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Nandiwada SL. Overview of human B-cell development and antibody deficiencies. J Immunol Methods 2023:113485. [PMID: 37150477 DOI: 10.1016/j.jim.2023.113485] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
B cells are a key component of the humoral (antibody-mediated) immune response which is responsible for defense against a variety of pathogens. Here we provide an overview of the current understanding of B cell development and function and briefly describe inborn errors of immunity associated with B cell development defects which can manifest as immune deficiency, malignancy, autoimmunity, or allergy. The knowledge and application of B cell biology are essential for laboratory evaluation and clinical assessment of these B cell disorders.
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Affiliation(s)
- Sarada L Nandiwada
- The Texas Children's Hospital, Section of Immunology, Allergy, and Retrovirology, Baylor College of Medicine, Houston, TX, United States.
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2
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Gullickson P, Xu YW, Niedernhofer LJ, Thompson EL, Yousefzadeh MJ. The Role of DNA Repair in Immunological Diversity: From Molecular Mechanisms to Clinical Ramifications. Front Immunol 2022; 13:834889. [PMID: 35432317 PMCID: PMC9010869 DOI: 10.3389/fimmu.2022.834889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/02/2022] [Indexed: 12/18/2022] Open
Abstract
An effective humoral immune response necessitates the generation of diverse and high-affinity antibodies to neutralize pathogens and their products. To generate this assorted immune repertoire, DNA damage is introduced at specific regions of the genome. Purposeful genotoxic insults are needed for the successful completion of multiple immunological diversity processes: V(D)J recombination, class-switch recombination, and somatic hypermutation. These three processes, in concert, yield a broad but highly specific immune response. This review highlights the importance of DNA repair mechanisms involved in each of these processes and the catastrophic diseases that arise from DNA repair deficiencies impacting immune system function. These DNA repair disorders underline not only the importance of maintaining genomic integrity for preventing disease but also for robust adaptive immunity.
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3
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Chansel-Da Cruz M, Hohl M, Ceppi I, Kermasson L, Maggiorella L, Modesti M, de Villartay JP, Ileri T, Cejka P, Petrini JHJ, Revy P. A Disease-Causing Single Amino Acid Deletion in the Coiled-Coil Domain of RAD50 Impairs MRE11 Complex Functions in Yeast and Humans. Cell Rep 2020; 33:108559. [PMID: 33378670 PMCID: PMC7788285 DOI: 10.1016/j.celrep.2020.108559] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/30/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
The MRE11-RAD50-NBS1 complex plays a central role in response to DNA double-strand breaks. Here, we identify a patient with bone marrow failure and developmental defects caused by biallelic RAD50 mutations. One of the mutations creates a null allele, whereas the other (RAD50E1035Δ) leads to the loss of a single residue in the heptad repeats within the RAD50 coiled-coil domain. This mutation represents a human RAD50 separation-of-function mutation that impairs DNA repair, DNA replication, and DNA end resection without affecting ATM-dependent DNA damage response. Purified recombinant proteins indicate that RAD50E1035Δ impairs MRE11 nuclease activity. The corresponding mutation in Saccharomyces cerevisiae causes severe thermosensitive defects in both DNA repair and Tel1ATM-dependent signaling. These findings demonstrate that a minor heptad break in the RAD50 coiled coil suffices to impede MRE11 complex functions in human and yeast. Furthermore, these results emphasize the importance of the RAD50 coiled coil to regulate MRE11-dependent DNA end resection in humans.
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Affiliation(s)
- Marie Chansel-Da Cruz
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France; Genomic Vision, R&D Innovation Department, Bagneux, France
| | - Marcel Hohl
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Laëtitia Kermasson
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | | | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Jean-Pierre de Villartay
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Talia Ileri
- Ankara University School of Medicine, Pediatric Hematology and Oncology, Ankara, Turkey
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - John H J Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée la Ligue contre le Cancer, Paris, France; University of Paris-Sorbonne Paris Cité University, Imagine Institute, Paris, France.
