111600. [DOI: 10.1016/j.celrep.2022.111600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022] Open
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Liu W, Lyu C, Wang W, Xue F, Chen L, Li H, Chi Y, Ma Y, Wu R, Fang Y, Zhang L, Yang R. Risk factors for inhibitors in hemophilia A based on RNA-seq and DNA methylation. Res Pract Thromb Haemost 2022; 6:e12794. [PMID: 36090157 PMCID: PMC9445143 DOI: 10.1002/rth2.12794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/03/2022] [Accepted: 07/23/2022] [Indexed: 11/08/2022] Open
Abstract
Background The development of factor VIII (FVIII) inhibitor is a severe complication during replacement therapy for hemophilia A patients. Objectives We investigated the potential risk factors for FVIII inhibitor formation based on genome-wide RNA-sequencing and whole-genome bisulfite sequencing analysis. Methods RNA-sequencing and whole-genome bisulfite sequencing analysis were applied on 17 blood samples with F8 intron 22 inversion, including seven with inhibitors and 10 without. Results Altogether, 344 mRNA transcripts and 20 long noncoding RNAs (lncRNA) transcripts were differentially expressed. Among the differentially expressed transcripts, 200 mRNAs and 12 lncRNAs were upregulated, and 144 mRNAs and eight lncRNAs were downregulated. Gene ontology enrichment analysis of differentially expressed mRNAs showed that genes involved in immune stimulation, especially those for T-cell activation, were upregulated, whereas genes involved in negative immune response regulation were downregulated. Coexpression analysis revealed that the targeted upregulated genes of differentially expressed lncRNA were similarly closely related to immune activation, especially T-cell activation. Methylation analysis showed inhibitor patients exhibited a slightly lower methylation status in the CpG islands, 5' untranslated region, and exon regions (p < 0.01). Genes with differentially methylated regions were also related to T-cell activation. Conclusions There is an upregulation of genes involved in activation of the immune system in hemophilia A patients with inhibitors. The lncRNA and methylation modifications may play important roles in inhibitor production. These findings are potentially to reveal novel therapeutic targets for prevention and treatment of inhibitors.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Cuicui Lyu
- Department of Hematology Tianjin First Central Hospital, School of Medicine, Nankai University Tianjin China
| | - Wentian Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Feng Xue
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Lingling Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Huiyuan Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Ying Chi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Yueshen Ma
- Office of Biostatics, Center for Information and Resources, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Runhui Wu
- Beijing Children's Hospital Affiliated to Capital Medical University Beijing China
| | - Yunhai Fang
- Shandong Blood Center, Shandong Hemophilia Treatment Center Shandong China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
| | - Renchi Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Laboratory of Blood Disease Gene Therapy, CAMS Key Laboratory of Gene Therapy for Blood Diseases, CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine Tianjin China
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Almutairi A, Amin MM, Rashwan MA, Elnagdy MH, Rizk R, Bahgat SA, Platt CD, Sobh A. Digenic inheritance of IL-36RA and SEC61A1 mutations underlies generalized pustular psoriasis with hypogammaglobulinemia. Clin Immunol 2022; 235:108930. [DOI: 10.1016/j.clim.2022.108930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/13/2022] [Indexed: 11/03/2022]
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12
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Chen JW, Schickel JN, Tsakiris N, Sng J, Arbogast F, Bouis D, Parisi D, Gera R, Boeckers JM, Delmotte FR, Veselits M, Schuetz C, Jacobsen EM, Posovszky C, Schulz AS, Schwarz K, Clark MR, Menard L, Meffre E. Positive and negative selection shape the human naïve B cell repertoire. J Clin Invest 2021; 132:150985. [PMID: 34813502 PMCID: PMC8759783 DOI: 10.1172/jci150985] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
Although negative selection of developing B cells in the periphery is well described, yet poorly understood, evidence of naive B cell positive selection remains elusive. Using 2 humanized mouse models, we demonstrate that there was strong skewing of the expressed immunoglobulin repertoire upon transit into the peripheral naive B cell pool. This positive selection of expanded naive B cells in humanized mice resembled that observed in healthy human donors and was independent of autologous thymic tissue. In contrast, negative selection of autoreactive B cells required thymus-derived Tregs and MHC class II–restricted self-antigen presentation by B cells. Indeed, both defective MHC class II expression on B cells of patients with rare bare lymphocyte syndrome and prevention of self-antigen presentation via HLA-DM inhibition in humanized mice resulted in the production of autoreactive naive B cells. These latter observations suggest that Tregs repressed autoreactive naive B cells continuously produced by the bone marrow. Thus, a model emerged, in which both positive and negative selection shaped the human naive B cell repertoire and that each process was mediated by fundamentally different molecular and cellular mechanisms.
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Affiliation(s)
- Jeff W Chen
- Department of Immunobiology, Yale University, New Haven, United States of America
| | | | - Nikolaos Tsakiris
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Joel Sng
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Florent Arbogast
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Delphine Bouis
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Daniele Parisi
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Ruchi Gera
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Joshua M Boeckers
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Fabien R Delmotte
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Margaret Veselits
- Department of Medicine, University of Chicago, Chicago, United States of America
| | - Catharina Schuetz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Eva-Maria Jacobsen
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Carsten Posovszky
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Ansgar S Schulz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Klaus Schwarz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Marcus R Clark
- Department of Medicine, University of Chicago, Chicago, United States of America
| | - Laurence Menard
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Eric Meffre
- Department of Immunobiology, Yale University, New Haven, United States of America
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13
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Abolhassani H, Vosughimotlagh A, Asano T, Landegren N, Boisson B, Delavari S, Bastard P, Aranda-Guillén M, Wang Y, Zuo F, Sardh F, Marcotte H, Du L, Zhang SY, Zhang Q, Rezaei N, Kämpe O, Casanova JL, Hammarström L, Pan-Hammarström Q. X-Linked TLR7 Deficiency Underlies Critical COVID-19 Pneumonia in a Male Patient with Ataxia-Telangiectasia. J Clin Immunol 2021. [PMID: 34686943 DOI: 10.1007/s10875-021-01151-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/03/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) exhibits a wide spectrum of clinical manifestations, ranging from asymptomatic to critical conditions. Understanding the mechanism underlying life-threatening COVID-19 is instrumental for disease prevention and treatment in individuals with a high risk. OBJECTIVES We aimed to identify the genetic cause for critical COVID-19 pneumonia in a patient with a preexisting inborn error of immunity (IEI). METHODS Serum levels of specific antibodies against the virus and autoantibodies against type I interferons (IFNs) were measured. Whole exome sequencing was performed, and the impacts of candidate gene variants were investigated. We also evaluated 247 ataxia-telangiectasia (A-T) patients in the Iranian IEI registry. RESULTS We report a 7-year-old Iranian boy with a preexisting hyper IgM syndrome who developed critical COVID-19 pneumonia. IgM only specific COVID-19 immune response was detected but no autoantibodies against type I IFN were observed. A homozygous deleterious mutation in the ATM gene was identified, which together with his antibody deficiency, radiosensitivity, and neurological signs, established a diagnosis of A-T. Among the 247 A-T patients evaluated, 36 had SARS-CoV-2 infection, but all had mild symptoms or were asymptomatic except the index patient. A hemizygous deleterious mutation in the TLR7 gene was subsequently identified in the patient. CONCLUSIONS We report a unique IEI patient with combined ATM and TLR7 deficiencies. The two genetic defects underlie A-T and critical COVID-19 in this patient, respectively.
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14
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Karlsen TR, Kong XY, Holm S, Quiles-Jiménez A, Dahl TB, Yang K, Sagen EL, Skarpengland T, S Øgaard JD, Holm K, Vestad B, Olsen MB, Aukrust P, Bjørås M, Hov JR, Halvorsen B, Gregersen I. NEIL3-deficiency increases gut permeability and contributes to a pro-atherogenic metabolic phenotype. Sci Rep 2021; 11:19749. [PMID: 34611194 PMCID: PMC8492623 DOI: 10.1038/s41598-021-98820-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
Atherosclerosis and its consequences cause considerable morbidity and mortality world-wide. We have previously shown that expression of the DNA glycosylase NEIL3 is regulated in human atherosclerotic plaques, and that NEIL3-deficiency enhances atherogenesis in Apoe-/- mice. Herein, we identified a time point prior to quantifiable differences in atherosclerosis between Apoe-/-Neil3-/- mice and Apoe-/- mice. Mice at this age were selected to explore the metabolic and pathophysiological processes preceding extensive atherogenesis in NEIL3-deficient mice. Untargeted metabolomic analysis of young Apoe-/-Neil3-/- mice revealed significant metabolic disturbances as compared to mice expressing NEIL3, particularly in metabolites dependent on the gut microbiota. 16S rRNA gene sequencing of fecal bacterial DNA indeed confirmed that the NEIL3-deficient mice had altered gut microbiota, as well as increased circulating levels of the bacterially derived molecule LPS. The mice were challenged with a FITC-conjugated dextran to explore gut permeability, which was significantly increased in the NEIL3-deficient mice. Further, immunohistochemistry showed increased levels of the proliferation marker Ki67 in the colonic epithelium of NEIL3-deficient mice, suggesting increased proliferation of intestinal cells and gut leakage. We suggest that these metabolic alterations serve as drivers of atherosclerosis in NEIL3-deficient mice.
