1
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Hayashi D, Hashimoto T, Mine M, Ishii N, Hashimoto K, Tsuchisaka A, Tsuruta D. Study of original B cells producing pathogenic IgG and IgA autoantibodies in anti-BP180-type mucous membrane pemphigoid. Arch Dermatol Res 2024; 316:169. [PMID: 38734797 DOI: 10.1007/s00403-024-02915-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/05/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Affiliation(s)
- Daisuke Hayashi
- Department of Dermatology, Graduate School of Medicine, Osaka Metropolitan University, 1-4-3 Asahimachi, Abeno, Osaka, 545-8585, Japan
| | - Takashi Hashimoto
- Department of Dermatology, Graduate School of Medicine, Osaka Metropolitan University, 1-4-3 Asahimachi, Abeno, Osaka, 545-8585, Japan.
| | - Mako Mine
- Department of Dermatology, Graduate School of Medicine, Osaka Metropolitan University, 1-4-3 Asahimachi, Abeno, Osaka, 545-8585, Japan
| | - Norito Ishii
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka, 830-0011, Japan
| | - Koji Hashimoto
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Atsunari Tsuchisaka
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka, 830-0011, Japan
| | - Daisuke Tsuruta
- Department of Dermatology, Graduate School of Medicine, Osaka Metropolitan University, 1-4-3 Asahimachi, Abeno, Osaka, 545-8585, Japan
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2
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Leeman-Neill RJ, Bhagat G, Basu U. AID in non-Hodgkin B-cell lymphomas: The consequences of on- and off-target activity. Adv Immunol 2024; 161:127-164. [PMID: 38763700 DOI: 10.1016/bs.ai.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Activation induced cytidine deaminase (AID) is a key element of the adaptive immune system, required for immunoglobulin isotype switching and affinity maturation of B-cells as they undergo the germinal center (GC) reaction in peripheral lymphoid tissue. The inherent DNA damaging activity of this enzyme can also have off-target effects in B-cells, producing lymphomagenic chromosomal translocations that are characteristic features of various classes of non-Hodgkin B-cell lymphoma (B-NHL), and generating oncogenic mutations, so-called aberrant somatic hypermutation (aSHM). Additionally, AID has been found to affect gene expression through demethylation as well as altered interactions between gene regulatory elements. These changes have been most thoroughly studied in B-NHL arising from GC B-cells. Here, we describe the most common classes of GC-derived B-NHL and explore the consequences of on- and off-target AID activity in B and plasma cell neoplasms. The relationships between AID expression, including effects of infection and other exposures/agents, mutagenic activity and lymphoma biology are also discussed.
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States; Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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3
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Mina ED, Jackson KJL, Crawford AJI, Faulks ML, Pathmanandavel K, Acquarola N, O'Sullivan M, Kerre T, Naesens L, Claes K, Goodnow CC, Haerynck F, Kracker S, Meyts I, D'Orsogna LJ, Ma CS, Tangye SG. A Novel Heterozygous Variant in AICDA Impairs Ig Class Switching and Somatic Hypermutation in Human B Cells and is Associated with Autosomal Dominant HIGM2 Syndrome. J Clin Immunol 2024; 44:66. [PMID: 38363477 PMCID: PMC10873450 DOI: 10.1007/s10875-024-01665-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/21/2024] [Indexed: 02/17/2024]
Abstract
B cells and their secreted antibodies are fundamental for host-defense against pathogens. The generation of high-affinity class switched antibodies results from both somatic hypermutation (SHM) of the immunoglobulin (Ig) variable region genes of the B-cell receptor and class switch recombination (CSR) which alters the Ig heavy chain constant region. Both of these processes are initiated by the enzyme activation-induced cytidine deaminase (AID), encoded by AICDA. Deleterious variants in AICDA are causal of hyper-IgM syndrome type 2 (HIGM2), a B-cell intrinsic primary immunodeficiency characterised by recurrent infections and low serum IgG and IgA levels. Biallelic variants affecting exons 2, 3 or 4 of AICDA have been identified that impair both CSR and SHM in patients with autosomal recessive HIGM2. Interestingly, B cells from patients with autosomal dominant HIGM2, caused by heterozygous variants (V186X, R190X) located in AICDA exon 5 encoding the nuclear export signal (NES) domain, show abolished CSR but variable SHM. We herein report the immunological and functional phenotype of two related patients presenting with common variable immunodeficiency who were found to have a novel heterozygous variant in AICDA (L189X). This variant led to a truncated AID protein lacking the last 10 amino acids of the NES at the C-terminal domain. Interestingly, patients' B cells carrying the L189X variant exhibited not only greatly impaired CSR but also SHM in vivo, as well as CSR and production of IgG and IgA in vitro. Our findings demonstrate that the NES domain of AID can be essential for SHM, as well as for CSR, thereby refining the correlation between AICDA genotype and SHM phenotype as well as broadening our understanding of the pathophysiology of HIGM disorders.
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Affiliation(s)
- Erika Della Mina
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Katherine J L Jackson
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Alexander J I Crawford
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Megan L Faulks
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Karrnan Pathmanandavel
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Nicolino Acquarola
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Michael O'Sullivan
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Murdoch, WA, Australia
- Department of Immunology, Perth Children's Hospital, Perth, WA, Australia
| | - Tessa Kerre
- Department of Hematology, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Primary Immunodeficiency Ghent (CPIG), Jeffrey Modell Diagnosis and Research Center, ERN Rita Network Center, Ghent University Hospital, Ghent, Belgium
| | - Leslie Naesens
- Center for Primary Immunodeficiency Ghent (CPIG), Jeffrey Modell Diagnosis and Research Center, ERN Rita Network Center, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Karlien Claes
- Center for Primary Immunodeficiency Ghent (CPIG), Jeffrey Modell Diagnosis and Research Center, ERN Rita Network Center, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Filomeen Haerynck
- Center for Primary Immunodeficiency Ghent (CPIG), Jeffrey Modell Diagnosis and Research Center, ERN Rita Network Center, Ghent University Hospital, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Sven Kracker
- Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, Imagine Institute, 75015, Paris, France
- Université Paris Cité, 75015, Paris, France
| | - Isabelle Meyts
- Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Louvain, Belgium
- Pediatric Immunodeficiency, Department of Pediatrics, University Hospitals Leuven, Louvain, Belgium
| | - Lloyd J D'Orsogna
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Murdoch, WA, Australia
- School of Medicine, University of Western Australia, Nedlands, WA, Australia
| | - Cindy S Ma
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Stuart G Tangye
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia.
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4
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Almasmoum HA. Molecular complexity of diffuse large B-cell lymphoma: a molecular perspective and therapeutic implications. J Appl Genet 2024; 65:57-72. [PMID: 38001281 DOI: 10.1007/s13353-023-00804-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) stands as a formidable challenge in the landscape of non-Hodgkin's lymphomas. This review illuminates the remarkable strides made in comprehending DLBCL's molecular intricacies and devising targeted treatments. DLBCL, the most prevalent non-Hodgkin's lymphoma, has seen transformative progress in its characterization. Genetic investigations, led by high-throughput sequencing, have unveiled recurrent mutations in genes such as MYC, BCL2, and BCL6, casting light on the underlying genetic chaos propelling DLBCL's aggressiveness. A pivotal facet of this understanding centers on cell signaling pathways. Dysregulation of B-cell receptor (BCR) signaling, NF-κB, PI3K/Akt/mTOR, JAK/STAT, Wnt/β-Catenin, and Toll-like receptor pathways plays a critical role in DLBCL pathogenesis, offering potential therapeutic targets. DLBCL's complex tumor microenvironment (TME) cannot be overlooked. The dynamic interplay among tumor cells, immune cells, stromal components, and the extracellular matrix profoundly influences DLBCL's course and response to therapies. Epigenetic modifications, including DNA methylation and histone changes, add another layer of intricacy. Aberrant epigenetic regulation plays a significant role in lymphomagenesis, offering prospects for epigenetic-based therapies. Promisingly, these molecular insights have spurred the development of personalized treatments. Targeted therapies and immunotherapies, guided by genomic profiling and molecular classification, are emerging as game-changers in DLBCL management. In conclusion, this review underscores the remarkable strides in understanding DLBCL's molecular underpinnings, spanning genetics, cell signaling, the tumor microenvironment, and epigenetics. These advances pave the way for more effective, personalized treatments, renewing hope for DLBCL patients.