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4
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Alos L, Fuster C, Castillo P, Jares P, Garcia-Herrera A, Marginet M, Agreda F, Arance A, Gonzalvo E, Garcia M, Puig S, Teixido C. TP53 mutation and tumoral PD-L1 expression are associated with depth of invasion in desmoplastic melanomas. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1218. [PMID: 33178750 PMCID: PMC7607103 DOI: 10.21037/atm-20-1846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background Desmoplastic melanoma (DM) is a rare subtype of spindle cell malignant melanoma characterized by frequent local recurrences and hematogenous spread, but without molecular classification. The aim of the study was to investigate in a DM series the incidence of relevant gene alterations in cancer, the programmed death-ligand 1 (PD-L1) expression status and the association with clinicopathological features and melanoma progression. Methods A total of 38 patients were included. Clinical follow-up and the histopathological features of all cases were retrospectively collected. PD-L1 expression by immunohistochemistry (IHC) and BRAF genomic alterations by real-time PCR were determined in 34 samples. Additionally, a molecular analysis by next-generation sequencing was performed in 25 DMs. Results Tumors occurred predominantly in men (76%) and in the head and neck region (50%). Most tumors were pure DMs (66%), containing less than 10% of conventional melanoma. Overall, 48% of our cohort harbored TP53 mutations, most of them showing a molecular signature associated with ultraviolet (UV)-oncogenesis, and 29%, BRAF mutations. A positive correlation between TP53 with depth of invasion (P=0.005) and presence of elastosis (P=0.002) was found. High-expression of PD-L1 in tumor cells was observed in 38% of cases and correlated with depth of tumoral infiltration (P=0.003), TP53 (P=0.016), PD-1 (P<0.001) and tumor-infiltrating lymphocytes (TILS) (P<0.001). PD-L1 expression in immune cells correlated with PD-1 (P=0.006), tumoral PD-L1 expression (P=0.029) and TP53 mutation (P=0.002). Survival correlated with depth of invasion (P=0.003), stage of tumors (P=0.015), positive sentinel lymph node (P=0.004), lymph node metastasis (P=0.024) and distant metastasis (P<0.001). Conclusions Our results suggest that progressed DMs with deep tumoral infiltration frequently harbor TP53 mutations, PD-L1 expression and present a high inflammatory response, probably related to adaptive immune resistance in this tumor-type.
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Affiliation(s)
- Llucia Alos
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Carla Fuster
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Paola Castillo
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Adriana Garcia-Herrera
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Marta Marginet
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Fernando Agreda
- Department of Urological Surgery, Hospital Trias I Pujol, Carretera de Canyet, Badalona, Spain
| | - Ana Arance
- Department of Medical Oncology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Elena Gonzalvo
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Mireia Garcia
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Susana Puig
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.,Department of Dermatology, Hospital Clínic of Barcelona, Barcelona, Spain
| | - Cristina Teixido
- Department of Pathology, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain.,August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
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5
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Ragu S, Matos-Rodrigues G, Lopez BS. Replication Stress, DNA Damage, Inflammatory Cytokines and Innate Immune Response. Genes (Basel) 2020; 11:E409. [PMID: 32283785 PMCID: PMC7230342 DOI: 10.3390/genes11040409] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/21/2022] Open
Abstract
Complete and accurate DNA replication is essential to genome stability maintenance during cellular division. However, cells are routinely challenged by endogenous as well as exogenous agents that threaten DNA stability. DNA breaks and the activation of the DNA damage response (DDR) arising from endogenous replication stress have been observed at pre- or early stages of oncogenesis and senescence. Proper detection and signalling of DNA damage are essential for the autonomous cellular response in which the DDR regulates cell cycle progression and controls the repair machinery. In addition to this autonomous cellular response, replicative stress changes the cellular microenvironment, activating the innate immune response that enables the organism to protect itself against the proliferation of damaged cells. Thereby, the recent descriptions of the mechanisms of the pro-inflammatory response activation after replication stress, DNA damage and DDR defects constitute important conceptual novelties. Here, we review the links of replication, DNA damage and DDR defects to innate immunity activation by pro-inflammatory paracrine effects, highlighting the implications for human syndromes and immunotherapies.