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Affiliation(s)
- Tom Rune Karlsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tuva B Dahl
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Research and Development, Division of Emergencies and Critical Care, Oslo University Hospital HF, Rikshospitalet, Oslo, Norway
| | - Kuan Yang
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ellen L Sagen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tonje Skarpengland
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jonas D S Øgaard
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Kristian Holm
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Maria B Olsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
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15
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Wang Q, Li Z, Yang J, Peng S, Zhou Q, Yao K, Cai W, Xie Z, Qin F, Li H, Chen X, Li K, Huang H. Loss of NEIL3 activates radiotherapy resistance in the progression of prostate cancer. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0550. [PMID: 34591415 PMCID: PMC9425180 DOI: 10.20892/j.issn.2095-3941.2020.0550] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE To explore the genetic changes in the progression of castration-resistant prostate cancer (CRPC) and neuroendocrine prostate cancer (NEPC) and the reason why these cancers resist existing therapies. METHODS We employed our CRPC cell line microarray and other CRPC or NEPC datasets to screen the target gene NEIL3. Lentiviral transfection and RNA interference were used to construct overexpression and knockdown cell lines. Cell and animal models of radiotherapy were established by using a medical electron linear accelerator. Flow cytometry was used to detect apoptosis or cell cycle progression. Western blot and qPCR were used to detect changes in the protein and RNA levels. RESULTS TCGA and clinical patient datasets indicated that NEIL3 was downregulated in CRPC and NEPC cell lines, and NEIL3 was correlated with a high Gleason score but a good prognosis. Further functional studies demonstrated that NEIL3 had no effect on the proliferation and migration of PCa cells. However, cell and animal radiotherapy models revealed that NEIL3 could facilitate the radiotherapy sensitivity of PCa cells, while loss of NEIL3 activated radiotherapy resistance. Mechanistically, we found that NEIL3 negatively regulated the expression of ATR, and higher NEIL3 expression repressed the ATR/CHK1 pathway, thus regulating the cell cycle. CONCLUSIONS We demonstrated that NEIL3 may serve as a diagnostic or therapeutic target for therapy-resistant patients.
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Affiliation(s)
- Qiong Wang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Zean Li
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jin Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Department of Radiation Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Shirong Peng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Qianghua Zhou
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Kai Yao
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Wenli Cai
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Xu Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Kaiwen Li
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Hai Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan 511518, China
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16
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Wang W, Yin Q, Guo S, Wang J. NEIL3 contributes toward the carcinogenesis of liver cancer and regulates PI3K/Akt/mTOR signaling. Exp Ther Med 2021; 22:1053. [PMID: 34434267 PMCID: PMC8353638 DOI: 10.3892/etm.2021.10487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/12/2021] [Indexed: 12/15/2022] Open
Abstract
Liver cancer is one of the top three fatal types of cancer and it causes several thousands of mortalities each year. The main treatment is surgical resection which shows little benefit for patients with recurrence or metastasis. NEIL3 promotes progression and predicts survival in cancer. However, its role in liver cancer remains unclear. Based on data in the TCGA database, NEIL3 exhibited much higher expression in liver cancer tissues and was clinically correlated with tumor grade in patients with liver cancer. Furthermore, high NEIL3 expression caused shorter survival times. In liver cancer cell lines, NEIL3 showed abundant expression. When NEIL3 was knocked down in HepG2 and Huh-7 cells, cell abilities including proliferation, growth, migration and invasion, exhibited deficiency to different extents. Cell cycle transition was blocked at the G2 phase and the cell apoptotic rate increased notably. In addition, the phosphorylation levels of Akt, PI3K and mTOR were increased following NEIL3-overexpression but decreased following NEIL3-knockdown. In conclusion, NEIL3 contributes toward development and/or progression in liver cancer and regulates PI3K/Akt/mTOR signaling.
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Affiliation(s)
- Weichen Wang
- Medical Research and Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Qing Yin
- Department of Medical Education, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Shanshan Guo
- Department of Food Science and Nutrition, University of Jinan, Jinan, Shandong 250022, P.R. China
| | - Jun Wang
- Medical Research and Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
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17
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Zhao Z, Gad H, Benitez-Buelga C, Sanjiv K, Xiangwei H, Kang H, Feng M, Zhao Z, Berglund UW, Xia Q, Helleday T. NEIL3 Prevents Senescence in Hepatocellular Carcinoma by Repairing Oxidative Lesions at Telomeres during Mitosis. Cancer Res 2021; 81:4079-4093. [PMID: 34045188 PMCID: PMC9398161 DOI: 10.1158/0008-5472.can-20-1028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
Patients with hepatocellular carcinoma (HCC) suffer from few treatment options and poor survival rates. Here we report that endonuclease VIII-like protein 3 (NEIL3) is overexpressed in HCC and correlates with poor survival. All six HCC cell lines investigated were dependent on NEIL3 catalytic activity for survival and prevention of senescence, while NEIL3 was dispensable for nontransformed cells. NEIL3-depleted HCC cell lines accumulated oxidative DNA lesions specifically at telomeres, resulting in telomere dysfunctional foci and 53BP1 foci formation. Following oxidative DNA damage during mitosis, NEIL3 relocated to telomeres and recruited apurinic endonuclease 1 (APE1), indicating activation of base excision repair. META-FISH revealed that NEIL3, but not NEIL1 or NEIL2, is required to initiate APE1 and polymerase beta (POLB)-dependent base excision repair at oxidized telomeres. Repeated exposure of NEIL3-depleted cells to oxidizing damage induced chromatin bridges and damaged telomeres. These results demonstrate a novel function for NEIL3 in repair of oxidative DNA damage at telomeres in mitosis, which is important to prevent senescence of HCC cells. Furthermore, these data suggest that NEIL3 could be a target for therapeutic intervention for HCC. SIGNIFICANCE: This study describes compartmentalization of base excision repair during mitosis that is dependent on NEIL3, APE1, and POLB to repair oxidative damage accumulating at telomeres in hepatocellular carcinoma.
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Affiliation(s)
- Zhenjun Zhao
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Helge Gad
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Carlos Benitez-Buelga
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Hua Xiangwei
- Organ Transplantation Center, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - He Kang
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingxuan Feng
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhicong Zhao
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Corresponding Authors: Thomas Helleday, Karolinska Institutet, Tomtebodavägen 23B, Stockholm S-171 65, Sweden. E-mail: ; and Xia Qiang, Renji Hospital, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200001, China. E-mail:
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.,Corresponding Authors: Thomas Helleday, Karolinska Institutet, Tomtebodavägen 23B, Stockholm S-171 65, Sweden. E-mail: ; and Xia Qiang, Renji Hospital, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200001, China. E-mail:
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18
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Abstract
DNA interstrand cross-links (ICLs) covalently connect the two strands of the double helix and are extremely cytotoxic. Defective ICL repair causes the bone marrow failure and cancer predisposition syndrome, Fanconi anemia, and upregulation of repair causes chemotherapy resistance in cancer. The central event in ICL repair involves resolving the cross-link (unhooking). In this review, we discuss the chemical diversity of ICLs generated by exogenous and endogenous agents. We then describe how proliferating and nonproliferating vertebrate cells unhook ICLs. We emphasize fundamentally new unhooking strategies, dramatic progress in the structural analysis of the Fanconi anemia pathway, and insights into how cells govern the choice between different ICL repair pathways. Throughout, we highlight the many gaps that remain in our knowledge of these fascinating DNA repair pathways.
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Affiliation(s)
- Daniel R Semlow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Current affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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19
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Zhao C, Liu J, Zhou H, Qian X, Sun H, Chen X, Zheng M, Bian T, Liu L, Liu Y, Zhang J. NEIL3 may act as a potential prognostic biomarker for lung adenocarcinoma. Cancer Cell Int 2021; 21:228. [PMID: 33879165 PMCID: PMC8059184 DOI: 10.1186/s12935-021-01938-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/13/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death. This study aimed to develop and validate reliable prognostic biomarkers and signature. METHODS Differentially expressed genes were identified based on three Gene Expression Omnibus (GEO) datasets. Based on 1052 samples' data from our cohort, GEO and The Cancer Genome Atlas, we explored the relationship of clinicopathological features and NEIL3 expression to determine clinical effect of NEIL3 in LUAD. Western blotting (22 pairs of tumor and normal tissues), Real-time quantitative PCR (19 pairs of tumor and normal tissues), and immunohistochemical analyses (406-tumor tissues subjected to microarray) were conducted. TIMER and ImmuCellAI analyzed relationship between NEIL3 expression and the abundance of tumor-infiltrating immune cells in LUAD. The co-expressed-gene prognostic signature was established based on the Cox regression analysis. RESULTS This study identified 502 common differentially expressed genes and confirmed that NEIL3 was significantly overexpressed in LUAD samples (P < 0.001). Increased NEIL3 expression was related to advanced stage, larger tumor size and poor overall survival (p < 0.001) in three LUAD cohorts. The proportions of natural T regulatory cells and induced T regulatory cells increased in the high NEIL3 group, whereas those of B cells, Th17 cells and dendritic cells decreased. Gene set enrichment analysis indicated that NEIL3 may activate cell cycle progression and P53 signaling pathway, leading to poor outcomes. We identified nine prognosis-associated hub genes among 370 genes co-expressed with NEIL3. A 10-gene prognostic signature including NEIL3 and nine key co-expressed genes was constructed. Higher risk-score was correlated with more advanced stage, larger tumor size and worse outcome (p < 0.05). Finally, the signature was verified in test cohort (GSE50081) with superior diagnostic accuracy. CONCLUSIONS This study suggested that NEIL3 has the potential to be an immune-related therapeutic target and an independent predictor of LUAD prognosis. We also developed a prognostic signature for LUAD with a precise diagnostic accuracy.
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Affiliation(s)
- Cui Zhao
- Nantong University, Nantong, 226001, China
| | - Jian Liu
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | | | - Xin Qian
- Nantong University, Nantong, 226001, China
| | - Hui Sun
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Xuewen Chen
- Department of Orthopedics, Second People's Hospital of Jingmen, Jingmen, 448000, China
| | | | - Tingting Bian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, 226001, China.
| | - Jianguo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, 226001, China.