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Affiliation(s)
- Hibah Ali Almasmoum
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
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5
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Mamidi MK, Huang J, Honjo K, Li R, Tabengwa EM, Neeli I, Randall NL, Ponnuchetty MV, Radic M, Leu CM, Davis RS. FCRL1 immunoregulation in B cell development and malignancy. Front Immunol 2023; 14:1251127. [PMID: 37822931 PMCID: PMC10562807 DOI: 10.3389/fimmu.2023.1251127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023] Open
Abstract
Immunotherapeutic targeting of surface regulatory proteins and pharmacologic inhibition of critical signaling pathways has dramatically shifted our approach to the care of individuals with B cell malignancies. This evolution in therapy reflects the central role of the B cell receptor (BCR) signaling complex and its co-receptors in the pathogenesis of B lineage leukemias and lymphomas. Members of the Fc receptor-like gene family (FCRL1-6) encode cell surface receptors with complex tyrosine-based regulation that are preferentially expressed by B cells. Among them, FCRL1 expression peaks on naïve and memory B cells and is unique in terms of its intracellular co-activation potential. Recent studies in human and mouse models indicate that FCRL1 contributes to the formation of the BCR signalosome, modulates B cell signaling, and promotes humoral responses. Progress in understanding its regulatory properties, along with evidence for its over-expression by mature B cell leukemias and lymphomas, collectively imply important yet unmet opportunities for FCRL1 in B cell development and transformation. Here we review recent advances in FCRL1 biology and highlight its emerging significance as a promising biomarker and therapeutic target in B cell lymphoproliferative disorders.
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Affiliation(s)
- Murali K. Mamidi
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jifeng Huang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kazuhito Honjo
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ran Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Edlue M. Tabengwa
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Nar’asha L. Randall
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Manasa V. Ponnuchetty
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Chuen-Miin Leu
- Institute of Microbiology and Immunology, National Yang Ming ChiaoTung University, Taipei, Taiwan
| | - Randall S. Davis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Departments of Microbiology, and Biochemistry & Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
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6
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Pasqualucci L. The germinal center in the pathogenesis of B cell lymphomas. Hematol Oncol 2023; 41 Suppl 1:62-69. [PMID: 37294970 DOI: 10.1002/hon.3141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 06/11/2023]
Abstract
The adaptive immune system has evolved to allow effective responses against a virtually unlimited number of invading pathogens. This process requires the transient formation of germinal centers (GC), a dynamic environment that ensures the generation and selection of B cells capable to produce antibodies with high antigen affinity, or to maintain the memory of that antigen for life. However, this comes at a cost, as the unique events accompanying the GC reaction pose a significant risk to the genome of B cells, which must endure elevated levels of replication stress, while proliferating at high rates and undergoing DNA breaks introduced by somatic hypermutation and class switch recombination. Indeed, the genetic/epigenetic disruption of programs implicated in normal GC biology has emerged as a hallmark of most B cell lymphomas. This improved understanding provides a conceptual framework for the identification of cellular pathways that could be exploited for precision medicine approaches.
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Affiliation(s)
- Laura Pasqualucci
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
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7
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Kobayashi M, Wakaguri H, Shimizu M, Higasa K, Matsuda F, Honjo T. Ago2 and a miRNA reduce Topoisomerase 1 for enhancing DNA cleavage in antibody diversification by activation-induced cytidine deaminase. Proc Natl Acad Sci U S A 2023; 120:e2216918120. [PMID: 37094168 PMCID: PMC10161001 DOI: 10.1073/pnas.2216918120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is the essential enzyme for imprinting immunological memory through class switch recombination (CSR) and somatic hypermutation (SHM) of the immunoglobulin (Ig) gene. AID-dependent reduction of Topoisomerase 1 (Top1) promotes DNA cleavage that occurs upon Ig gene diversification, whereas the mechanism behind AID-induced Top1 reduction remains unclear. Here, we clarified the contribution of the microRNA-Ago2 complex in AID-dependent Top1 decrease. Ago2 binds to Top1 3'UTR with two regions of AID-dependent Ago2-binding sites (5'- and 3'dABs). Top1 3'UTR knockout (3'UTRKO) in B lymphoma cells leads to decreases in DNA break efficiency in the IgH gene accompanied by a reduction in CSR and SHM frequencies. Furthermore, AID-dependent Top1 protein reduction and Ago2-binding to Top1 mRNA are down-regulated in 3'UTRKO cells. Top1 mRNA in the highly translated fractions of the sucrose gradient is decreased in an AID-dependent and Top1 3'UTR-mediated manner, resulting in a decrease in Top1 protein synthesis. Both AID and Ago2 localize in the mRNA-binding protein fractions and they interact with each other. Furthermore, we found some candidate miRNAs which possibly bind to 5'- and 3'dAB in Top1 mRNA. Among them, miR-92a-3p knockdown induces the phenotypes of 3'UTRKO cells to wild-type cells whereas it does not impact on 3'UTRKO cells. Taken together, the Ago2-miR-92a-3p complex will be recruited to Top1 3'UTR in an AID-dependent manner and posttranscriptionally reduces Top1 protein synthesis. These consequences cause the increase in a non-B-DNA structure, enhance DNA cleavage by Top1 in the Ig gene and contribute to immunological memory formation.
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Affiliation(s)
- Maki Kobayashi
- Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Hiroyuki Wakaguri
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Masakazu Shimizu
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Koichiro Higasa
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Tasuku Honjo
- Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
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8
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Refaat AM, Nakata M, Husain A, Kosako H, Honjo T, Begum NA. HNRNPU facilitates antibody class-switch recombination through C-NHEJ promotion and R-loop suppression. Cell Rep 2023; 42:112284. [PMID: 36943867 DOI: 10.1016/j.celrep.2023.112284] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/23/2022] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
B cells generate functionally different classes of antibodies through class-switch recombination (CSR), which requires classical non-homologous end joining (C-NHEJ) to join the DNA breaks at the donor and acceptor switch (S) regions. We show that the RNA-binding protein HNRNPU promotes C-NHEJ-mediated S-S joining through the 53BP1-shieldin DNA-repair complex. Notably, HNRNPU binds to the S region RNA/DNA G-quadruplexes, contributing to regulating R-loop and single-stranded DNA (ssDNA) accumulation. HNRNPU is an intrinsically disordered protein that interacts with both C-NHEJ and R-loop complexes in an RNA-dependent manner. Strikingly, recruitment of HNRNPU and the C-NHEJ factors is highly sensitive to liquid-liquid phase separation inhibitors, suggestive of DNA-repair condensate formation. We propose that HNRNPU facilitates CSR by forming and stabilizing the C-NHEJ ribonucleoprotein complex and preventing excessive R-loop accumulation, which otherwise would cause persistent DNA breaks and aberrant DNA repair, leading to genomic instability.
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Affiliation(s)
- Ahmed M Refaat
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Afzal Husain
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Hidetaka Kosako
- Division of Cell Signaling, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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9
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Stoler-Barak L, Harris E, Peres A, Hezroni H, Kuka M, Di Lucia P, Grenov A, Gurwicz N, Kupervaser M, Yip BH, Iannacone M, Yaari G, Crispino JD, Shulman Z. B cell class switch recombination is regulated by DYRK1A through MSH6 phosphorylation. Nat Commun 2023; 14:1462. [PMID: 36927854 PMCID: PMC10020581 DOI: 10.1038/s41467-023-37205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Protection from viral infections depends on immunoglobulin isotype switching, which endows antibodies with effector functions. Here, we find that the protein kinase DYRK1A is essential for B cell-mediated protection from viral infection and effective vaccination through regulation of class switch recombination (CSR). Dyrk1a-deficient B cells are impaired in CSR activity in vivo and in vitro. Phosphoproteomic screens and kinase-activity assays identify MSH6, a DNA mismatch repair protein, as a direct substrate for DYRK1A, and deletion of a single phosphorylation site impaired CSR. After CSR and germinal center (GC) seeding, DYRK1A is required for attenuation of B cell proliferation. These findings demonstrate DYRK1A-mediated biological mechanisms of B cell immune responses that may be used for therapeutic manipulation in antibody-mediated autoimmunity.
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Affiliation(s)
- Liat Stoler-Barak
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ethan Harris
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 52900, Israel
| | - Hadas Hezroni
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Mirela Kuka
- Vita-Salute San Raffaele University and Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Di Lucia
- Vita-Salute San Raffaele University and Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Amalie Grenov
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Meital Kupervaser
- De Botton Institute for Proteomics, Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Bon Ham Yip
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matteo Iannacone
- Vita-Salute San Raffaele University and Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 52900, Israel
| | - John D Crispino
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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10
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Ma N, Jin A, Sun Y, Jin Y, Sun Y, Xiao Q, Sha X, Yu F, Yang L, Liu W, Gao X, Zhang X, Li L. Comprehensive investigating of MMR gene in hepatocellular carcinoma with chronic hepatitis B virus infection in Han Chinese population. Front Oncol 2023; 13:1124459. [PMID: 37035153 PMCID: PMC10079871 DOI: 10.3389/fonc.2023.1124459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Hepatocellular carcinoma associated with chronic hepatitis B virus infection seriously affects human health. Present studies suggest that genetic susceptibility plays an important role in the mechanism of cancer development. Therefore, this study focused on single nucleotide polymorphisms (SNPs) of MMR genes associated with HBV-HCC. Five groups of participants were included in this study, which were healthy control group (HC), spontaneous clearance (SC), chronic hepatitis B group (CHB), HBV-related liver cirrhosis group (LC) and HBV-related hepatocellular carcinoma group (HBV-HCC). A total of 3128 participants met the inclusion and exclusion criteria for this study. 20 polymorphic loci on MSH2, MSH3 and MSH6 were selected for genotyping. There were four case-control studies, which were HC vs. HCC, SC vs. HCC, CHB vs. HCC and LC vs. HCC. We used Hardy-Weinberg equilibrium test, unconditional logistic regression, haplotype analysis, and gene-gene interaction for genetic analysis. Ultimately, after excluding confounding factors such as age, gender, smoking and drinking, 12 polymorphisms were found to be associated with genetic susceptibility to HCC. Haplotype analysis showed the risk haplotype GTTT (rs1805355_G, rs3776968_T, rs1428030_C, rs181747_C) was more frequent in the HCC group compared with the HC group. The GMDR analysis showed that the best interaction model was the three-factor model of MSH2-rs1981928, MSH3-rs26779 and MSH6-rs2348244 in SC vs. HCC group (P=0.001). In addition, we found multiplicative or additive interactions between genes in our selected SNPs. These findings provide new ideas to further explore the etiology and pathogenesis of HCC. We have attempted to explain the molecular mechanisms by which certain SNPs (MSH2-rs4952887, MSH3-rs26779, MSH3-rs181747 and MSH3-rs32950) affect genetic susceptibility to HCC from the perspectives of eQTL, TFBS, cell cycle and so on. We also explained the results of haplotypes and gene-gene interactions. These findings provide new ideas to further explore the etiology and pathogenesis of HCC.