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Affiliation(s)
| | | | - Bernard S. Lopez
- Institut Cochin, INSERM U1016, UMR 8104 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, 24 rue du Faubourg St Jacques, 75014 Paris, France; (S.R.); (G.M.-R.)
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6
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Keenan CR, Allan RS. Epigenomic drivers of immune dysfunction in aging. Aging Cell 2019; 18:e12878. [PMID: 30488545 PMCID: PMC6351880 DOI: 10.1111/acel.12878] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 12/17/2022] Open
Abstract
Aging inevitably leads to reduced immune function, leaving the elderly more susceptible to infections, less able to respond to pathogen challenges, and less responsive to preventative vaccinations. No cell type is exempt from the ravages of age, and extensive studies have found age-related alterations in the frequencies and functions of both stem and progenitor cells, as well as effector cells of both the innate and adaptive immune systems. The intrinsic functional reduction in immune competence is also associated with low-grade chronic inflammation, termed "inflamm-aging," which further perpetuates immune dysfunction. While many of these age-related cellular changes are well characterized, understanding the molecular changes that underpin the functional decline has proven more difficult. Changes in chromatin are increasingly appreciated as a causative mechanism of cellular and organismal aging across species. These changes include increased genomic instability through loss of heterochromatin and increased DNA damage, telomere attrition, and epigenetic alterations. In this review, we discuss the connections between chromatin, immunocompetence, and the loss of function associated with mammalian immune aging. Through understanding the molecular events which underpin the phenotypic changes observed in the aged immune system, it is hoped that the aged immune system can be restored to provide youthful immunity once more.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
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7
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Abstract
PURPOSE OF REVIEW Natural killer cells are innate lymphoid cells (ILCs) that play critical roles in human host defense and are especially useful in combating viral pathogens and malignancy. RECENT FINDINGS The NK cell deficiency (NKD) is particularly underscored in patients with a congenital immunodeficiency in which NK cell development or function is affected. The classical NK cell deficiency (cNKD) is a result of absent or a profound decrease in the number of circulating NK cells. In contrast, functional NKD (fNKD) is characterized by abnormal NK cell function but with normal number of NK cells. The combined immune deficiencies with significant impact on NK cells are not considered classical or functional NK cell deficiencies. In these disorders, the impairment of NK cells represents an important aspect of the overall immunodeficiency. In turn, this leads to improved insights on the NK cell development and function. Here, we detail the NK cell biology based upon recent natural killer cell defects described in combined immune deficiencies.
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8
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The therapeutic significance of mutational signatures from DNA repair deficiency in cancer. Nat Commun 2018; 9:3292. [PMID: 30120226 PMCID: PMC6098043 DOI: 10.1038/s41467-018-05228-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
Cancer is fundamentally a disease of the genome and inherited deficiencies in DNA repair pathways are well established to increase lifetime cancer risk. Computational analysis of pan-cancer data has identified signatures of mutational processes thought to be responsible for the pattern of mutations in any given cancer. These analyses identified altered DNA repair pathways in a much broader spectrum of cancers than previously appreciated with significant therapeutic implications. The development of DNA repair deficiency biomarkers is critical to the implementation of therapeutic targeting of repair-deficient tumors, using either DNA damaging agents or immunotherapy for the personalization of cancer therapy. Targeting DNA repair-deficient tumors is one of the most promising therapeutic strategies in cancer research; however, accurately predicting which tumors will respond can be a challenge. Here the authors present a review of the current state of knowledge in DNA repair deficiency across human cancers.