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20
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Gámez-Díaz L, Grimbacher B. Immune checkpoint deficiencies and autoimmune lymphoproliferative syndromes. Biomed J 2021; 44:400-411. [PMID: 34384744 PMCID: PMC8514790 DOI: 10.1016/j.bj.2021.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 04/15/2021] [Indexed: 12/30/2022] Open
Abstract
Autoimmune lymphoproliferative syndrome (ALPS) is an inherited non-malignant and non-infectious lymphoproliferative syndrome caused by mutations in genes affecting the extrinsic apoptotic pathway (FAS, FASL, CASP10). The resulting FAS-mediated apoptosis defect accounts for the expansion and accumulation of autoreactive (double-negative) T cells leading to cytopenias, splenomegaly, lymphadenopathy, autoimmune disorders, and risk of lymphoma. However, there are other monogenetic disorders known as ALPS-like syndromes that can be clinically similar to ALPS but are genetically and biologically different, such as observed in patients with immune checkpoint deficiencies, particularly cytotoxic T-lymphocyte antigen 4 (CTLA-4) insufficiency and lipopolysaccharide-responsive beige-like anchor protein LRBA deficiency. CTLA-4 insufficiency is caused by heterozygous mutations in CTLA-4, an essential negative immune regulator that is constitutively expressed on regulatory T (Treg) cells. Mutations in CTLA-4 affect CTLA-4 binding to CD80-CD86 costimulatory molecules, CTLA-4 homodimerization, or CTLA-4 intracellular vesicle trafficking upon cell activation. Abnormal CTLA-4 trafficking is also observed in patients with LRBA deficiency, a syndrome caused by biallelic mutations in LRBA that abolishes the LRBA protein expression. Both immune checkpoint deficiencies are biologically characterized by low levels of CTLA-4 protein on the cell surface of Tregs, accounting for the autoimmune manifestations observed in CTLA4-insufficient and LRBA-deficient patients. In addition, both immune checkpoint deficiencies present with an overlapping but heterogeneous clinical picture despite the difference in inheritance and penetrance. In this review, we describe the most prominent clinical features of ALPS, CTLA-4 insufficiency and LRBA deficiency, emphasizing their corresponding biological mechanisms. We also provide some clinical and laboratory approaches to diagnose these three rare immune disorders, together with therapeutic strategies that have worked best at improving prognosis and quality life of patients.
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Affiliation(s)
- Laura Gámez-Díaz
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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21
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Wang Y, Xu L, Shi S, Wu S, Meng R, Chen H, Jiang Z. Deficiency of NEIL3 Enhances the Chemotherapy Resistance of Prostate Cancer. Int J Mol Sci 2021; 22:4098. [PMID: 33921035 PMCID: PMC8071437 DOI: 10.3390/ijms22084098] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 01/04/2023] Open
Abstract
Acquired treatment resistance is an important cause of death in prostate cancer, and this study aimed to explore the mechanisms of chemotherapy resistance in prostate cancer. We employed castration-resistant prostate cancer (CRPC), neuroendocrine prostate cancer (NEPC), and chemotherapy-resistant prostate cancer datasets to screen for potential target genes. The Cancer Genome Atlas (TCGA) was used to detect the correlation between the target genes and prognosis and clinical characteristics. Nei endonuclease VIII-like 3 (NEIL3) knockdown cell lines were constructed with RNA interference. Prostate cancer cells were treated with enzalutamide for the androgen deprivation therapy (ADT) model, and with docetaxel and cisplatin for the chemotherapy model. Apoptosis and the cell cycle were examined using flow cytometry. RNA sequencing and western blotting were performed in the knockdown Duke University 145 (DU145) cell line to explore the possible mechanisms. The TCGA dataset demonstrated that high NEIL3 was associated with a high T stage and Gleason score, and indicated a possibility of lymph node metastasis, but a good prognosis. The cell therapy models showed that the loss of NEIL3 could promote the chemotherapy resistance (but not ADT resistance) of prostate cancer (PCa). Flow cytometry revealed that the loss of NEIL3 in PCa could inhibit cell apoptosis and cell cycle arrest under cisplatin treatment. RNA sequencing showed that the knockdown of NEIL3 changes the expression of neuroendocrine-related genes. Further western blotting revealed that the loss of NEIL3 could significantly promote the phosphorylation of ATR serine/threonine kinase (ATR) and ATM serine/threonine kinase (ATM) under chemotherapy, thus initiating downstream pathways related to DNA repair. In summary, the loss of NEIL3 promotes chemotherapy resistance in prostate cancer, and NEIL3 may serve as a diagnostic marker for chemotherapy-resistant patients.
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Affiliation(s)
- Yiwei Wang
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Liuyue Xu
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Shanshan Shi
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Sha Wu
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Ruijie Meng
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
| | - Huifang Chen
- School of Pharmacy, Guangdong Lingnan Institute of Technology, Guangzhou 510663, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, College of Basic Medicine and Public Hygiene, Jinan University, Guangzhou 510632, China; (Y.W.); (L.X.); (S.S.); (S.W.); (R.M.)
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22
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Salami F, Shirkani A, Shahrooei M, Azizi G, Yazdani R, Abolhassani H, Aghamohammadi A. Leishmaniasis and Autoimmunity in Patient with LPS-Responsive Beige-Like Anchor Protein (LRBA) Deficiency. Endocr Metab Immune Disord Drug Targets 2021; 20:479-484. [PMID: 31389321 DOI: 10.2174/1871530319666190807161546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/26/2019] [Accepted: 05/30/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND/OBJECTIVE LPS-responsive beige-like anchor protein (LRBA) deficiency is a combined immunodeficiency and immune dysregulation. The authors present a case report of LPSresponsive beige-like anchor protein (LRBA) deficiency with the history of autoimmunity, enteropathy and visceral leishmaniasis. Sirolimus therapy was started for autoimmunity and enteropathy but was discontinued due to recurrent leishmaniasis. Therefore, a common side-effect of many immunosuppressive drugs in patients with LRBA deficiency is increased susceptibility to infections. METHODS Whole exome sequencing was performed to detect the underlying genetic mutation and Leishmania DNA was detected by the PCR technique in this patient. RESULTS Whole exome sequencing of the patient reported a homozygous frameshift deletion mutation in the LRBA gene (NM_006726: exon29: c.4638delC, p. S1546fs). Leishmania DNA PCR was positive in this case. CONCLUSION Parasite infections manifestations report in LRBA deficiency. Leishmania infections in patients with chronic diarrhea and autoimmunity should be considered for immunodeficiency.
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Affiliation(s)
- Fereshte Salami
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Afshin Shirkani
- Allergy and Clinical Immunology Department, School of Medicine, Bushehr University of Medical Science, Bushehr, Iran
| | - Mohammad Shahrooei
- Department of Immunology, Specialised Immunology Laboratory of Dr. Shahrooei, Ahvaz, Iran
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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23
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Rodriguez AA, Wojtaszek JL, Greer BH, Haldar T, Gates KS, Williams RS, Eichman BF. An autoinhibitory role for the GRF zinc finger domain of DNA glycosylase NEIL3. J Biol Chem 2020; 295:15566-15575. [PMID: 32878989 PMCID: PMC7667957 DOI: 10.1074/jbc.ra120.015541] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/30/2020] [Indexed: 01/07/2023] Open
Abstract
The NEIL3 DNA glycosylase maintains genome integrity during replication by excising oxidized bases from single-stranded DNA (ssDNA) and unhooking interstrand cross-links (ICLs) at fork structures. In addition to its N-terminal catalytic glycosylase domain, NEIL3 contains two tandem C-terminal GRF-type zinc fingers that are absent in the other NEIL paralogs. ssDNA binding by the GRF-ZF motifs helps recruit NEIL3 to replication forks converged at an ICL, but the nature of DNA binding and the effect of the GRF-ZF domain on catalysis of base excision and ICL unhooking is unknown. Here, we show that the tandem GRF-ZFs of NEIL3 provide affinity and specificity for DNA that is greater than each individual motif alone. The crystal structure of the GRF domain shows that the tandem ZF motifs adopt a flexible head-to-tail configuration well-suited for binding to multiple ssDNA conformations. Functionally, we establish that the NEIL3 GRF domain inhibits glycosylase activity against monoadducts and ICLs. This autoinhibitory activity contrasts GRF-ZF domains of other DNA-processing enzymes, which typically use ssDNA binding to enhance catalytic activity, and suggests that the C-terminal region of NEIL3 is involved in both DNA damage recruitment and enzymatic regulation.
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Affiliation(s)
- Alyssa A Rodriguez
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Briana H Greer
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Tuhin Haldar
- Department of Chemistry, University of Missouri, Columbia, Missouri, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA.
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.
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24
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Paludan SR, Pradeu T, Masters SL, Mogensen TH. Constitutive immune mechanisms: mediators of host defence and immune regulation. Nat Rev Immunol 2021; 21:137-50. [PMID: 32782357 DOI: 10.1038/s41577-020-0391-5] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2020] [Indexed: 02/07/2023]
Abstract
The immune system enables organisms to combat infections and to eliminate endogenous challenges. Immune responses can be evoked through diverse inducible pathways. However, various constitutive mechanisms are also required for immunocompetence. The inducible responses of pattern recognition receptors of the innate immune system and antigen-specific receptors of the adaptive immune system are highly effective, but they also have the potential to cause extensive immunopathology and tissue damage, as seen in many infectious and autoinflammatory diseases. By contrast, constitutive innate immune mechanisms, including restriction factors, basal autophagy and proteasomal degradation, tend to limit immune responses, with loss-of-function mutations in these pathways leading to inflammation. Although they function through a broad and heterogeneous set of mechanisms, the constitutive immune responses all function as early barriers to infection and aim to minimize any disruption of homeostasis. Supported by recent human and mouse data, in this Review we compare and contrast the inducible and constitutive mechanisms of immunosurveillance.
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25
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Ghaini M, Arzanian MT, Shamsian BS, Sadr S, Rohani P, Keramatipour M, Mesdaghi M, Eskandarzadeh S, Lo B, Jamee M, Chavoshzadeh Z. Identifying Novel Mutations in Iranian Patients with LPS-responsive Beige-like Anchor Protein (LRBA) Deficiency. Immunol Invest 2020; 50:399-405. [PMID: 32476511 DOI: 10.1080/08820139.2020.1770784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
LPS-responsive beige-like anchor protein (LRBA) deficiency is a monogenic primary immunodeficiency characterized by a heterogeneous spectrum of clinical manifestations associated with immune dysregulation. In this study, we reported clinical, immunologic, and genetic evaluation of two Iranian patients from unrelated families, both suffering from recurrent respiratory tract infections, failure to thrive, interstitial lung disease, autoimmune cytopenia, and hypogammaglobulinemia. Pulmonary abscess in one patient and persistent enteropathy in another were also observed. Further investigations revealed causative mutations in the exon (c.2166_2766del) and intron (c.4730-3 T > G) of the LRBA gene. These results may provide further elucidation of the clinical phenotypes and responsible genetic factors of LRBA deficiency.