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Affiliation(s)
- Ning Ma
- Hebei Key Laboratory of Environment and Human Health, Department of Social Medicine and Health Care Management, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Ao Jin
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Yitong Sun
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Yiyao Jin
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Yucheng Sun
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Qian Xiao
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - XuanYi Sha
- Hebei Key Laboratory of Environment and Human Health, School of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Fengxue Yu
- The Hebei Key Laboratory of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lei Yang
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Wenxuan Liu
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xia Gao
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Xiaolin Zhang
- Hebei Key Laboratory of Environment and Human Health, Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Xiaolin Zhang, ; Lu Li,
| | - Lu Li
- Hebei Key Laboratory of Environment and Human Health, Department of Social Medicine and Health Care Management, School of Public Health, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Xiaolin Zhang, ; Lu Li,
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11
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López C, Burkhardt B, Chan JKC, Leoncini L, Mbulaiteye SM, Ogwang MD, Orem J, Rochford R, Roschewski M, Siebert R. Burkitt lymphoma. Nat Rev Dis Primers 2022; 8:78. [PMID: 36522349 DOI: 10.1038/s41572-022-00404-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/19/2022] [Indexed: 12/16/2022]
Abstract
Burkitt lymphoma (BL) is an aggressive form of B cell lymphoma that can affect children and adults. The study of BL led to the identification of the first recurrent chromosomal aberration in lymphoma, t(8;14)(q24;q32), and subsequent discovery of the central role of MYC and Epstein-Barr virus (EBV) in tumorigenesis. Most patients with BL are cured with chemotherapy but those with relapsed or refractory disease usually die of lymphoma. Historically, endemic BL, non-endemic sporadic BL and the immunodeficiency-associated BL have been recognized, but differentiation of these epidemiological variants is confounded by the frequency of EBV positivity. Subtyping into EBV+ and EBV- BL might better describe the biological heterogeneity of the disease. Phenotypically resembling germinal centre B cells, all types of BL are characterized by dysregulation of MYC due to enhancer activation via juxtaposition with one of the three immunoglobulin loci. Additional molecular changes commonly affect B cell receptor and sphingosine-1-phosphate signalling, proliferation, survival and SWI-SNF chromatin remodelling. BL is diagnosed on the basis of morphology and high expression of MYC. BL can be effectively treated in children and adolescents with short durations of high dose-intensity multiagent chemotherapy regimens. Adults are more susceptible to toxic effects but are effectively treated with chemotherapy, including modified versions of paediatric regimens. The outcomes in patients with BL are good in high-income countries with low mortality and few late effects, but in low-income and middle-income countries, BL is diagnosed late and is usually treated with less-effective regimens affecting the overall good outcomes in patients with this lymphoma.
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Affiliation(s)
- Cristina López
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Birgit Burkhardt
- Non-Hodgkin's Lymphoma Berlin-Frankfurt-Münster (NHL-BFM) Study Center and Paediatric Hematology, Oncology and BMT, University Hospital Muenster, Muenster, Germany
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Lorenzo Leoncini
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | | | | | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mark Roschewski
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany.
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12
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Mallaby J, Ng J, Stewart A, Sinclair E, Dunn-Walters D, Hershberg U. Chickens, more than humans, focus the diversity of their immunoglobulin genes on the complementarity-determining region but utilise amino acids, indicative of a more cross-reactive antibody repertoire. Front Immunol 2022; 13:837246. [PMID: 36569888 PMCID: PMC9772431 DOI: 10.3389/fimmu.2022.837246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanisms of B-cell diversification differ greatly between aves and mammals, but both produce B cells and antibodies capable of supporting an effective immune response. To see how differences in the generation of diversity might affect overall repertoire diversity, we have compared the diversity characteristics of immunoglobulin genes from domestic chickens to those from humans. Both use V(D)J gene rearrangement and somatic hypermutation, but only chickens use somatic gene conversion. A range of diversity analysis tools were used to investigate multiple aspects of amino acid diversity at both the germline and repertoire levels. The effect of differing amino acid usages on antibody characteristics was assessed. At both the germline and repertoire levels, chickens exhibited lower amino acid diversity in comparison to the human immunoglobulin genes, especially outside of the complementarity-determining region (CDR). Chickens were also found to possess much larger and more hydrophilic CDR3s with a higher predicted protein binding potential, suggesting that the antigen-binding site in chicken antibodies is more flexible and more polyreactive than that seen in human antibodies.
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Affiliation(s)
- Jessica Mallaby
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Joseph Ng
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Alex Stewart
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Emma Sinclair
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Deborah Dunn-Walters
- Department of Bioscience and Medicine, University of Surrey, Guildford, United Kingdom
| | - Uri Hershberg
- Department of Human Biology, University of Haifa, Haifa, Israel
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13
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Pan-cancer landscape of AID-related mutations, composite mutations, and their potential role in the ICI response. NPJ Precis Oncol 2022; 6:89. [PMID: 36456685 PMCID: PMC9715662 DOI: 10.1038/s41698-022-00331-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
Activation-induced cytidine deaminase, AICDA or AID, is a driver of somatic hypermutation and class-switch recombination in immunoglobulins. In addition, this deaminase belonging to the APOBEC family may have off-target effects genome-wide, but its effects at pan-cancer level are not well elucidated. Here, we used different pan-cancer datasets, totaling more than 50,000 samples analyzed by whole-genome, whole-exome, or targeted sequencing. AID mutations are present at pan-cancer level with higher frequency in hematological cancers and higher presence at transcriptionally active TAD domains. AID synergizes initial hotspot mutations by a second composite mutation. AID mutational load was found to be independently associated with a favorable outcome in immune-checkpoint inhibitors (ICI) treated patients across cancers after analyzing 2000 samples. Finally, we found that AID-related neoepitopes, resulting from mutations at more frequent hotspots if compared to other mutational signatures, enhance CXCL13/CCR5 expression, immunogenicity, and T-cell exhaustion, which may increase ICI sensitivity.
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14
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Abstract
Activation-induced cytidine deaminase (AID) initiates somatic hypermutation of immunoglobulin (Ig) gene variable regions and class switch recombination (CSR) of Ig heavy chain constant regions. Two decades of intensive research has greatly expanded our knowledge of how AID functions in peripheral B cells to optimize antibody responses against infections, while maintaining tight regulation of AID to restrain its activity to protect B cell genomic integrity. The many exciting recent advances in the field include: 1) the first description of AID's molecular structure, 2) remarkable advances in high throughput approaches that precisely track AID targeting genome-wide, and 3) the discovery that the cohesion-mediate loop extrusion mechanism [initially discovered in V(D)J recombination studies] also governs AID-medicated CSR. These advances have significantly advanced our understanding of AID's biochemical properties in vitro and AID's function and regulation in vivo. This mini review will discuss these recent discoveries and outline the challenges and questions that remain to be addressed.