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9
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Li KP, Shanmuganad S, Carroll K, Katz JD, Jordan MB, Hildeman DA. Dying to protect: cell death and the control of T-cell homeostasis. Immunol Rev 2017; 277:21-43. [PMID: 28462527 PMCID: PMC5416827 DOI: 10.1111/imr.12538] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 02/23/2017] [Accepted: 02/26/2017] [Indexed: 02/07/2023]
Abstract
T cells play a critical role in immune responses as they specifically recognize peptide/MHC complexes with their T-cell receptors and initiate adaptive immune responses. While T cells are critical for performing appropriate effector functions and maintaining immune memory, they also can cause autoimmunity or neoplasia if misdirected or dysregulated. Thus, T cells must be tightly regulated from their development onward. Maintenance of appropriate T-cell homeostasis is essential to promote protective immunity and limit autoimmunity and neoplasia. This review will focus on the role of cell death in maintenance of T-cell homeostasis and outline novel therapeutic strategies tailored to manipulate cell death to limit T-cell survival (eg, autoimmunity and transplantation) or enhance T-cell survival (eg, vaccination and immune deficiency).
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Affiliation(s)
- Kun-Po Li
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sharmila Shanmuganad
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Kaitlin Carroll
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Jonathan D. Katz
- Division of Immunobiology, Cincinnati, OH 45229, USA
- Division of Endocrinology, Diabetes Research Center, Cincinnati, OH 45229, USA
| | - Michael B. Jordan
- Division of Immunobiology, Cincinnati, OH 45229, USA
- Division of Bone Marrow Transplantation and Immune Deficiency, Department of Pediatrics, Cincinnati Children’s Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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10
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Govindaraj GM, Karuthedath Vellarikkal S, Jayarajan R, Ravi R, Verma A, Chakkiyar K, Jayakrishnan MP, Arakkal R, Raj R, Kunnaruvath R, Sivasubbu S, Scaria V. Case Report: Whole exome sequencing identifies variation c.2308G>A p.E770K in RAG1 associated with B- T- NK+ severe combined immunodeficiency. F1000Res 2016; 5:2532. [PMID: 29067161 PMCID: PMC5635439 DOI: 10.12688/f1000research.9473.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2017] [Indexed: 11/20/2022] Open
Abstract
Severe combined immunodeficiency is a large clinically heterogeneous group of disorders caused by a defect in the development of humoral or cellular immune responses. At least 13 genes are known to be involved in the pathophysiology of the disease and the mutation spectrum in SCID has been well documented. Mutations of the recombination-activating genes RAG 1 and RAG 2 are associated with a range of clinical presentations including, severe combined immunodeficiency and autoimmunity. Recently, our understanding of the molecular basis of immune dysfunction in RAG deficiency has improved tremendously with newer insights into the ultrastructure of the RAG complex. In this report, we describe the application of whole exome sequencing for arriving at a molecular diagnosis in a child suffering from B- T- NK+ severe combined immunodeficiency. Apart from making the accurate molecular diagnosis, we also add a genetic variation c.2308G>A p.E770K to the compendium of variations associated with the disease.
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Affiliation(s)
- Geeta Madathil Govindaraj
- Department of Pediatrics, Institute of Maternal and Child Health, Government Medical College, Kozhikode, India
| | - Shamsudheen Karuthedath Vellarikkal
- Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Delhi, India.,Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Rowmika Ravi
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Ankit Verma
- Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Krishnan Chakkiyar
- Department of Pediatrics, Institute of Maternal and Child Health, Government Medical College, Kozhikode, India
| | | | - Riyaz Arakkal
- Department of Pediatrics, Institute of Maternal and Child Health, Government Medical College, Kozhikode, India
| | | | | | - Sridhar Sivasubbu
- Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Delhi, India.,Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Delhi, India.,GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India
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11
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Nagel ZD, Chaim IA, Samson LD. Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research. DNA Repair (Amst) 2014; 19:199-213. [PMID: 24780560 DOI: 10.1016/j.dnarep.2014.03.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Why does a constant barrage of DNA damage lead to disease in some individuals, while others remain healthy? This article surveys current work addressing the implications of inter-individual variation in DNA repair capacity for human health, and discusses the status of DNA repair assays as potential clinical tools for personalized prevention or treatment of disease. In particular, we highlight research showing that there are significant inter-individual variations in DNA repair capacity (DRC), and that measuring these differences provides important biological insight regarding disease susceptibility and cancer treatment efficacy. We emphasize work showing that it is important to measure repair capacity in multiple pathways, and that functional assays are required to fill a gap left by genome wide association studies, global gene expression and proteomics. Finally, we discuss research that will be needed to overcome barriers that currently limit the use of DNA repair assays in the clinic.