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Affiliation(s)
- Mehdi Ghaini
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Mohammad Taghi Arzanian
- Department of Pediatric Hematology and Oncology, Mofid Children's Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Bibi Shahin Shamsian
- Department of Pediatric Hematology and Oncology, Mofid Children's Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Saeed Sadr
- Department of Pediatric Pulmonology, Mofid Children's Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Pejman Rohani
- Department of Pediatric Gastroenterology and Hepatology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Keramatipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrnaz Mesdaghi
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Shabnam Eskandarzadeh
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Bernice Lo
- Department of Human Genetics, Research Branch, Sidra Medicine, Doha, Qatar
| | - Mahnaz Jamee
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran.,Alborz Office of USERN, Universal Scientific Education and Research Network (USERN), Alborz University of Medical Sciences, Karaj, Iran
| | - Zahra Chavoshzadeh
- Immunology and Allergy Department, Mofid Children's Hospital, Shahid Beheshti University of Medical Science, Tehran, Iran
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26
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Abstract
Primary immunodeficiencies (PIDs) comprise a diverse group of over 400 genetic disorders that result in clinically apparent immune dysfunction. Although PIDs are classically considered as Mendelian disorders with complete penetrance, we now understand that absent or partial clinical disease is often noted in individuals harboring disease-causing genotypes. Despite the frequency of incomplete penetrance in PID, no conceptual framework exists to categorize and explain these occurrences. Here, by reviewing decades of reports on incomplete penetrance in PID we identify four recurrent themes of incomplete penetrance, namely genotype quality, (epi)genetic modification, environmental influence, and mosaicism. For each of these principles, we review what is known, underscore what remains unknown, and propose future experimental approaches to fill the gaps in our understanding. Although the content herein relates specifically to inborn errors of immunity, the concepts are generalizable across genetic diseases.
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Affiliation(s)
- Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Department of Pediatrics, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
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27
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Stratigopoulou M, van Dam TP, Guikema JEJ. Base Excision Repair in the Immune System: Small DNA Lesions With Big Consequences. Front Immunol 2020; 11:1084. [PMID: 32547565 PMCID: PMC7272602 DOI: 10.3389/fimmu.2020.01084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
The integrity of the genome is under constant threat of environmental and endogenous agents that cause DNA damage. Endogenous damage is particularly pervasive, occurring at an estimated rate of 10,000–30,000 per cell/per day, and mostly involves chemical DNA base lesions caused by oxidation, depurination, alkylation, and deamination. The base excision repair (BER) pathway is primary responsible for removing and repairing these small base lesions that would otherwise lead to mutations or DNA breaks during replication. Next to preventing DNA mutations and damage, the BER pathway is also involved in mutagenic processes in B cells during immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM), which are instigated by uracil (U) lesions derived from activation-induced cytidine deaminase (AID) activity. BER is required for the processing of AID-induced lesions into DNA double strand breaks (DSB) that are required for CSR, and is of pivotal importance for determining the mutagenic outcome of uracil lesions during SHM. Although uracils are generally efficiently repaired by error-free BER, this process is surprisingly error-prone at the Ig loci in proliferating B cells. Breakdown of this high-fidelity process outside of the Ig loci has been linked to mutations observed in B-cell tumors and DNA breaks and chromosomal translocations in activated B cells. Next to its role in preventing cancer, BER has also been implicated in immune tolerance. Several defects in BER components have been associated with autoimmune diseases, and animal models have shown that BER defects can cause autoimmunity in a B-cell intrinsic and extrinsic fashion. In this review we discuss the contribution of BER to genomic integrity in the context of immune receptor diversification, cancer and autoimmune diseases.
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Affiliation(s)
- Maria Stratigopoulou
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tijmen P van Dam
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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28
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Tran OT, Tadesse S, Chu C, Kidane D. Overexpression of NEIL3 associated with altered genome and poor survival in selected types of human cancer. Tumour Biol 2020; 42:1010428320918404. [PMID: 32364878 DOI: 10.1177/1010428320918404] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Base excision repair, which is initiated by the DNA N-glycosylase proteins, is the frontline for repairing potentially mutagenic DNA base damage. Several base excision repair genes are deregulated in cancer and affect cellular outcomes to chemotherapy and carcinogenesis. Endonuclease VIII-like 3 (NEIL3) is a DNA glycosylase protein that is involved in oxidative and interstrand crosslink DNA damage repair. Our previous work has showed that NEIL3 is required to maintain replication fork integrity. It is unknown whether NEIL3 overexpression could contribute to cancer phenotypes, and its prognostic value and use as potential drug target remain unexplored. Our analysis of cancer genomics data sets reveals that NEIL3 frequently undergoes overexpression in several cancers. Furthermore, patients who exhibited NEIL3 overexpression with pancreatic adenocarcinoma, lung adenocarcinoma, lower grade glioma, kidney renal clear cell carcinoma, and kidney papillary cell carcinoma had worse overall survival. Importantly, NEIL3 overexpressed tumors accumulate mutation and chromosomal variations. Furthermore, NEIL3 overexpressed tumors exhibit simultaneous overexpression of homologous recombination genes (BRCA1/2) and mismatch repair genes (MSH2/MSH6). However, NEIL3 overexpression is negatively correlated with tumor overexpressing nucleotide excision repair genes (XPA, XPC, ERCC1/2). Our results suggest that NEIL3 might be a potential prognosis marker for high-risk patients, and/or an attractive therapeutic target for selected cancers.
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Affiliation(s)
- Oanh Tn Tran
- College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA.,Department of Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Serkalem Tadesse
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, USA
| | - Christopher Chu
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, USA
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, Dell Pediatric Research Institute, The University of Texas at Austin, Austin, TX, USA
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29
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Li N, Wang J, Wallace SS, Chen J, Zhou J, D’Andrea AD. Cooperation of the NEIL3 and Fanconi anemia/BRCA pathways in interstrand crosslink repair. Nucleic Acids Res 2020; 48:3014-3028. [PMID: 31980815 PMCID: PMC7102959 DOI: 10.1093/nar/gkaa038] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 12/12/2019] [Accepted: 01/22/2020] [Indexed: 12/19/2022] Open
Abstract
The NEIL3 DNA glycosylase is a base excision repair enzyme that excises bulky base lesions from DNA. Although NEIL3 has been shown to unhook interstrand crosslinks (ICL) in Xenopus extracts, how NEIL3 participants in ICL repair in human cells and its corporation with the canonical Fanconi anemia (FA)/BRCA pathway remain unclear. Here we show that the NEIL3 and the FA/BRCA pathways are non-epistatic in psoralen-ICL repair. The NEIL3 pathway is the major pathway for repairing psoralen-ICL, and the FA/BRCA pathway is only activated when NEIL3 is not present. Mechanistically, NEIL3 is recruited to psoralen-ICL in a rapid, PARP-dependent manner. Importantly, the NEIL3 pathway repairs psoralen-ICLs without generating double-strand breaks (DSBs), unlike the FA/BRCA pathway. In addition, we found that the RUVBL1/2 complex physically interact with NEIL3 and function within the NEIL3 pathway in psoralen-ICL repair. Moreover, TRAIP is important for the recruitment of NEIL3 but not FANCD2, and knockdown of TRAIP promotes FA/BRCA pathway activation. Interestingly, TRAIP is non-epistatic with both NEIL3 and FA pathways in psoralen-ICL repair, suggesting that TRAIP may function upstream of the two pathways. Taken together, the NEIL3 pathway is the major pathway to repair psoralen-ICL through a unique DSB-free mechanism in human cells.
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Affiliation(s)
- Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Jing Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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30
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Vodicka P, Urbanova M, Makovicky P, Tomasova K, Kroupa M, Stetina R, Opattova A, Kostovcikova K, Siskova A, Schneiderova M, Vymetalkova V, Vodickova L. Oxidative Damage in Sporadic Colorectal Cancer: Molecular Mapping of Base Excision Repair Glycosylases in Colorectal Cancer Patients. Int J Mol Sci 2020; 21:E2473. [PMID: 32252452 DOI: 10.3390/ijms21072473] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress with subsequent premutagenic oxidative DNA damage has been implicated in colorectal carcinogenesis. The repair of oxidative DNA damage is initiated by lesion-specific DNA glycosylases (hOGG1, NTH1, MUTYH). The direct evidence of the role of oxidative DNA damage and its repair is proven by hereditary syndromes (MUTYH-associated polyposis, NTHL1-associated tumor syndrome), where germline mutations cause loss-of-function in glycosylases of base excision repair, thus enabling the accumulation of oxidative DNA damage and leading to the adenoma-colorectal cancer transition. Unrepaired oxidative DNA damage often results in G:C>T:A mutations in tumor suppressor genes and proto-oncogenes and widespread occurrence of chromosomal copy-neutral loss of heterozygosity. However, the situation is more complicated in complex and heterogeneous disease, such as sporadic colorectal cancer. Here we summarized our current knowledge of the role of oxidative DNA damage and its repair on the onset, prognosis and treatment of sporadic colorectal cancer. Molecular and histological tumor heterogeneity was considered. Our study has also suggested an additional important source of oxidative DNA damage due to intestinal dysbiosis. The roles of base excision repair glycosylases (hOGG1, MUTYH) in tumor and adjacent mucosa tissues of colorectal cancer patients, particularly in the interplay with other factors (especially microenvironment), deserve further attention. Base excision repair characteristics determined in colorectal cancer tissues reflect, rather, a disease prognosis. Finally, we discuss the role of DNA repair in the treatment of colon cancer, since acquired or inherited defects in DNA repair pathways can be effectively used in therapy.
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31
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Kim DV, Makarova AV, Miftakhova RR, Zharkov DO. Base Excision DNA Repair Deficient Cells: From Disease Models to Genotoxicity Sensors. Curr Pharm Des 2020; 25:298-312. [PMID: 31198112 DOI: 10.2174/1381612825666190319112930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022]
Abstract
Base excision DNA repair (BER) is a vitally important pathway that protects the cell genome from many kinds of DNA damage, including oxidation, deamination, and hydrolysis. It involves several tightly coordinated steps, starting from damaged base excision and followed by nicking one DNA strand, incorporating an undamaged nucleotide, and DNA ligation. Deficiencies in BER are often embryonic lethal or cause morbid diseases such as cancer, neurodegeneration, or severe immune pathologies. Starting from the early 1980s, when the first mammalian cell lines lacking BER were produced by spontaneous mutagenesis, such lines have become a treasure trove of valuable information about the mechanisms of BER, often revealing unexpected connections with other cellular processes, such as antibody maturation or epigenetic demethylation. In addition, these cell lines have found an increasing use in genotoxicity testing, where they provide increased sensitivity and representativity to cell-based assay panels. In this review, we outline current knowledge about BER-deficient cell lines and their use.