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15
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Wu M, Zhao H, Tang X, Zhao W, Yi X, Li Q, Sun X. Organization and Complexity of the Yak (Bos Grunniens) Immunoglobulin Loci. Front Immunol 2022; 13:876509. [PMID: 35615368 PMCID: PMC9124968 DOI: 10.3389/fimmu.2022.876509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
As important livestock in Qinghai-Tibet Plateau, yak provides meat and other necessities for Tibetans living. Plateau yak has resistance to diseases and stress, yet is nearly unknown in the structure and expression mechanism of yak immunoglobulin loci. Based on the published immunoglobulin genes of bovids (cattle, sheep and goat), the genomic organization of the yak immunoglobulin heavy chain (IgH) and immunoglobulin light chain (IgL) were described. The assemblage diversity of IgH, Igλ and Igκ in yak was similar to that in bovids, and contributes little to the antibody lineage compared with that in humans and mice. Somatic hypermutation (SHM) had a greater effect on immunoglobulin diversity in yak than in goat and sheep, and in addition to the complementarity-determining region (CDR), some loci in the framework region (FR) also showed high frequency mutations. CDR3 diversity showed that immunological lineages in yak were overwhelmingly generated through linkage diversity in IgH rearrangements. The emergence of new high-throughput sequencing technologies and the yak whole genome (2019) publication have greatly improved our understanding of the immune response in yaks. We had a more comprehensive analysis of yak immunoglobulin expression diversity by PE300, which avoided the disadvantage of missing low-frequency recombination in traditional Sanger sequencing. In summary, we described the schematic structure of the genomic organization of yak IgH loci and IgL loci. The analysis of immunoglobulin expression diversity showed that yak made up for the deficiency of V(D)J recombinant diversity by junctional diversity and CDR3 diversity. In addition, yak, like cattle, also had the same ultra-long IgH CDR3 (CDR3H), which provided more contribution to the diverse expression of yak immunoglobulin. These findings might provide a theoretical basis for disease resistance breeding and vaccine development in yak.
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Affiliation(s)
- Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wanxia Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
- *Correspondence: Xiuzhu Sun,
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16
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Lombard-Vadnais F, Collin R, Daudelin JF, Chabot-Roy G, Labrecque N, Lesage S. The Idd2 Locus Confers Prominent Resistance to Autoimmune Diabetes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:898-909. [PMID: 35039332 DOI: 10.4049/jimmunol.2100456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Type 1 diabetes is an autoimmune disease characterized by pancreatic β cell destruction. It is a complex genetic trait driven by >30 genetic loci with parallels between humans and mice. The NOD mouse spontaneously develops autoimmune diabetes and is widely used to identify insulin-dependent diabetes (Idd) genetic loci linked to diabetes susceptibility. Although many Idd loci have been extensively studied, the impact of the Idd2 locus on autoimmune diabetes susceptibility remains to be defined. To address this, we generated a NOD congenic mouse bearing B10 resistance alleles on chromosome 9 in a locus coinciding with part of the Idd2 locus and found that NOD.B10-Idd2 congenic mice are highly resistant to diabetes. Bone marrow chimera and adoptive transfer experiments showed that the B10 protective alleles provide resistance in an immune cell-intrinsic manner. Although no T cell-intrinsic differences between NOD and NOD.B10-Idd2 mice were observed, we found that the Idd2 resistance alleles limit the formation of spontaneous and induced germinal centers. Comparison of B cell and dendritic cell transcriptome profiles from NOD and NOD.B10-Idd2 mice reveal that resistance alleles at the Idd2 locus affect the expression of specific MHC molecules, a result confirmed by flow cytometry. Altogether, these data demonstrate that resistance alleles at the Idd2 locus impair germinal center formation and influence MHC expression, both of which likely contribute to reduced diabetes incidence.
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Affiliation(s)
- Félix Lombard-Vadnais
- Immunology-Oncology Axis, Research Center, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Roxanne Collin
- Immunology-Oncology Axis, Research Center, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada; and
| | - Jean-François Daudelin
- Immunology-Oncology Axis, Research Center, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Geneviève Chabot-Roy
- Immunology-Oncology Axis, Research Center, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Nathalie Labrecque
- Immunology-Oncology Axis, Research Center, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada; and
- Département de Médecine, Université de Montréal, Montreal, Quebec, Canada
| | - Sylvie Lesage
- Immunology-Oncology Axis, Research Center, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada;
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada; and
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17
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Jiang L, Yin J, Qian M, Rong S, Zhang S, Chen K, Zhao C, Tan Y, Guo J, Chen H, Gao S, Liu T, Liu Y, Shen B, Yang J, Zhang Y, Meng FL, Hu J, Ma H, Chen YH. UdgX-Mediated Uracil Sequencing at Single-Nucleotide Resolution. J Am Chem Soc 2022; 144:1323-1331. [PMID: 35037455 DOI: 10.1021/jacs.1c11269] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As an aberrant base in DNA, uracil is generated by either deoxyuridine (dU) misincorporation or cytosine deamination, and involved in multiple physiological and pathological processes. Genome-wide profiles of uracil are important for study of these processes. Current methods for whole-genome mapping of uracil all rely on uracil-DNA N-glycosylase (UNG) and are limited in resolution, specificity, and/or sensitivity. Here, we developed a UdgX cross-linking and polymerase stalling sequencing ("Ucaps-seq") method to detect dU at single-nucleotide resolution. First, the specificity of Ucaps-seq was confirmed on synthetic DNA. Then the effectiveness of the approach was verified on two genomes from different sources. Ucaps-seq not only identified the enrichment of dU at dT sites in pemetrexed-treated cancer cells with globally elevated uracil but also detected dU at dC sites within the "WRC" motif in activated B cells which have increased dU in specific regions. Finally, Ucaps-seq was utilized to detect dU introduced by the cytosine base editor (nCas9-APOBEC) and identified a novel off-target site in cellular context. In conclusion, Ucaps-seq is a powerful tool with many potential applications, especially in evaluation of base editing fidelity.
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Affiliation(s)
- Liudan Jiang
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China
| | - Jiayong Yin
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Maoxiang Qian
- Institute of Pediatrics and Department of Hematology and Oncology, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Shaoqin Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Shengqi Zhang
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China
| | - Kejing Chen
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China
| | - Chengchen Zhao
- School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Yuanqing Tan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiayin Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hao Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Siyun Gao
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China
| | - Tingting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Liu
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jian Yang
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China
| | - Yong Zhang
- School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinchuan Hu
- Shanghai Fifth People's Hospital, Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Honghui Ma
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China.,Research Units of Origin and Regulation of Heart Rhythm, Chinese Academy of Medical Sciences, Shanghai 200092, China
| | - Yi-Han Chen
- Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai, 200092, China
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18
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Gulbudak H, Qu Z, Milner F, Tuncer N. Sensitivity Analysis in an Immuno-Epidemiological Vector-Host Model. Bull Math Biol 2022; 84:27. [PMID: 34982249 PMCID: PMC8724773 DOI: 10.1007/s11538-021-00979-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022]
Abstract
Sensitivity Analysis (SA) is a useful tool to measure the impact of changes in model parameters on the infection dynamics, particularly to quantify the expected efficacy of disease control strategies. SA has only been applied to epidemic models at the population level, ignoring the effect of within-host virus-with-immune-system interactions on the disease spread. Connecting the scales from individual to population can help inform drug and vaccine development. Thus the value of understanding the impact of immunological parameters on epidemiological quantities. Here we consider an age-since-infection structured vector-host model, in which epidemiological parameters are formulated as functions of within-host virus and antibody densities, governed by an ODE system. We then use SA for these immuno-epidemiological models to investigate the impact of immunological parameters on population-level disease dynamics such as basic reproduction number, final size of the epidemic or the infectiousness at different phases of an outbreak. As a case study, we consider Rift Valley Fever Disease utilizing parameter estimations from prior studies. SA indicates that \documentclass[12pt]{minimal}
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\begin{document}$$1\%$$\end{document}1% increase in within-host pathogen growth rate can lead up to \documentclass[12pt]{minimal}
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\begin{document}$$\mathcal R_0,$$\end{document}R0, up to \documentclass[12pt]{minimal}
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\begin{document}$$1 \%$$\end{document}1% increase in steady-state infected host abundance, and up to \documentclass[12pt]{minimal}
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\begin{document}$$4\%$$\end{document}4% increase in infectiousness of hosts when the reproduction number \documentclass[12pt]{minimal}
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\begin{document}$$\mathcal R_0$$\end{document}R0 is larger than one. These significant increases in population-scale disease quantities suggest that control strategies that reduce the within-host pathogen growth can be important in reducing disease prevalence.