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Affiliation(s)
- Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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12
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Dhingra N, Yadav SP, de Villartay JP, Picard C, Sabharwal RK, Dinand V, Ghuman SS, Sachdeva A. Severe combined immunodeficiency caused by a new homozygous RAG1 mutation with progressive encephalopathy. Hematol Oncol Stem Cell Ther 2013; 7:44-9. [PMID: 24333136 DOI: 10.1016/j.hemonc.2013.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 10/31/2013] [Accepted: 11/18/2013] [Indexed: 10/25/2022] Open
Abstract
We describe an unusual case of severe combined immunodeficiency (SCID) with neutropenia and central nervous system (CNS) manifestations in which a novel RAG1 mutation was identified. A 15-month-old boy presented with failure to thrive, neutropenia and recurrent infections. He was diagnosed with T-B-NK+ SCID. He subsequently developed right partial seizures with ipsilateral hemiparesis and became comatose. Magnetic resonance imaging (MRI) of the brain revealed an inflammatory lesion in the left thalamus which later progressed to diffuse meningo-encephalitis on serial imaging. No CNS infection was documented. Genetic work-up in the child revealed a novel homozygous deleterious mutation in the RAG1 gene (c:2881T>C; p:I794T), for which both parents were heterozygous. He underwent a haploidentical bone marrow transplant without conditioning and died on day +35 with no improvement in his neurological status. The features of neutropenia and progressive encephalopathy could be linked to the novel genetic defect but more data is required to establish this conclusively.
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Affiliation(s)
- Nivedita Dhingra
- Division of Pediatric Hematology-Oncology and Bone Marrow Transplantation, Sir Ganga Ram Hospital, New Delhi, India
| | - Satya Prakash Yadav
- Division of Pediatric Hematology-Oncology and Bone Marrow Transplantation, Sir Ganga Ram Hospital, New Delhi, India.
| | | | - Capucine Picard
- Centre d'Étude des Déficits Immunitaires, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - R K Sabharwal
- Pediatric Neurology Unit, Department of Pediatrics, Sir Ganga Ram Hospital, New Delhi, India
| | - Veronique Dinand
- Division of Pediatric Hematology-Oncology and Bone Marrow Transplantation, Sir Ganga Ram Hospital, New Delhi, India
| | | | - Anupam Sachdeva
- Division of Pediatric Hematology-Oncology and Bone Marrow Transplantation, Sir Ganga Ram Hospital, New Delhi, India
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13
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Brachner A, Braun J, Ghodgaonkar M, Castor D, Zlopaša L, Ehrlich V, Jiricny J, Gotzmann J, Knasmüller S, Foisner R. The endonuclease Ankle1 requires its LEM and GIY-YIG motifs for DNA cleavage in vivo. J Cell Sci 2012; 125:1048-57. [PMID: 22399800 PMCID: PMC4335191 DOI: 10.1242/jcs.098392] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The LEM domain (for lamina-associated polypeptide, emerin, MAN1 domain) defines a group of nuclear proteins that bind chromatin through interaction of the LEM motif with the conserved DNA crosslinking protein, barrier-to-autointegration factor (BAF). Here, we describe a LEM protein annotated in databases as 'Ankyrin repeat and LEM domain-containing protein 1' (Ankle1). We show that Ankle1 is conserved in metazoans and contains a unique C-terminal GIY-YIG motif that confers endonuclease activity in vitro and in vivo. In mammals, Ankle1 is predominantly expressed in hematopoietic tissues. Although most characterized LEM proteins are components of the inner nuclear membrane, ectopic Ankle1 shuttles between cytoplasm and nucleus. Ankle1 enriched in the nucleoplasm induces DNA cleavage and DNA damage response. This activity requires both the catalytic C-terminal GIY-YIG domain and the LEM motif, which binds chromatin via BAF. Hence, Ankle1 is an unusual LEM protein with a GIY-YIG-type endonuclease activity in higher eukaryotes.