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Affiliation(s)
- Daria V Kim
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., Moscow 123182, Russian Federation
| | - Regina R Miftakhova
- Kazan Federal University, 18 Kremlevsakaya St., Kazan 420008, Russian Federation
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation.,SB RAS Institute of Chemical Biology and Fu ndamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russian Federation
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Cabral-Marques O, Schimke LF, de Oliveira EB, El Khawanky N, Ramos RN, Al-Ramadi BK, Segundo GRS, Ochs HD, Condino-Neto A. Flow Cytometry Contributions for the Diagnosis and Immunopathological Characterization of Primary Immunodeficiency Diseases With Immune Dysregulation. Front Immunol 2019; 10:2742. [PMID: 31849949 PMCID: PMC6889851 DOI: 10.3389/fimmu.2019.02742] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/08/2019] [Indexed: 12/24/2022] Open
Abstract
Almost 70 years after establishing the concept of primary immunodeficiency disorders (PIDs), more than 320 monogenic inborn errors of immunity have been identified thanks to the remarkable contribution of high-throughput genetic screening in the last decade. Approximately 40 of these PIDs present with autoimmune or auto-inflammatory symptoms as the primary clinical manifestation instead of infections. These PIDs are now recognized as diseases of immune dysregulation. Loss-of function mutations in genes such as FOXP3, CD25, LRBA, IL-10, IL10RA, and IL10RB, as well as heterozygous gain-of-function mutations in JAK1 and STAT3 have been reported as causative of these disorders. Identifying these syndromes has considerably contributed to expanding our knowledge on the mechanisms of immune regulation and tolerance. Although whole exome and whole genome sequencing have been extremely useful in identifying novel causative genes underlying new phenotypes, these approaches are time-consuming and expensive. Patients with monogenic syndromes associated with autoimmunity require faster diagnostic tools to delineate therapeutic strategies and avoid organ damage. Since these PIDs present with severe life-threatening phenotypes, the need for a precise diagnosis in order to initiate appropriate patient management is necessary. More traditional approaches such as flow cytometry are therefore a valid option. Here, we review the application of flow cytometry and discuss the relevance of this powerful technique in diagnosing patients with PIDs presenting with immune dysregulation. In addition, flow cytometry represents a fast, robust, and sensitive approach that efficiently uncovers new immunopathological mechanisms underlying monogenic PIDs.
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Affiliation(s)
- Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lena F Schimke
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, University of Freiburg, Freiburg im Breisgau, Germany
| | | | - Nadia El Khawanky
- Department of Hematology, Oncology and Stem Cell Transplantation, Freiburg University Medical Center, Freiburg im Breisgau, Germany.,Precision Medicine Theme, The South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia
| | - Rodrigo Nalio Ramos
- INSERM U932, SiRIC Translational Immunotherapy Team, Institut Curie, Paris Sciences et Lettres Research University, Paris, France
| | - Basel K Al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | | | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, United States
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Tirosh I, Spielman S, Barel O, Ram R, Stauber T, Paret G, Rubinsthein M, Pessach IM, Gerstein M, Anikster Y, Shukrun R, Dagan A, Adler K, Pode-Shakked B, Volkov A, Perelman M, Greenberger S, Somech R, Lahav E, Majmundar AJ, Padeh S, Hildebrandt F, Vivante A. Whole exome sequencing in childhood-onset lupus frequently detects single gene etiologies. Pediatr Rheumatol Online J 2019; 17:52. [PMID: 31362757 PMCID: PMC6668194 DOI: 10.1186/s12969-019-0349-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) comprise a diverse range of clinical manifestations. To date, more than 30 single gene causes of lupus/lupus like syndromes in humans have been identified. In the clinical setting, identifying the underlying molecular diagnosis is challenging due to phenotypic and genetic heterogeneity. METHODS We employed whole exome sequencing (WES) in patients presenting with childhood-onset lupus with severe and/or atypical presentations to identify cases that are explained by a single-gene (monogenic) cause. RESULTS From January 2015 to June 2018 15 new cases of childhood-onset SLE were diagnosed in Edmond and Lily Safra Children's Hospital. By WES we identified causative mutations in four subjects in five different genes: C1QC, SLC7A7, MAN2B1, PTEN and STAT1. No molecular diagnoses were established on clinical grounds prior to genetic testing. CONCLUSIONS We identified a significant fraction of monogenic SLE etiologies using WES and confirm the genetic locus heterogeneity in childhood-onset lupus. These results highlight the importance of establishing a genetic diagnosis for children with severe or atypical lupus by providing accurate and early etiology-based diagnoses and improving subsequent clinical management.
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Affiliation(s)
- Irit Tirosh
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0001 2107 2845grid.413795.dRheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shiri Spielman
- 0000 0001 2107 2845grid.413795.dRheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ortal Barel
- 0000 0001 2107 2845grid.413795.dThe Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Reut Ram
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel
| | - Tali Stauber
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics A Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gideon Paret
- 0000 0001 2107 2845grid.413795.dIntensive care unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Marina Rubinsthein
- 0000 0001 2107 2845grid.413795.dIntensive care unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Itai M. Pessach
- 0000 0001 2107 2845grid.413795.dIntensive care unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Maya Gerstein
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yair Anikster
- 0000 0001 2107 2845grid.413795.dMetabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Shukrun
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Adi Dagan
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Katerina Adler
- 0000 0001 2107 2845grid.413795.dThe Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ben Pode-Shakked
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0001 2107 2845grid.413795.dMetabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Alexander Volkov
- 0000 0001 2107 2845grid.413795.dPathology Department, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Marina Perelman
- 0000 0001 2107 2845grid.413795.dPathology Department, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shoshana Greenberger
- 0000 0001 2107 2845grid.413795.dDepartment of Dermatology, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Raz Somech
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics A Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Einat Lahav
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics A Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel ,0000 0001 2107 2845grid.413795.dNephrology Unit, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601 Ramat Gan, Israel
| | - Amar J. Majmundar
- 000000041936754Xgrid.38142.3cDivision of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Shai Padeh
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Friedhelm Hildebrandt
- 000000041936754Xgrid.38142.3cDivision of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel. .,Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel.
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Albelazi MS, Martin PR, Mohammed S, Mutti L, Parsons JL, Elder RH. The Biochemical Role of the Human NEIL1 and NEIL3 DNA Glycosylases on Model DNA Replication Forks. Genes (Basel) 2019; 10:genes10040315. [PMID: 31018584 PMCID: PMC6523847 DOI: 10.3390/genes10040315] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/22/2022] Open
Abstract
Endonuclease VIII-like (NEIL) 1 and 3 proteins eliminate oxidative DNA base damage and psoralen DNA interstrand crosslinks through initiation of base excision repair. Current evidence points to a DNA replication associated repair function of NEIL1 and NEIL3, correlating with induced expression of the proteins in S/G2 phases of the cell cycle. However previous attempts to express and purify recombinant human NEIL3 in an active form have been challenging. In this study, both human NEIL1 and NEIL3 have been expressed and purified from E. coli, and the DNA glycosylase activity of these two proteins confirmed using single- and double-stranded DNA oligonucleotide substrates containing the oxidative bases, 5-hydroxyuracil, 8-oxoguanine and thymine glycol. To determine the biochemical role that NEIL1 and NEIL3 play during DNA replication, model replication fork substrates were designed containing the oxidized bases at one of three specific sites relative to the fork. Results indicate that whilst specificity for 5- hydroxyuracil and thymine glycol was observed, NEIL1 acts preferentially on double-stranded DNA, including the damage upstream to the replication fork, whereas NEIL3 preferentially excises oxidized bases from single stranded DNA and within open fork structures. Thus, NEIL1 and NEIL3 act in concert to remove oxidized bases from the replication fork.
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Affiliation(s)
- Mustafa S Albelazi
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
| | - Peter R Martin
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
| | - Soran Mohammed
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
- Chemical Biology, Diagnostics and Therapeutics Group, Chemistry Faculty, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Luciano Mutti
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA.
| | - Jason L Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, 200 London Road, Liverpool L3 9TA, UK.
| | - Rhoderick H Elder
- Biomedical Research Centre, School of Environment and Life Sciences, Peel Building, University of Salford, Salford, M5 4NT, UK.
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Habibi S, Zaki-Dizaji M, Rafiemanesh H, Lo B, Jamee M, Gámez-Díaz L, Salami F, Kamali AN, Mohammadi H, Abolhassani H, Yazdani R, Aghamohammadi A, Anaya JM, Azizi G. Clinical, Immunologic, and Molecular Spectrum of Patients with LPS-Responsive Beige-Like Anchor Protein Deficiency: A Systematic Review. J Allergy Clin Immunol Pract 2019; 7:2379-2386.e5. [PMID: 30995531 DOI: 10.1016/j.jaip.2019.04.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND LPS-responsive beige-like anchor protein (LRBA) deficiency is a primary immunodeficiency and immune dysregulation syndrome caused by biallelic mutations in the LRBA gene. These mutations usually abrogate the protein expression of LRBA, leading to a broad spectrum of clinical phenotypes including autoimmunity, chronic diarrhea, hypogammaglobulinemia, and recurrent infections. OBJECTIVE Our aim was to systematically collect all studies reporting on the clinical manifestations, molecular and laboratory findings, and management of patients with LRBA deficiency. METHODS We searched in PubMed, Web of Science, and Scopus without any restrictions on study design and publication time. A total of 109 LRBA-deficient cases were identified from 45 eligible articles. For all patients, demographic information, clinical records, and immunologic and molecular data were collected. RESULTS Of the patients with LRBA deficiency, 93 had homozygous and 16 had compound heterozygous mutations in LRBA. The most common clinical manifestations were autoimmunity (82%), enteropathy (63%), splenomegaly (57%), and pneumonia (49%). Reduction in numbers of CD4+ T cells and regulatory T cells as well as IgG levels was recorded for 21.6%, 65.6%, and 54.2% of evaluated patients, respectively. B-cell subpopulation analysis revealed low numbers of switched-memory and increased numbers of CD21low B cells in 73.5% and 77.8% of patients, respectively. Eighteen (16%) patients underwent hematopoietic stem cell transplantation due to the severity of complications and the outcomes improved in 13 of them. CONCLUSIONS Autoimmune disorders are the main clinical manifestations of LRBA deficiency. Therefore, LRBA deficiency should be included in the list of monogenic autoimmune diseases, and screening for LRBA mutations should be routinely performed for patients with these conditions.