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Affiliation(s)
- Hayriye Gulbudak
- Department of Mathematics, University of Louisiana at Lafayette, 217 Maxim Doucet Hall, Lafayette, LA, P.O. Box 43568, USA.
| | - Zhuolin Qu
- Department of Mathematics, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Fabio Milner
- School of Mathematical and Statistical Sciences, Arizona State University, 825 Wexler Hall, P.O. Box 871804, Tempe, AZ, 85287, USA
| | - Necibe Tuncer
- Department of Mathematical Sciences, Florida Atlantic University, Science Building, Room 234 777 Glades Road, Boca Raton, FL, 33431, USA
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19
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Baptista BO, de Souza ABL, Riccio EKP, Bianco-Junior C, Totino PRR, Martins da Silva JH, Theisen M, Singh SK, Amoah LE, Ribeiro-Alves M, Souza RM, Lima-Junior JC, Daniel-Ribeiro CT, Pratt-Riccio LR. Naturally acquired antibody response to a Plasmodium falciparum chimeric vaccine candidate GMZ2.6c and its components (MSP-3, GLURP, and Pfs48/45) in individuals living in Brazilian malaria-endemic areas. Malar J 2022; 21:6. [PMID: 34983540 PMCID: PMC8729018 DOI: 10.1186/s12936-021-04020-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/09/2021] [Indexed: 12/19/2022] Open
Abstract
Background The GMZ2.6c malaria vaccine candidate is a multi-stage Plasmodium falciparum chimeric protein which contains a fragment of the sexual-stage Pfs48/45-6C protein genetically fused to GMZ2, a fusion protein of GLURP and MSP-3, that has been shown to be well tolerated, safe and immunogenic in clinical trials performed in a malaria-endemic area of Africa. However, there is no data available on the antigenicity or immunogenicity of GMZ2.6c in humans. Considering that circulating parasites can be genetically distinct in different malaria-endemic areas and that host genetic factors can influence the immune response to vaccine antigens, it is important to verify the antigenicity, immunogenicity and the possibility of associated protection in individuals living in malaria-endemic areas with different epidemiological scenarios. Herein, the profile of antibody response against GMZ2.6c and its components (MSP-3, GLURP and Pfs48/45) in residents of the Brazilian Amazon naturally exposed to malaria, in areas with different levels of transmission, was evaluated. Methods This study was performed using serum samples from 352 individuals from Cruzeiro do Sul and Mâncio Lima, in the state of Acre, and Guajará, in the state of Amazonas. Specific IgG, IgM, IgA and IgE antibodies and IgG subclasses were detected by Enzyme-Linked Immunosorbent Assay. Results The results showed that GMZ2.6c protein was widely recognized by naturally acquired antibodies from individuals of the Brazilian endemic areas with different levels of transmission. The higher prevalence of individuals with antibodies against GMZ2.6c when compared to its individual components may suggest an additive effect of GLURP, MSP-3, and Pfs48/45 when inserted in a same construct. Furthermore, naturally malaria-exposed individuals predominantly had IgG1 and IgG3 cytophilic anti-GMZ2.6c antibodies, an important fact considering that the acquisition of anti-malaria protective immunity results from a delicate balance between cytophilic/non-cytophilic antibodies. Interestingly, anti-GMZ2.6c antibodies seem to increase with exposure to malaria infection and may contribute to parasite immunity. Conclusions The data showed that GMZ2.6c protein is widely recognized by naturally acquired antibodies from individuals living in malaria-endemic areas in Brazil and that these may contribute to parasite immunity. These data highlight the importance of GMZ2.6c as a candidate for an anti-malarial vaccine. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-04020-6.
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Affiliation(s)
- Barbara Oliveira Baptista
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.,Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brazil
| | - Ana Beatriz Lopes de Souza
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.,Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brazil
| | - Evelyn Kety Pratt Riccio
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.,Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brazil
| | - Cesare Bianco-Junior
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.,Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brazil
| | - Paulo Renato Rivas Totino
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.,Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brazil
| | | | - Michael Theisen
- Centre for Medical Parasitology at Department of International Health, Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Susheel Kumar Singh
- Centre for Medical Parasitology at Department of International Health, Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Linda Eva Amoah
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Marcelo Ribeiro-Alves
- Laboratório de Pesquisa Clínica em DST e AIDS, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
| | - Rodrigo Medeiros Souza
- Laboratório de Doenças Infecciosas na Amazônia Ocidental, Universidade Federal do Acre, Acre, Brazil
| | | | - Cláudio Tadeu Daniel-Ribeiro
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.,Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brazil
| | - Lilian Rose Pratt-Riccio
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. .,Centro de Pesquisa, Diagnóstico e Treinamento em Malária, Fiocruz, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brazil.
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20
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Kawanami T, Kawanami-Iwao H, Takata T, Ishigaki Y, Tomosugi N, Takegami T, Yanagisawa H, Fujimoto S, Sakai T, Fujita Y, Yamada K, Mizuta S, Kawabata H, Fukushima T, Hirose Y, Masaki Y. Comprehensive analysis of protein-expression changes specific to immunoglobulin G4-related disease. Clin Chim Acta 2021; 523:45-57. [PMID: 34453919 DOI: 10.1016/j.cca.2021.08.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/30/2021] [Accepted: 08/20/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Immunoglobulin 4 (IgG4)-related disease (IgG4-RD) is a lymphoproliferative disorder characterized by elevated serum IgG4 levels and tissue infiltration of IgG4-positive plasma cells. We analyzed the serum proteins, whose levels varied based on the disease state and treatment. MATERIALS AND METHODS Serum proteins from patients with IgG4-related disease and healthy subjects were resolved using two-dimensional electrophoresis, silver-stained, and scanned. Alternatively, the proteins were labeled with Cy2, Cy3, and Cy5 before electrophoresis. The proteins, whose expression differed significantly between patients and healthy individuals, and between before and after steroid treatment, were identified and validated using enzyme-linked immunosorbent assays. RESULTS Pre-treatment sera from patients with IgG4-related disease was characterized by increased levels of immunoglobulins such as IgG1, IgG4; inflammatory factors such as α-1 antitrypsin (A1AT); and proteins associated with immune system regulation such as clusterin and leucine-rich α-2-glycoprotein (LRG-1). The serum levels of A1AT, LRG-1 and clusterin, during treatment with prednisolone for up to 12 months revealed that LRG-1 levels were halved after 1 month of treatment, comparable to those in healthy subjects; LRG-1 levels remained normal until the end of treatment. CONCLUSION LRG-1 could serve as a novel biomarker of IgG4-related diseases.
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Affiliation(s)
- Takafumi Kawanami
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan.
| | - Haruka Kawanami-Iwao
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Takanobu Takata
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yasuhito Ishigaki
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Naohisa Tomosugi
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Tsutomu Takegami
- Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Hiroto Yanagisawa
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Shino Fujimoto
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Tomoyuki Sakai
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yoshimasa Fujita
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Kazunori Yamada
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Shuichi Mizuta
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Hiroshi Kawabata
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan; Department of Hematology, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa Mukaihata-cho, Fushimi-ku, Kyoto, Japan
| | - Toshihiro Fukushima
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yuko Hirose
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
| | - Yasufumi Masaki
- Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa-ken 920-0293, Japan
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21
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Tikhonov A, Smoldovskaya O, Feyzkhanova G, Kushlinskii N, Rubina A. Glycan-specific antibodies as potential cancer biomarkers: a focus on microarray applications. Clin Chem Lab Med 2021; 58:1611-1622. [PMID: 32324152 DOI: 10.1515/cclm-2019-1161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/10/2020] [Indexed: 02/06/2023]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins and lipids. In the case of tumors, cell transformation accompanied by aberrant glycosylation results in the expression of tumor-associated glycans that promote tumor invasion. As part of the innate immunity, anti-glycan antibodies recognize tumor-associated glycans, and these antibodies can be present in the bloodstream in the early stages of cancer. Recently, anti-glycan antibody profiles have been of interest in various cancer studies. Novel advantages in the field of analytical techniques have simplified the analysis of anti-glycan antibodies and made it easier to have more comprehensive knowledge about their functions. One of the robust approaches for studying anti-glycan antibodies engages in microarray technology. The analysis of glycan microarrays can provide more expanded information to simultaneously specify or suggest the role of antibodies to a wide variety of glycans in the progression of different diseases, therefore making it possible to identify new biomarkers for diagnosing cancer and/or the state of the disease. Thus, in this review, we discuss antibodies to various glycans, their application for diagnosing cancer and one of the most promising tools for the investigation of these molecules, microarrays.
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Affiliation(s)
- Aleksei Tikhonov
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Smoldovskaya
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Guzel Feyzkhanova
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay Kushlinskii
- Laboratory of Clinical Biochemistry, Federal State Budgetary Institution «N.N. Blokhin National Medical Research Center of Oncology» оf the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alla Rubina
- Laboratory of Biological Microchips, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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22
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Thiruvengadam M, Subramanian U, Venkidasamy B, Thirupathi P, Samynathan R, Shariati MA, Rebezov M, Chung IM, Rengasamy KRR. Emerging role of nutritional short-chain fatty acids (SCFAs) against cancer via modulation of hematopoiesis. Crit Rev Food Sci Nutr 2021; 63:827-844. [PMID: 34319824 DOI: 10.1080/10408398.2021.1954874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The understanding of gut microbiota has emerged as a significant frontier in development of strategies to maintain normal human body's homeostasis and preventing the disease development over the last decade. The composition of the gut microbiota influences the clinical benefit of immune checkpoints in patients with advanced cancer, but the mechanisms underlying this relationship are unclear. Cancer is among the leading causes of mortality worldwide. So far, there is no universal treatment for cancer and despite significant advances, a lot of improvement on cancer therapy is required. Owing to its role in preserving the host's health and maintaining cellular integrity, the human gut microbiome has recently drawn a lot of interest as a target for cancer treatment. Dietary fiber is fermented by the gut microbiota to generate short-chain fatty acids (SCFAs), such as acetate, butyrate, and propionate, which are physiologically active metabolites. SCFAs can modulate the pathophysiology of the tumor environment through various critical signaling pathways. In addition, SCFAs can bind to carcinogens and other toxic chemicals, thus facilitating their biotransformation and elimination through different excretory mechanisms. This review discusses the mechanisms of action of short-chain fatty acids in modulating hematopoiesis of various immune system cells and the resultant beneficial anti-cancer effects. It also provides future perspectives on cancer therapy.