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Affiliation(s)
- Andreas Brachner
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Juliane Braun
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Medini Ghodgaonkar
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | - Dennis Castor
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | - Livija Zlopaša
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Veronika Ehrlich
- Institute of Cancer Research, Inner Medicine I, Medical University of Vienna, Austria
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | - Josef Gotzmann
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
| | - Siegfried Knasmüller
- Institute of Cancer Research, Inner Medicine I, Medical University of Vienna, Austria
| | - Roland Foisner
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9, Vienna, Austria
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14
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Aloj G, Giardino G, Valentino L, Maio F, Gallo V, Esposito T, Naddei R, Cirillo E, Pignata C. Severe Combined Immunodeficiences: New and Old Scenarios. Int Rev Immunol 2012; 31:43-65. [DOI: 10.3109/08830185.2011.644607] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Lan L, Ui A, Nakajima S, Hatakeyama K, Hoshi M, Watanabe R, Janicki SM, Ogiwara H, Kohno T, Kanno SI, Yasui A. The ACF1 complex is required for DNA double-strand break repair in human cells. Mol Cell 2011; 40:976-87. [PMID: 21172662 DOI: 10.1016/j.molcel.2010.12.003] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 07/11/2010] [Accepted: 10/18/2010] [Indexed: 01/23/2023]
Abstract
DNA double-strand breaks (DSBs) are repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR), but cellular repair processes remain elusive. We show here that the ATP-dependent chromatin-remodeling factors, ACF1 and SNF2H, accumulate rapidly at DSBs and are required for DSB repair in human cells. If the expression of ACF1 or SNF2H is suppressed, cells become extremely sensitive to X-rays and chemical treatments producing DSBs, and DSBs remain unrepaired. ACF1 interacts directly with KU70 and is required for the accumulation of KU proteins at DSBs. The KU70/80 complex becomes physically more associated with the chromatin-remodeling factors of the CHRAC complex, which includes ACF1, SNF2H, CHRAC15, and CHRAC17, after treatments producing DSBs. Furthermore, the frequency of NHEJ as well as HR induced by DSBs in chromosomal DNA is significantly decreased in cells depleted of either of these factors. Thus, ACF1 and its complexes play important roles in DSBs repair.
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Affiliation(s)
- Li Lan
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Seiryomachi 4-1, Sendai 980-8575, Japan
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16
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Briggs FBS, Goldstein BA, McCauley JL, Zuvich RL, De Jager PL, Rioux JD, Ivinson AJ, Compston A, Hafler DA, Hauser SL, Oksenberg JR, Sawcer SJ, Pericak-Vance MA, Haines JL, Barcellos LF. Variation within DNA repair pathway genes and risk of multiple sclerosis. Am J Epidemiol 2010; 172:217-24. [PMID: 20522537 DOI: 10.1093/aje/kwq086] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multiple sclerosis (MS) is a complex autoimmune disease of the central nervous system with a prominent genetic component. The primary genetic risk factor is the human leukocyte antigen (HLA)-DRB1*1501 allele; however, much of the remaining genetic contribution to MS has not been elucidated. The authors investigated the relation between variation in DNA repair pathway genes and risk of MS. Single-locus association testing, epistatic tests of interactions, logistic regression modeling, and nonparametric Random Forests analyses were performed by using genotypes from 1,343 MS cases and 1,379 healthy controls of European ancestry. A total of 485 single nucleotide polymorphisms within 72 genes related to DNA repair pathways were investigated, including base excision repair, nucleotide excision repair, and double-strand breaks repair. A single nucleotide polymorphism variant within the general transcription factor IIH, polypeptide 4 gene, GTF2H4, on chromosome 6p21.33 was significantly associated with MS (odds ratio = 0.7, P = 3.5 x 10(-5)) after accounting for multiple testing and was not due to linkage disequilibrium with HLA-DRB1*1501. Although other candidate genes examined here warrant further follow-up studies, collectively, these results derived from a well-powered study do not support a strong role for common variation within DNA repair pathway genes in MS.