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Affiliation(s)
- Sima Habibi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Hosein Rafiemanesh
- Student Research Committee, Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bernice Lo
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
| | - Mahnaz Jamee
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran
| | - Laura Gámez-Díaz
- Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg im Breisgau, Germany
| | - Fereshte Salami
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali N Kamali
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Hamed Mohammadi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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Wu RA, Semlow DR, Kamimae-Lanning AN, Kochenova OV, Chistol G, Hodskinson MR, Amunugama R, Sparks JL, Wang M, Deng L, Mimoso CA, Low E, Patel KJ, Walter JC. TRAIP is a master regulator of DNA interstrand crosslink repair. Nature 2019; 567:267-272. [PMID: 30842657 PMCID: PMC6417926 DOI: 10.1038/s41586-019-1002-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/01/2019] [Indexed: 12/24/2022]
Abstract
Cells often use multiple pathways to repair the same DNA lesion, and the choice of pathway has substantial implications for the fidelity of genome maintenance. DNA interstrand crosslinks covalently link the two strands of DNA, and thereby block replication and transcription; the cytotoxicity of these crosslinks is exploited for chemotherapy. In Xenopus egg extracts, the collision of replication forks with interstrand crosslinks initiates two distinct repair pathways. NEIL3 glycosylase can cleave the crosslink1; however, if this fails, Fanconi anaemia proteins incise the phosphodiester backbone that surrounds the interstrand crosslink, generating a double-strand-break intermediate that is repaired by homologous recombination2. It is not known how the simpler NEIL3 pathway is prioritized over the Fanconi anaemia pathway, which can cause genomic rearrangements. Here we show that the E3 ubiquitin ligase TRAIP is required for both pathways. When two replisomes converge at an interstrand crosslink, TRAIP ubiquitylates the replicative DNA helicase CMG (the complex of CDC45, MCM2-7 and GINS). Short ubiquitin chains recruit NEIL3 through direct binding, whereas longer chains are required for the unloading of CMG by the p97 ATPase, which enables the Fanconi anaemia pathway. Thus, TRAIP controls the choice between the two known pathways of replication-coupled interstrand-crosslink repair. These results, together with our other recent findings3,4 establish TRAIP as a master regulator of CMG unloading and the response of the replisome to obstacles.
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Affiliation(s)
- R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Daniel R Semlow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Olga V Kochenova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Gheorghe Chistol
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Ravindra Amunugama
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Justin L Sparks
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Meng Wang
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Lin Deng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Emily Low
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ketan J Patel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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Al-Herz W, Chou J, Delmonte OM, Massaad MJ, Bainter W, Castagnoli R, Klein C, Bryceson YT, Geha RS, Notarangelo LD. Comprehensive Genetic Results for Primary Immunodeficiency Disorders in a Highly Consanguineous Population. Front Immunol 2019; 9:3146. [PMID: 30697212 PMCID: PMC6340972 DOI: 10.3389/fimmu.2018.03146] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/20/2018] [Indexed: 01/31/2023] Open
Abstract
Objective: To present the genetic causes of patients with primary immune deficiencies (PIDs) in Kuwait between 2004 and 2017. Methods: The data was obtained from the Kuwait National Primary Immunodeficiency Disorders Registry. Genomic DNA from patients with clinical and immunological features of PID was sequenced using Sanger sequencing (SS), next generation sequencing (NGS) of targeted genes, whole exome sequencing (WES), and/or whole genome sequencing (WGS). Functional assays were utilized to assess the biologic effect of identified variants. Fluorescence in situ hybridization (FISH) for 22q11.2 deletion and genomic hybridizations arrays were performed when thymic defects were suspected. Results: A total of 264 patients were registered during the study period with predominance of patients with immunodeficiencies affecting cellular and humoral immunity (35.2%), followed by combined immunodeficiencies with associated syndromic features (24%). Parental consanguinity and family history suggestive of PID were reported in 213 (81%) and 145 patients (55%), respectively. Genetic testing of 206 patients resulted in a diagnostic yield of 70%. Mutations were identified in 46 different genes and more than 90% of the reported genetic defects were transmitted by in an autosomal recessive pattern. The majority of the mutations were missense mutations (57%) followed by deletions and frame shift mutations. Five novel disease-causing genes were discovered. Conclusions: Genetic testing should be an integral part in the management of primary immunodeficiency patients. This will help the delivery of precision medicine and facilitate proper genetic counseling. Studying inbred populations using sophisticated diagnostic methods can allow better understanding of the genetics of primary immunodeficiency disorders.
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Affiliation(s)
- Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.,Allergy and Clinical Immunology Unit, Pediatric Department, Al-Sabah Hospital, Kuwait City, Kuwait
| | - Janet Chou
- Division of Immunology, Department of Pediatrics, Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Ottavia Maria Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michel J Massaad
- Department of Experimental Pathology, Immunology, and Microbiology, Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Wayne Bainter
- Division of Immunology, Department of Pediatrics, Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Riccardo Castagnoli
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.,Department of Pediatrics, University of Pavia, Foundation IRCCS Policlinico San Matteo, Pavia, Italy
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Yenan T Bryceson
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Raif S Geha
- Division of Immunology, Department of Pediatrics, Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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38
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Jørgensen SF, Fevang B, Aukrust P. Autoimmunity and Inflammation in CVID: a Possible Crosstalk between Immune Activation, Gut Microbiota, and Epigenetic Modifications. J Clin Immunol 2018; 39:30-36. [PMID: 30465180 DOI: 10.1007/s10875-018-0574-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022]
Abstract
Common variable immunodeficiency (CVID) is the most common symptomatic primary immunodeficiency among adults and is characterized by a B cell dysfunction and increased risk of respiratory tract infections with encapsulated bacteria. However, a large proportion of patients also has inflammatory and autoimmune complications. It may seem like a paradox that immunodeficiency and inflammation/autoimmunity coexist within the same individuals. In this commentary, we propose that CVID immunopathogenesis involves an interplay of genes, environmental factors, and dysregulation of immune cells, where gut microbiota and gastrointestinal inflammation can both be important contributors or endpoints to the systemic immune activation seen in CVID, and where epigenetic mechanism may be the undiscovered link between these contributors. In our opinion, these pathways could represent novel targets for therapy in CVID directed against autoimmune and inflammatory manifestations that represent the most severe complications in these patients. Considering the heterogeneous nature of CVID, these mechanisms may not be present in all patients, and different complications may be triggered by different risk factors. CVID is really a variable disease and in the future there is clearly a need for a more personalized medicine based on both genotypic and phenotypic findings.
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Affiliation(s)
- Silje F Jørgensen
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Nydalen, P.O. Box 4950, 0424, Oslo, Norway. .,Section of Clinical Immunology and Infectious Diseases, Department of Rheumatology, Dermatology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
| | - Børre Fevang
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Nydalen, P.O. Box 4950, 0424, Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Department of Rheumatology, Dermatology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Nydalen, P.O. Box 4950, 0424, Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Department of Rheumatology, Dermatology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
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39
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Zhou J, Chan J, Lambelé M, Yusufzai T, Stumpff J, Opresko PL, Thali M, Wallace SS. NEIL3 Repairs Telomere Damage during S Phase to Secure Chromosome Segregation at Mitosis. Cell Rep 2018; 20:2044-2056. [PMID: 28854357 DOI: 10.1016/j.celrep.2017.08.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/05/2017] [Accepted: 08/01/2017] [Indexed: 12/28/2022] Open
Abstract
Oxidative damage to telomere DNA compromises telomere integrity. We recently reported that the DNA glycosylase NEIL3 preferentially repairs oxidative lesions in telomere sequences in vitro. Here, we show that loss of NEIL3 causes anaphase DNA bridging because of telomere dysfunction. NEIL3 expression increases during S phase and reaches maximal levels in late S/G2. NEIL3 co-localizes with TRF2 and associates with telomeres during S phase, and this association increases upon oxidative stress. Mechanistic studies reveal that NEIL3 binds to single-stranded DNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner. Moreover, NEIL3 is recruited to telomeres through its interaction with TRF1, and this interaction enhances the enzymatic activity of purified NEIL3. Finally, we show that NEIL3 interacts with AP Endonuclease 1 (APE1) and the long-patch base excision repair proteins PCNA and FEN1. Taken together, we propose that NEIL3 protects genome stability through targeted repair of oxidative damage in telomeres during S/G2 phase.
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Affiliation(s)
- Jia Zhou
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jany Chan
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Marie Lambelé
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, College of Medicine, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Markus Thali
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
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40
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Dhande IS, Cranford SM, Zhu Y, Kneedler SC, Hicks MJ, Wenderfer SE, Braun MC, Doris PA. Susceptibility to Hypertensive Renal Disease in the Spontaneously Hypertensive Rat Is Influenced by 2 Loci Affecting Blood Pressure and Immunoglobulin Repertoire. Hypertension 2018; 71:700-708. [PMID: 29437896 DOI: 10.1161/hypertensionaha.117.10593] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/02/2017] [Accepted: 12/27/2017] [Indexed: 12/11/2022]
Abstract
High blood pressure exerts its deleterious effects on health largely through acceleration of end-organ diseases. Among these, progressive loss of renal function is particularly important, not only for the direct consequences of kidney damage but also because loss of renal function is associated with amplification of other adverse cardiovascular outcomes. Genetic susceptibility to hypertension and associated end-organ disease is non-Mendelian in both humans and in a rodent model, the spontaneously hypertensive rat (SHR). Here, we report that hypertensive end-organ disease in the inbred SHR-A3 line is attributable to genetic variation in the immunoglobulin heavy chain on chromosome 6. This variation coexists with variation in a 10 Mb block on chromosome 17 that contains genetic variation in 2 genes involved in immunoglobulin Fc receptor signaling. Substitution of these genomic regions into the SHR-A3 genome from the closely related, but injury-resistant, SHR-B2 line normalizes both biomarker and histological measures of renal injury. Our findings indicate that genetic variation leads to a contribution by immune mechanisms hypertensive end-organ injury and that, in this rat model, disease is influenced by differences in germ line antibody repertoire.