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Affiliation(s)
- Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
| | - Umadevi Subramanian
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Baskar Venkidasamy
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore, India
| | - Prabhu Thirupathi
- Translational Research Platform for Veterinary Biologicals, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | | | - Mohammad Ali Shariati
- Department of Technology of Food Products, K.G. Razumovsky Moscow State University of Technologies and Management (The First Cossack University), Moscow, Russian Federation
| | - Maksim Rebezov
- V M Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow, Russian Federation.,Prokhorov General Physics Institute of the Russian Academy of Science, Moscow, Russian Federation
| | - Ill-Min Chung
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
| | - Kannan R R Rengasamy
- Green Biotechnologies Research Centre of Excellence, University of Limpopo, Mankweng, South Africa
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23
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Aizik L, Dror Y, Taussig D, Barzel A, Carmi Y, Wine Y. Antibody Repertoire Analysis of Tumor-Infiltrating B Cells Reveals Distinct Signatures and Distributions Across Tissues. Front Immunol 2021; 12:705381. [PMID: 34349765 PMCID: PMC8327180 DOI: 10.3389/fimmu.2021.705381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The role of B cells in the tumor microenvironment (TME) has largely been under investigated, and data regarding the antibody repertoire encoded by B cells in the TME and the adjacent lymphoid organs are scarce. Here, we utilized B cell receptor high-throughput sequencing (BCR-Seq) to profile the antibody repertoire signature of tumor-infiltrating lymphocyte B cells (TIL−Bs) in comparison to B cells from three anatomic compartments in a mouse model of triple-negative breast cancer. We found that TIL-Bs exhibit distinct antibody repertoire measures, including high clonal polarization and elevated somatic hypermutation rates, suggesting a local antigen-driven B-cell response. Importantly, TIL-Bs were highly mutated but non-class switched, suggesting that class-switch recombination may be inhibited in the TME. Tracing the distribution of TIL-B clones across various compartments indicated that they migrate to and from the TME. The data thus suggests that antibody repertoire signatures can serve as indicators for identifying tumor-reactive B cells.
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Affiliation(s)
- Ligal Aizik
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Dror
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - David Taussig
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Adi Barzel
- The School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Carmi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yariv Wine
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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24
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Mori H, Masahata K, Umeda S, Morine Y, Ishibashi H, Usui N, Shimada M. Risk of carcinogenesis in the biliary epithelium of children with congenital biliary dilatation through epigenetic and genetic regulation. Surg Today 2021; 52:215-223. [PMID: 34132887 DOI: 10.1007/s00595-021-02325-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022]
Abstract
PURPOSES Congenital biliary dilatation (CBD), defined as pancreaticobiliary maljunction (PBM) with biliary dilatation, is a high risk factor for biliary tract cancer (BTC). KRAS and p53 mutations reportedly affect this process, but the mechanisms are unclear, as is the likelihood of BTC later in life in children with CBD. We investigated potential carcinogenetic pathways in children with CBD compared with adults. METHODS The subjects of this study were nine children with CBD and 13 adults with PBM (10 dilated, 3 non-dilated) without BTC who underwent extrahepatic bile duct resections, as well as four control patients who underwent pancreaticoduodenectomy for non-biliary cancer. We evaluated expressions of Ki-67, KRAS, p53, histone deacetylase (HDAC) and activation-induced cytidine deaminase (AID) in the biliary tract epithelium immunohistochemically. RESULTS The Ki-67 labeling index (LI) and expressions of KRAS, p53, HDAC, and AID in the gallbladder epithelium were significantly higher or tended to be higher in both the children with CBD and the adults with PBM than in the controls. CONCLUSIONS BTC may develop later in children with CBD and in adults with PBM, via HDAC and AID expression and through epigenetic and genetic regulation.
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Affiliation(s)
- Hiroki Mori
- Department of Surgery, Institute of Health Biosciences, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan.
| | - Kazunori Masahata
- Department of Pediatric Surgery, Osaka Women's and Children's Hospital, Murodoucho 840, Izumi, Osaka, 594-1101, Japan
| | - Satoshi Umeda
- Department of Pediatric Surgery, Osaka Women's and Children's Hospital, Murodoucho 840, Izumi, Osaka, 594-1101, Japan
| | - Yuji Morine
- Department of Surgery, Institute of Health Biosciences, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Hiroki Ishibashi
- Department of Surgery, Institute of Health Biosciences, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Noriaki Usui
- Department of Pediatric Surgery, Osaka Women's and Children's Hospital, Murodoucho 840, Izumi, Osaka, 594-1101, Japan
| | - Mitsuo Shimada
- Department of Surgery, Institute of Health Biosciences, The University of Tokushima, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
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25
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Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
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Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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26
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Català-Moll F, Ferreté-Bonastre AG, Li T, Weichenhan D, Lutsik P, Ciudad L, Álvarez-Prado ÁF, Rodríguez-Ubreva J, Klemann C, Speckmann C, Vilas-Zornoza A, Abolhassani H, Martínez-Gallo M, Dieli-Crimi R, Rivière JG, Martín-Nalda A, Colobran R, Soler-Palacín P, Kracker S, Hammarström L, Prosper F, Durandy A, Grimbacher B, Plass C, Ballestar E. Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction. Nucleic Acids Res 2021; 49:5057-5073. [PMID: 33950194 PMCID: PMC8136777 DOI: 10.1093/nar/gkab322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. In this study, using whole-genome bisulfite sequencing of HIGM2 B cells, we investigated direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation alterations, of which ∼25% are attributable to active DNA demethylation. For genes that undergo active demethylation that is impaired in HIGM2 individuals, our analysis indicates that AID is not directly involved. We demonstrate that the widespread alterations in the DNA methylation and expression profiles of HIGM2 naïve B cells result from premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data support a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns.
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Affiliation(s)
- Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Anna G Ferreté-Bonastre
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Ángel F Álvarez-Prado
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Christian Klemann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, Center for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Germany
| | - Amaya Vilas-Zornoza
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Mónica Martínez-Gallo
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Romina Dieli-Crimi
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Jacques G Rivière
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Sven Kracker
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Felipe Prosper
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Anne Durandy
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Center for Infection Research (DZIF), Satellite Center Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs University, Freiburg, Germany
- RESIST, Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
- Institute of Immunity & Transplantation, Royal Free Hospital, University College London, UK
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
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27
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Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.
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Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
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28
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Nakanishi R, Shimizu T, Kumagai K, Takai A, Marusawa H. Genetic Pathogenesis of Inflammation-Associated Cancers in Digestive Organs. Pathogens 2021; 10:453. [PMID: 33918902 PMCID: PMC8069378 DOI: 10.3390/pathogens10040453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/12/2021] [Accepted: 04/08/2021] [Indexed: 12/20/2022] Open
Abstract
Epidemiological, clinical, and biological studies convincingly demonstrate that chronic inflammation predisposes to the development of human cancers. In digestive organs, inflammation-associated cancers include colitis-associated colorectal cancers, Helicobacter pylori-associated gastric cancer, as well as Barrett's esophagus and esophageal adenocarcinoma associated with chronic duodenogastric-esophageal reflux. Cancer is a genomic disease, and stepwise accumulation of genetic and epigenetic alterations of tumor-related genes leads to the development of tumor cells. Recent genome analyses show that genetic alterations, which are evoked by inflammation, are latently accumulated in inflamed epithelial cells of digestive organs. Production of reactive oxygen and aberrant expression of activation-induced cytidine deaminase, a nucleotide-editing enzyme, could be induced in inflamed gastrointestinal epithelial cells and play a role as a genomic modulator of inflammation-associated carcinogenesis. Understanding the molecular linkage between inflammation and genetic alterations will open up a new field of tumor biology and provide a novel strategy for the prevention of inflammation-associated tumorigenesis.
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Affiliation(s)
- Risa Nakanishi
- Department of Gastroenterology, Red Cross Osaka Hospital, Osaka 543-8555, Japan;
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Ken Kumagai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; (T.S.); (K.K.); (A.T.)
| | - Hiroyuki Marusawa
- Department of Gastroenterology, Red Cross Osaka Hospital, Osaka 543-8555, Japan;
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29
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Ghosh D, Raghavan SC. Nonhomologous end joining: new accessory factors fine tune the machinery. Trends Genet 2021; 37:582-599. [PMID: 33785198 DOI: 10.1016/j.tig.2021.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major DNA double-strand break (DSB) repair pathways in eukaryotes. The well-known critical proteins involved in NHEJ include Ku70/80, DNA-PKcs, Artemis, DNA pol λ/μ, DNA ligase IV-XRCC4, and XLF. Recent studies have added a number of new proteins to the NHEJ repertoire namely paralog of XRCC4 and XLF (PAXX), modulator of retroviral infection (MRI)/ cell cycle regulator of NHEJ (CYREN), transactivation response DNA-binding protein (TARDBP) of 43 kDa (TDP-43), intermediate filament family orphan (IFFO1), ERCC excision repair 6 like 2 (ERCC6L2), and RNase H2. PAXX acts as a stabilizing factor for the main NHEJ components. MRI/CYREN seems to play a dual role stimulating NHEJ in the G1 phase of the cell cycle, while inhibiting the pathway in the S and G2 phases. TDP-43 can recruit the ligase IV-XRCC4 complex to the DSB sites and stimulate ligation in neuronal cells. RNase H2 excises out the ribonucleotides inserted during repair by DNA polymerase μ/TdT. This review provides a brief glimpse into how these new partners were discovered and their contribution to the mechanism and regulation of NHEJ.