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17
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Niehues T, Perez-Becker R, Schuetz C. More than just SCID--the phenotypic range of combined immunodeficiencies associated with mutations in the recombinase activating genes (RAG) 1 and 2. Clin Immunol 2010; 135:183-92. [PMID: 20172764 DOI: 10.1016/j.clim.2010.01.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/23/2010] [Accepted: 01/25/2010] [Indexed: 01/08/2023]
Abstract
Combined immunodeficiencies with impaired numbers and function of T- and B-cells can be attributed to defects in the recombinase activating genes (RAG). The products of these genes, the RAG1 and 2 proteins, are key players in the V(D)J recombination process leading to the assembly of antigen receptor genes. Complete RAG deficiency (RAGD) with no V(D)J (<1% recombination activity of wild type) is associated with classical SCID and absence of T- and B-cells. In RAGD with residual V(D)J activity (>1% recombination activity of wild type), several clinical and immunological subtypes have been described: RAGD with skin inflammation and alphabeta T-cell expansion (classical Omenn syndrome), RAGD with skin inflammation and without T-cell expansion (incomplete Omenn syndrome), RAGD with gammadelta T-cell expansion and RAGD with granulomas. Engraftment of maternal T-cells can add to variation in phenotype. The potential role of epigenetic factors that influence the emergence of these phenotypes is discussed. Thorough assessment and interpretation of clinical and immunological findings will guide treatment modalities as intense as hematopoietic stem cell transplantation.
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Affiliation(s)
- Tim Niehues
- HELIOS Klinikum Krefeld, Center for Child and Adolescent Health, Krefeld, Germany.
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18
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Holland SM, Rosenzweig SD, Schumacher RF, Notarangelo L. Immunodeficiencies. Infect Dis (Lond) 2010. [DOI: 10.1016/b978-0-323-04579-7.00072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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19
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Pessach I, Walter J, Notarangelo LD. Recent advances in primary immunodeficiencies: identification of novel genetic defects and unanticipated phenotypes. Pediatr Res 2009; 65:3R-12R. [PMID: 19190530 DOI: 10.1203/pdr.0b013e31819dbe1e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Primary immunodeficiencies (PIDs) have traditionally been defined according to their immunologic phenotype. Far from being concluded, the search for human genes that, when mutated, cause PID is actively being pursued. During the last year, four novel genetic defects that cause severe combined immunodeficiency and severe congenital neutropenia have been identified. At the same time, the immunologic definition of primary immunodeficiencies has been expanded by the recognition that genetic defects affecting innate immunity may result in selective predisposition to certain infections, such as mycobacterial disease, herpes simplex encephalitis, and invasive pneumococcal infections. Studies of genetically determined susceptibility to infections have recently shown that immunologic defects may also account for novel infectious phenotypes, such as malaria or leprosy. Finally, a growing body of evidence indicates that primary immunodeficiencies may present with a noninfectious clinical phenotype that may be restricted to single organs, as in the case of atypical hemolytic uremic syndrome or pulmonary alveolar proteinosis. Overall, these achievements highlight the importance of human models, which often differ from the corresponding animal models.
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Affiliation(s)
- Itai Pessach
- Division of Immunology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA
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