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Affiliation(s)
- Isha S Dhande
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX
| | - Stacy M Cranford
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX
| | - Yaming Zhu
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX
| | - Sterling C Kneedler
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX
| | - M John Hicks
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX
| | - Scott E Wenderfer
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX
| | - Michael C Braun
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX
| | - Peter A Doris
- From the Institute of Molecular Medicine, University of Texas HSC at Houston (I.S.D., S.M.C., Y.Z., S.C.K., P.A.D.); and Department of Pediatrics (S.E.W., M.C.B.) and Department of Pathology and Immunology (M.J.H.), Baylor College of Medicine, Houston, TX.
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41
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Ameratunga R, Woon ST, Bryant VL, Steele R, Slade C, Leung EY, Lehnert K. Clinical Implications of Digenic Inheritance and Epistasis in Primary Immunodeficiency Disorders. Front Immunol 2018; 8:1965. [PMID: 29434582 PMCID: PMC5790765 DOI: 10.3389/fimmu.2017.01965] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/19/2017] [Indexed: 12/16/2022] Open
Abstract
The existence of epistasis in humans was first predicted by Bateson in 1909. Epistasis describes the non-linear, synergistic interaction of two or more genetic loci, which can substantially modify disease severity or result in entirely new phenotypes. The concept has remained controversial in human genetics because of the lack of well-characterized examples. In humans, it is only possible to demonstrate epistasis if two or more genes are mutated. In most cases of epistasis, the mutated gene products are likely to be constituents of the same physiological pathway leading to severe disruption of a cellular function such as antibody production. We have recently described a digenic family, who carry mutations of TNFRSF13B/TACI as well as TCF3 genes. Both genes lie in tandem along the immunoglobulin isotype switching and secretion pathway. We have shown they interact in an epistatic way causing severe immunodeficiency and autoimmunity in the digenic proband. With the advent of next generation sequencing, it is likely other families with digenic inheritance will be identified. Since digenic inheritance does not always cause epistasis, we propose an epistasis index which may help quantify the effects of the two mutations. We also discuss the clinical implications of digenic inheritance and epistasis in humans with primary immunodeficiency disorders.
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Affiliation(s)
- Rohan Ameratunga
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand.,Department of Clinical Immunology, Auckland City Hospital, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand
| | - Vanessa L Bryant
- Department of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Richard Steele
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand
| | - Charlotte Slade
- Department of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Allergy and Clinical Immunology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Euphemia Yee Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Giardino G, De Luca M, Cirillo E, Palma P, Romano R, Valeriani M, Papetti L, Saunders C, Cancrini C, Pignata C. Two Brothers with Atypical UNC13D-Related Hemophagocytic Lymphohistiocytosis Characterized by Massive Lung and Brain Involvement. Front Immunol 2017; 8:1892. [PMID: 29312353 PMCID: PMC5742579 DOI: 10.3389/fimmu.2017.01892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/11/2017] [Indexed: 01/05/2023] Open
Abstract
Hemophagocytic lymphohistiocytosis (HLH) is a potentially fatal hyperinflammatory condition. Variants in different genes have been associated with the familial forms of the syndrome (FHL), usually presenting within the first 2 years of life. Due to increasing awareness of the signs and symptoms of HLH and a better understanding of the genetic basis of the disease, FHL has been increasingly diagnosed in patients presenting beyond infancy. Here, we report on two brothers with atypical, late-onset HLH in which whole exome sequencing revealed a homozygous pathogenic UNC13D variant. In the first brother, the clinical phenotype was dominated by a massive lung involvement. In the second brother a progressive neurological deterioration was observed. In both cases, the clinical manifestations at symptom onset were misleading, making the diagnosis difficult to achieve. This report expands the spectrum of clinical presentations of FLH3. Moreover, it highlights the importance to warn clinicians to keep a high level of suspicion in patients presenting with fever, cytopenia, splenomegaly of unknown origin, and unresponsiveness to conventional treatment even beyond early childhood. Moreover, this report emphasizes that insidious neurologic symptoms may represent the initial or sole presenting sign of FHL, even in the absence of peripheral signs of activation.
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Affiliation(s)
- Giuliana Giardino
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Maia De Luca
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Paolo Palma
- Research Unit in Congenital and Perinatal Infection, Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - Roberta Romano
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | | | - Laura Papetti
- Neurology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, United States.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States.,Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, United States
| | - Caterina Cancrini
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy.,Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
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43
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Klattenhoff AW, Thakur M, Chu CS, Ray D, Habib SL, Kidane D. Loss of NEIL3 DNA glycosylase markedly increases replication associated double strand breaks and enhances sensitivity to ATR inhibitor in glioblastoma cells. Oncotarget 2017; 8:112942-112958. [PMID: 29348879 PMCID: PMC5762564 DOI: 10.18632/oncotarget.22896] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/16/2017] [Indexed: 01/07/2023] Open
Abstract
DNA endonuclease eight-like glycosylase 3 (NEIL3) is one of the DNA glycosylases that removes oxidized DNA base lesions from single-stranded DNA (ssDNA) and non-B DNA structures. Approximately seven percent of human tumors have an altered NEIL3 gene. However, the role of NEIL3 in replication-associated repair and its impact on modulating treatment response is not known. Here, we report that NEIL3 is localized at the DNA double-strand break (DSB) sites during oxidative DNA damage and replication stress. Loss of NEIL3 significantly increased spontaneous replication-associated DSBs and recruitment of replication protein A (RPA). In contrast, we observed a marked decrease in Rad51 on nascent DNA strands at the replication fork, suggesting that HR-dependent repair is compromised in NEIL3-deficient cells. Interestingly, NEIL3-deficient cells were sensitive to ataxia–telangiectasia and Rad3 related protein (ATR) inhibitor alone or in combination with PARP1 inhibitor. This study elucidates the mechanism by which NEIL3 is critical to overcome oxidative and replication-associated genotoxic stress. Our findings may have important clinical implications to utilize ATR and PARP1 inhibitors to enhance cytotoxicity in tumors that carry altered levels of NEIL3.
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Affiliation(s)
- Alex W Klattenhoff
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, TX, United States
| | - Megha Thakur
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, TX, United States
| | - Christopher S Chu
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, TX, United States
| | - Debolina Ray
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, TX, United States
| | - Samy L Habib
- South Texas Veterans Health System and Department of Cellular and Structural Biology, The University of Texas Health Science Center, San Antonio, TX, United States
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, TX, United States
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Hoyos-Bachiloglu R, Chou J, Sodroski CN, Beano A, Bainter W, Angelova M, Al Idrissi E, Habazi MK, Alghamdi HA, Almanjomi F, Al Shehri M, Elsidig N, Alaa Eldin M, Knipe DM, AlZahrani M, Geha RS. A digenic human immunodeficiency characterized by IFNAR1 and IFNGR2 mutations. J Clin Invest 2017; 127:4415-4420. [PMID: 29106381 DOI: 10.1172/jci93486] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/14/2017] [Indexed: 01/29/2023] Open
Abstract
Primary immunodeficiencies are often monogenic disorders characterized by vulnerability to specific infectious pathogens. Here, we performed whole-exome sequencing of a patient with disseminated Mycobacterium abscessus, Streptococcus viridians bacteremia, and cytomegalovirus (CMV) viremia and identified mutations in 2 genes that regulate distinct IFN pathways. The patient had a homozygous frameshift deletion in IFNGR2, which encodes the signal transducing chain of the IFN-γ receptor, that resulted in minimal protein expression and abolished downstream signaling. The patient also harbored a homozygous deletion in IFNAR1 (IFNAR1*557Gluext*46), which encodes the IFN-α receptor signaling subunit. The IFNAR1*557Gluext*46 resulted in replacement of the stop codon with 46 additional codons at the C-terminus. The level of IFNAR1*557Gluext*46 mutant protein expressed in patient fibroblasts was comparable to levels of WT IFNAR1 in control fibroblasts. IFN-α-induced signaling was impaired in the patient fibroblasts, as evidenced by decreased STAT1/STAT2 phosphorylation, nuclear translocation of STAT1, and expression of IFN-α-stimulated genes critical for CMV immunity. Pretreatment with IFN-α failed to suppress CMV protein expression in patient fibroblasts, whereas expression of WT IFNAR1 restored IFN-α-mediated suppression of CMV. This study identifies a human IFNAR1 mutation and describes a digenic immunodeficiency specific to type I and type II IFNs.
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Affiliation(s)
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, and
| | - Catherine N Sodroski
- Department of Microbiology and Immunobiology and Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Abdallah Beano
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, and
| | - Wayne Bainter
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, and
| | - Magdalena Angelova
- Department of Microbiology and Immunobiology and Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eman Al Idrissi
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Murad K Habazi
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Fahd Almanjomi
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Mohamed Al Shehri
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Nagi Elsidig
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Morsi Alaa Eldin
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - David M Knipe
- Department of Microbiology and Immunobiology and Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mofareh AlZahrani
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, and
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Abstract
PURPOSE OF REVIEW Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease known for its clinical heterogeneity. Over time, new insights into the complex genetic origin of SLE have started to explain some of this clinical variability. These findings, reviewed here, have also yielded important understanding in the immune mechanisms behind SLE pathogenesis. RECENT FINDINGS Several new monogenic disorders with lupus-like phenotype have been described. These can be organized into physiologic pathways that parallel mechanisms of disease in SLE. Examples include genes important for DNA damage repair (e.g., TREX1), nucleic acid sensing and type I interferon overproduction (e.g., STING, TREX1), apoptosis (FASLG), tolerance (PRKCD), and clearance of self-antigen (DNASE1L3). Further study of monogenic lupus may lead to better genotype/phenotype correlations in SLE. Eventually, the ability to understand individual patients according to their genetic profile may allow the development of more targeted and personalized approaches to therapy.