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Affiliation(s)
- Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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30
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Repair of programmed DNA lesions in antibody class switch recombination: common and unique features. ACTA ACUST UNITED AC 2021; 2:115-125. [PMID: 33817557 PMCID: PMC7996122 DOI: 10.1007/s42764-021-00035-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023]
Abstract
The adaptive immune system can diversify the antigen receptors to eliminate various pathogens through programmed DNA lesions at antigen receptor genes. In immune diversification, general DNA repair machineries are applied to transform the programmed DNA lesions into gene mutation or recombination events with common and unique features. Here we focus on antibody class switch recombination (CSR), and review the initiation of base damages, the conversion of damaged base to DNA double-strand break, and the ligation of broken ends. With an emphasis on the unique features in CSR, we discuss recent advances in the understanding of DNA repair/replication coordination, and ERCC6L2-mediated deletional recombination. We further elaborate the application of CSR in end-joining, resection and translesion synthesis assays. In the time of the COVID-19 pandemic, we hope it help to understand the generation of therapeutic antibodies.
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31
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IgH 3' regulatory region increases ectopic class switch recombination. PLoS Genet 2021; 17:e1009288. [PMID: 33556079 PMCID: PMC7869978 DOI: 10.1371/journal.pgen.1009288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
DNA lesions inflicted by activation-induced deaminase (AID) instrumentally initiate the processes reshaping immunoglobulin genes in mature B-cells, from local somatic hypermutation (SHM) to junctions of distant breaks during class switch recombination (CSR). It remains incompletely understood how these divergent outcomes of AID attacks are differentially and temporally focused, with CSR strictly occurring in the Ig heavy chain (IgH) locus while SHM concentrates on rearranged V(D)J regions in the IgH and Ig light chain loci. In the IgH locus, disruption of either the 3’Regulatory Region (3’RR) super-enhancer or of switch (S) regions preceding constant genes, profoundly affects CSR. Reciprocally, we now examined if these elements are sufficient to induce CSR in a synthetic locus based on the Igκ locus backbone. Addition of a surrogate “core 3’RR” (c3’RR) and of a pair of transcribed and spliced Switch regions, together with a reporter system for “κ-CSR” yielded a switchable Igκ locus. While the c3’RR stimulated SHM at S regions, it also lowered the local SHM threshold necessary for switch recombination to occur. The 3’RR thus both helps recruit AID to initiate DNA lesions, but then also promotes their resolution through long-distance synapses and recombination following double-strand breaks. Class switching allows B lymphocytes to replace expression of immunoglobin M with that of immunoglobulins G, A or E. The genetic support of class switching, is a unique and large deletion uniquely occuring within the immunoglobulin heavy chain (IgH) locus. This recombination is triggered after DNA lesions inflicted by the activation-induced deaminase (AID) enzyme. In immunoglobulin light chain loci, AID only stimulates somatic hypermutation. In such a non-IgH locus, we now show that the IgH 3’ superenhancer can promote junctions between distant DNA breaks and ectopic class switch recombination. This study identifies the minimal elements necessary for class-switch recombination to occur instead of hypermutation in a locus targeted by AID, i.e. transcribed (and spliced) target sites for AID in so-called S regions, and the 3’IgH superenhancer which both helps recruit AID for DNA lesions, and helps repair these lesions through distant gene synapsis and recombination.
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32
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Luong TMH, Matsuda K, Niino D, Kurohama H, Ito M, Nakashima M. Significance of abnormal 53BP1 expression as a novel molecular pathologic parameter of follicular-shaped B-cell lymphoid lesions in human digestive tract. Sci Rep 2021; 11:3074. [PMID: 33542453 PMCID: PMC7862599 DOI: 10.1038/s41598-021-82867-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/19/2021] [Indexed: 11/24/2022] Open
Abstract
The digestive tract is a common site of extranodal malignant lymphomas (MLs) and benign lymphoid lesions (BLs). TP53-binding protein 1 (53BP1) expression has been widely investigated in class switch recombination but rarely in human lymphoid tissues with respect to tumorigenesis. We previously reported that immunofluorescence (IF) analysis of 53BP1 nuclear foci (NF), reflecting DNA double strand breaks, is useful for estimating genomic instability in different tumor types. In this study, we evaluated the potential of IF-based analysis of 53BP1 expression in differentiating MLs from BLs. We examined 231 biopsied tissue samples of primary MLs and BLs in the digestive tract. The 53BP1 immunoreactivity pattern was determined by multicolor IF. Compared to BLs, MLs showed a high frequency of abnormal 53BP1 expression (p < 0.0001). Statistically, abnormal 53BP1 expression is an effective test for distinguishing follicular lymphomas from BLs (specificity 98.6%, sensitivity 86.8%) and for distinguishing small B-cell lymphomas from BLs (specificity 98.3%, sensitivity 77.6%). Furthermore, a high frequency of abnormal 53BP1 expression was associated with “high-risk” MALT lymphomas, which exhibited t(11;18)(q21;21) (p = 0.0145). Collectively, these results suggest that IF-based analysis of 53BP1 expression in biopsy samples is a promising technique for diagnosing MLs in the digestive system.
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Affiliation(s)
- Thi My Hanh Luong
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Katsuya Matsuda
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Daisuke Niino
- Department of Pathology, Local Incorporated Administrative Agency Sasebo City General Hospital, Sasebo, Japan
| | - Hirokazu Kurohama
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Masahiro Ito
- Department of Pathology, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Masahiro Nakashima
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
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33
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Jiang Y, Dong Y, Luo Y, Jiang S, Meng FL, Tan M, Li J, Zang Y. AMPK-mediated phosphorylation on 53BP1 promotes c-NHEJ. Cell Rep 2021; 34:108713. [PMID: 33596428 DOI: 10.1016/j.celrep.2021.108713] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 11/12/2020] [Accepted: 01/12/2021] [Indexed: 12/25/2022] Open
Abstract
AMP-activated protein kinase (AMPK) is an energy sensor that plays roles in multiple biological processes beyond metabolism. Several studies have suggested that AMPK is involved in the DNA damage response (DDR), but the mechanisms remain unclear. Herein, we demonstrate that AMPK promotes classic non-homologous end joining (c-NHEJ) in double-strand break (DSB) repair through recruiting a key chromatin-based mediator named p53-binding protein 1 (53BP1), which facilitates the end joining of distal DNA ends during DDR. We find that the interaction of AMPK and 53BP1 spatially occurs under DSB stress. In the context of DSBs, AMPK directly phosphorylates 53BP1 at Ser1317 and promotes 53BP1 recruitment during DDR for an efficient c-NHEJ, thus maintaining genomic stability and diversity of the immune repertoire. Taken together, our study demonstrates that AMPK is a regulator of 53BP1 and controls c-NHEJ choice by phospho-regulation.
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Affiliation(s)
- Yuejing Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Ying Dong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yifeng Luo
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shangwen Jiang
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fei-Long Meng
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Minjia Tan
- University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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34
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Ochiai K, Yamaoka M, Swaminathan A, Shima H, Hiura H, Matsumoto M, Kurotaki D, Nakabayashi J, Funayama R, Nakayama K, Arima T, Ikawa T, Tamura T, Sciammas R, Bouvet P, Kundu TK, Igarashi K. Chromatin Protein PC4 Orchestrates B Cell Differentiation by Collaborating with IKAROS and IRF4. Cell Rep 2020; 33:108517. [PMID: 33357426 DOI: 10.1016/j.celrep.2020.108517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/10/2020] [Accepted: 11/22/2020] [Indexed: 12/24/2022] Open
Abstract
The chromatin protein positive coactivator 4 (PC4) has multiple functions, including chromatin compaction. However, its role in immune cells is largely unknown. We show that PC4 orchestrates chromatin structure and gene expression in mature B cells. B-cell-specific PC4-deficient mice show impaired production of antibody upon antigen stimulation. The PC4 complex purified from B cells contains the transcription factors (TFs) IKAROS and IRF4. IKAROS protein is reduced in PC4-deficient mature B cells, resulting in de-repression of their target genes in part by diminished interactions with gene-silencing components. Upon activation, the amount of IRF4 protein is not increased in PC4-deficient B cells, resulting in reduction of plasma cells. Importantly, IRF4 reciprocally induces PC4 expression via a super-enhancer. PC4 knockdown in human B cell lymphoma and myeloma cells reduces IKAROS protein as an anticancer drug, lenalidomide. Our findings establish PC4 as a chromatin regulator of B cells and a possible therapeutic target adjoining IKAROS in B cell malignancies.