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Affiliation(s)
- Mindy S Lo
- Division of Immunology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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46
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Alroqi FJ, Charbonnier LM, Keles S, Ghandour F, Mouawad P, Sabouneh R, Mohammed R, Almutairi A, Chou J, Massaad MJ, Geha RS, Baz Z, Chatila TA. DOCK8 Deficiency Presenting as an IPEX-Like Disorder. J Clin Immunol 2017; 37:811-819. [PMID: 29058101 DOI: 10.1007/s10875-017-0451-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/09/2017] [Indexed: 12/13/2022]
Abstract
PURPOSE The dedicator of cytokinesis 8 (DOCK8) deficiency is an autosomal recessive-combined immunodeficiency whose clinical spectra include recurrent infections, autoimmunity, malignancies, elevated serum IgE, eczema, and food allergies. Here, we report on patients with loss of function DOCK8 mutations with profound immune dysregulation suggestive of an immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX)-like disorder. METHODS Immunophenotyping of lymphocyte subpopulations and analysis of DOCK8 protein expression were evaluated by flow cytometry. T regulatory (Treg) cells were isolated by cell sorting, and their suppressive activity was analyzed by flow cytometry. Gene mutational analysis was performed by whole-exome and Sanger sequencing. RESULTS Patient 1 (P1) presented at 10 months of age with chronic severe diarrhea and active colitis in the absence of an infectious trigger, severe eczema with elevated serum IgE, and autoimmune hemolytic anemia, suggestive of an IPEX-related disorder. Whole-exome sequencing revealed a homozygous nonsense mutation in DOCK8 at the DOCK-homology region (DHR)-1 (c.1498C>T; p. R500X). Patient P2, a cousin of P1 who carries the same DOCK8 nonsense mutation, presented with eczema and recurrent ear infections in early infancy, and she developed persistent diarrhea by 3 years of age. Patient P3 presented with lymphoproliferation, severe eczema with allergic dysregulation, and chronic diarrhea with colitis. She harbored a homozygous loss of function DOCK8 mutation (c.2402 -1G→A). Treg cell function was severely compromised by both DOCK8 mutations. CONCLUSION DOCK8 deficiency may present severe immune dysregulation with features that may overlap with those of IPEX and other IPEX-like disorders.
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Affiliation(s)
- Fayhan J Alroqi
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Karp Family Building, Room 10-214. 1 Blackfan Street, Boston, MA, 02115, USA
- Department of Pediatrics, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Karp Family Building, Room 10-214. 1 Blackfan Street, Boston, MA, 02115, USA
| | - Sevgi Keles
- Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Konya, Turkey
| | - Fatima Ghandour
- Department of Pathology, St George Hospital University Medical Center, Beirut, Lebanon
| | - Pierre Mouawad
- Department of Pediatrics, St George Hospital University Medical Center, Beirut, Lebanon
| | - Rami Sabouneh
- Department of Pediatrics, St George Hospital University Medical Center, Beirut, Lebanon
| | - Reem Mohammed
- Department of Pediatrics, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abduarahman Almutairi
- Department of Pediatrics, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Karp Family Building, Room 10-214. 1 Blackfan Street, Boston, MA, 02115, USA
| | - Michel J Massaad
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Karp Family Building, Room 10-214. 1 Blackfan Street, Boston, MA, 02115, USA
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Karp Family Building, Room 10-214. 1 Blackfan Street, Boston, MA, 02115, USA
| | - Zeina Baz
- Department of Pediatrics, St George Hospital University Medical Center, Beirut, Lebanon
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Karp Family Building, Room 10-214. 1 Blackfan Street, Boston, MA, 02115, USA.
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Ameratunga R, Koopmans W, Woon ST, Leung E, Lehnert K, Slade CA, Tempany JC, Enders A, Steele R, Browett P, Hodgkin PD, Bryant VL. Epistatic interactions between mutations of TACI ( TNFRSF13B) and TCF3 result in a severe primary immunodeficiency disorder and systemic lupus erythematosus. Clin Transl Immunology 2017; 6:e159. [PMID: 29114388 PMCID: PMC5671988 DOI: 10.1038/cti.2017.41] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 07/21/2017] [Accepted: 07/21/2017] [Indexed: 12/22/2022] Open
Abstract
Common variable immunodeficiency disorders (CVID) are a group of primary immunodeficiencies where monogenetic causes account for only a fraction of cases. On this evidence, CVID is potentially polygenic and epistatic although there are, as yet, no examples to support this hypothesis. We have identified a non-consanguineous family, who carry the C104R (c.310T>C) mutation of the Transmembrane Activator Calcium-modulator and cyclophilin ligand Interactor (TACI, TNFRSF13B) gene. Variants in TNFRSF13B/TACI are identified in up to 10% of CVID patients, and are associated with, but not solely causative of CVID. The proband is heterozygous for the TNFRSF13B/TACI C104R mutation and meets the Ameratunga et al. diagnostic criteria for CVID and the American College of Rheumatology criteria for systemic lupus erythematosus (SLE). Her son has type 1 diabetes, arthritis, reduced IgG levels and IgA deficiency, but has not inherited the TNFRSF13B/TACI mutation. Her brother, homozygous for the TNFRSF13B/TACI mutation, is in good health despite profound hypogammaglobulinemia and mild cytopenias. We hypothesised that a second unidentified mutation contributed to the symptomatic phenotype of the proband and her son. Whole-exome sequencing of the family revealed a de novo nonsense mutation (T168fsX191) in the Transcription Factor 3 (TCF3) gene encoding the E2A transcription factors, present only in the proband and her son. We demonstrate mutations of TNFRSF13B/TACI impair immunoglobulin isotype switching and antibody production predominantly via T-cell-independent signalling, while mutations of TCF3 impair both T-cell-dependent and -independent pathways of B-cell activation and differentiation. We conclude that epistatic interactions between mutations of the TNFRSF13B/TACI and TCF3 signalling networks lead to the severe CVID-like disorder and SLE in the proband.
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Affiliation(s)
- Rohan Ameratunga
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand.,Department of Clinical Immunology, Auckland City Hospital, Auckland, New Zealand
| | - Wikke Koopmans
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand
| | - Euphemia Leung
- Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Charlotte A Slade
- Department of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Department of Allergy and Clinical Immunology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Jessica C Tempany
- Department of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Anselm Enders
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research and Centre for Personalised Immunology, Australian National University, Canberra, ACT, Australia
| | - Richard Steele
- Department of Virology and Immunology, Auckland City Hospital, Auckland, New Zealand
| | - Peter Browett
- Department of Hematology, LabPlus, Auckland City Hospital, Auckland, New Zealand.,Department of Molecular Medicine, and Pathology University of Auckland, Auckland, New Zealand
| | - Philip D Hodgkin
- Department of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Vanessa L Bryant
- Department of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Department of Allergy and Clinical Immunology, Royal Melbourne Hospital, Parkville, VIC, Australia
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Chinen J, Badran YR, Geha RS, Chou JS, Fried AJ. Advances in basic and clinical immunology in 2016. J Allergy Clin Immunol 2017; 140:959-973. [DOI: 10.1016/j.jaci.2017.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/22/2017] [Indexed: 10/19/2022]
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Seleman M, Hoyos-Bachiloglu R, Geha RS, Chou J. Uses of Next-Generation Sequencing Technologies for the Diagnosis of Primary Immunodeficiencies. Front Immunol 2017; 8:847. [PMID: 28791010 PMCID: PMC5522848 DOI: 10.3389/fimmu.2017.00847] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/05/2017] [Indexed: 12/11/2022] Open
Abstract
Primary immunodeficiencies (PIDs) are genetic disorders impairing host immunity, leading to life-threatening infections, autoimmunity, and/or malignancies. Genomic technologies have been critical for expediting the discovery of novel genetic defects underlying PIDs, expanding our knowledge of the complex clinical phenotypes associated with PIDs, and in shifting paradigms of PID pathogenesis. Once considered Mendelian, monogenic, and completely penetrant disorders, genomic studies have redefined PIDs as a heterogeneous group of diseases found in the global population that may arise through multigenic defects, non-germline transmission, and with variable penetrance. This review examines the uses of next-generation DNA sequencing (NGS) in the diagnosis of PIDs. While whole genome sequencing identifies variants throughout the genome, whole exome sequencing sequences only the protein-coding regions within a genome, and targeted gene panels sequence only a specific cohort of genes. The advantages and limitations of each sequencing approach are compared. The complexities of variant interpretation and variant validation remain the major challenge in wide-spread implementation of these technologies. Lastly, the roles of NGS in newborn screening and precision therapeutics for individuals with PID are also addressed.
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Affiliation(s)
- Michael Seleman
- Division of Immunology, Boston Children's Hospital, Boston, MA, United States
| | | | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Boston, MA, United States
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Boston, MA, United States
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50
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Al-Mousa H, Al-Saud B. Primary Immunodeficiency Diseases in Highly Consanguineous Populations from Middle East and North Africa: Epidemiology, Diagnosis, and Care. Front Immunol 2017; 8:678. [PMID: 28694805 PMCID: PMC5483440 DOI: 10.3389/fimmu.2017.00678] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/24/2017] [Indexed: 12/27/2022] Open
Abstract
Middle East and North Africa region (MENA)1 populations are of different ethnic origins. Consanguineous marriages are common practice with an overall incidence ranging between 20 and 50%. Primary immunodeficiency diseases (PIDs) are a group of heterogeneous genetic disorders caused by defects in the immune system that predisposes patients to recurrent infections, autoimmune diseases, and malignancies. PIDs are more common in areas with high rates of consanguineous marriage since most have an autosomal recessive mode of inheritance. Studies of PIDs in the region had contributed into the discovery and the understanding of several novel immunodeficiency disorders. Few MENA countries have established national registries that helped in estimating the prevalence and defining common PID phenotypes. Available reports from those registries suggest a predominance of combined immunodeficiency disorders in comparison to antibody deficiencies seen in other populations. Access to a comprehensive clinical immunology management services is limited in most MENA countries. Few countries had established advanced clinical immunology service, capable to provide extensive genetic testing and stem cell transplantation for various immunodeficiency disorders. Newborn screening for PIDs is an essential need in this population considering the high incidence of illness and can be implemented and incorporated into existing newborn screening programs in some MENA countries. Increased awareness, subspecialty training in clinical immunology, and establishing collaborating research centers are necessary to improve patient care. In this review, we highlight some of the available epidemiological data, challenges in establishing diagnosis, and available therapy for PID patients in the region.
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Affiliation(s)
- Hamoud Al-Mousa
- Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.,Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Bandar Al-Saud
- Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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