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Affiliation(s)
- Kyoko Ochiai
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan.
| | - Mari Yamaoka
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Amrutha Swaminathan
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Daisuke Kurotaki
- Department of Immunology, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Yokohama 236-0004, Japan
| | - Jun Nakabayashi
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Yokohama 236-0004, Japan
| | - Ryo Funayama
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Keiko Nakayama
- Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Tomokatsu Ikawa
- Division of Immunobiology, Tokyo University of Science, Yamazaki 2669, Noda 278-0022, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Yokohama 236-0004, Japan; Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Yokohama 236-0004, Japan
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, Centre de Recherche en Cancérologie de Lyon, Cancer Cell Plasticity Department, UMR INSERM 1052 CNRS 5286, Centre Léon Bérard, Lyon, France
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India.
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan.
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35
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Kalfaoglu B, Almeida-Santos J, Tye CA, Satou Y, Ono M. T-cell dysregulation in COVID-19. Biochem Biophys Res Commun 2020; 538:204-210. [PMID: 33220925 PMCID: PMC7648511 DOI: 10.1016/j.bbrc.2020.10.079] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
T-cells play key roles in immunity to COVID-19 as well as the development of severe disease. T-cell immunity to COVID-19 is mediated through differentiated CD4+ T-cells and cytotoxic CD8+ T-cells, although their differentiation is often atypical and ambiguous in COVID-19 and single cell dynamics of key genes need to be characterized. Notably, T-cells are dysregulated in severe COVID-19 patients, although their molecular features are still yet to be fully revealed. Importantly, it is not clear which T-cell activities are beneficial and protective and which ones can contribute to the development of severe COVID-19. In this article, we examine the latest evidence and discuss the key features of T-cell responses in COVID-19, showing how T-cells are dysregulated in severe COVID-19 patients. Particularly, we highlight the impairment of FOXP3 induction in CD4+ T-cells and how the impaired FOXP3 expression can lead to the differentiation of abnormally activated (hyperactivated) T-cells and the dysregulated T-cell responses in severe patients. Furthermore, we characterise the feature of hyperactivated T-cells, showing their potential contribution to T-cell dysregulation and immune-mediated tissue destruction (immunopathology) in COVID-19.
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Affiliation(s)
| | - José Almeida-Santos
- Department of Life Sciences, Imperial College London, UK; Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Yorifumi Satou
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Japan
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, UK; International Research Center for Medical Sciences, Kumamoto University, Japan.
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36
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Bagno FF, Godói LC, Figueiredo MM, Sérgio SAR, Moraes TDFS, Salazar NDC, Kim YC, Reyes-Sandoval A, da Fonseca FG. Chikungunya E2 Protein Produced in E. coli and HEK293-T Cells-Comparison of Their Performances in ELISA. Viruses 2020; 12:E939. [PMID: 32858804 PMCID: PMC7552038 DOI: 10.3390/v12090939] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 12/29/2022] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne pathogen that causes a disease characterized by the acute onset of fever accompanied by arthralgia and intense joint pain. Clinical similarities and cocirculation of this and other arboviruses in many tropical countries highlight the necessity for efficient and accessible diagnostic tools. CHIKV envelope proteins are highly conserved among alphaviruses and, particularly, the envelope 2 glycoprotein (CHIKV-E2) appears to be immunodominant and has a considerable serodiagnosis potential. Here, we investigate how glycosylation of CHIKV-E2 affects antigen/antibody interaction and how this affects the performance of CHIKV-E2-based Indirect ELISA tests. We compare two CHIKV-E2 recombinant antigens produced in different expression systems: prokaryotic-versus eukaryotic-made recombinant proteins. CHIKV-E2 antigens are expressed either in E. coli BL21(DE3)-a prokaryotic system unable to produce post-translational modifications-or in HEK-293T mammalian cells-a eukaryotic system able to add post-translational modifications, including glycosylation sites. Both prokaryotic and eukaryotic recombinant CHIKV-E2 react strongly to anti-CHIKV IgG antibodies, showing accuracy levels that are higher than 90%. However, the glycan-added viral antigen presents better sensitivity and specificity (85 and 98%) than the non-glycosylated antigen (81 and 71%, respectively) in anti-CHIKV IgM ELISA assays.
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Affiliation(s)
- Flávia Fonseca Bagno
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico da UFMG (BH-Tec), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte-MG 31320-000, Brazil; (F.F.B.); (L.C.G.); (M.M.F.); (S.A.R.S.); (T.d.F.S.M.); (N.d.C.S.)
- Laboratório de Virologia Molecular e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB/UFMG), Belo Horizonte-MG 31270-901, Brazil
| | - Lara Carvalho Godói
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico da UFMG (BH-Tec), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte-MG 31320-000, Brazil; (F.F.B.); (L.C.G.); (M.M.F.); (S.A.R.S.); (T.d.F.S.M.); (N.d.C.S.)
- Colégio Técnico da Universidade Federal de Minas Gerais (COLTEC), Belo Horizonte-MG 31270-901, Brazil
| | - Maria Marta Figueiredo
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico da UFMG (BH-Tec), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte-MG 31320-000, Brazil; (F.F.B.); (L.C.G.); (M.M.F.); (S.A.R.S.); (T.d.F.S.M.); (N.d.C.S.)
| | - Sarah Aparecida Rodrigues Sérgio
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico da UFMG (BH-Tec), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte-MG 31320-000, Brazil; (F.F.B.); (L.C.G.); (M.M.F.); (S.A.R.S.); (T.d.F.S.M.); (N.d.C.S.)
| | - Thaís de Fátima Silva Moraes
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico da UFMG (BH-Tec), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte-MG 31320-000, Brazil; (F.F.B.); (L.C.G.); (M.M.F.); (S.A.R.S.); (T.d.F.S.M.); (N.d.C.S.)
- Laboratório de Virologia Molecular e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB/UFMG), Belo Horizonte-MG 31270-901, Brazil
| | - Natália de Castro Salazar
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico da UFMG (BH-Tec), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte-MG 31320-000, Brazil; (F.F.B.); (L.C.G.); (M.M.F.); (S.A.R.S.); (T.d.F.S.M.); (N.d.C.S.)
| | - Young Chan Kim
- The Jenner Institute, Nuffield Department of Medicine, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK; (Y.C.K.); (A.R.-S.)
| | - Arturo Reyes-Sandoval
- The Jenner Institute, Nuffield Department of Medicine, The Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK; (Y.C.K.); (A.R.-S.)
| | - Flávio Guimarães da Fonseca
- Centro de Tecnologia em Vacinas (CT-Vacinas), Parque Tecnológico da UFMG (BH-Tec), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte-MG 31320-000, Brazil; (F.F.B.); (L.C.G.); (M.M.F.); (S.A.R.S.); (T.d.F.S.M.); (N.d.C.S.)
- Laboratório de Virologia Molecular e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB/UFMG), Belo Horizonte-MG 31270-901, Brazil
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Abstract
A current challenge for disease modeling and public health is understanding pathogen dynamics across scales since their ecology and evolution ultimately operate on several coupled scales. This is particularly true for vector-borne diseases, where within-vector, within-host, and between vector–host populations all play crucial roles in diversity and distribution of the pathogen. Despite recent modeling efforts to determine the effect of within-host virus-immune response dynamics on between-host transmission, the role of within-vector viral dynamics on disease spread is overlooked. Here, we formulate an age-since-infection-structured epidemic model coupled to nonlinear ordinary differential equations describing within-host immune-virus dynamics and within-vector viral kinetics, with feedbacks across these scales. We first define the within-host viral-immune response and within-vector viral kinetics-dependent basic reproduction number [Formula: see text] Then we prove that whenever [Formula: see text] the disease-free equilibrium is locally asymptotically stable, and under certain biologically interpretable conditions, globally asymptotically stable. Otherwise, if [Formula: see text] it is unstable and the system has a unique positive endemic equilibrium. In the special case of constant vector to host inoculum size, we show the positive equilibrium is locally asymptotically stable and the disease is weakly uniformly persistent. Furthermore, numerical results suggest that within-vector-viral kinetics and dynamic inoculum size may play a substantial role in epidemics. Finally, we address how the model can be utilized to better predict the success of control strategies such as vaccination and drug treatment.
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Affiliation(s)
- HAYRIYE GULBUDAK
- Department of Mathematics, University of Louisiana at Lafayette, 104 E. University Circle, Lafayette, LA 70503, USA
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38
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Yang D, Sun Y, Chen J, Zhang Y, Fan S, Huang M, Xie X, Cai Y, Shang Y, Gui T, Sun L, Hu J, Dong J, Yeap LS, Wang X, Xiao W, Meng FL. REV7 is required for processing AID initiated DNA lesions in activated B cells. Nat Commun 2020; 11:2812. [PMID: 32499490 PMCID: PMC7272641 DOI: 10.1038/s41467-020-16632-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 05/13/2020] [Indexed: 01/10/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates both antibody class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. DNA double-strand break response (DSBR) factors promote rearrangement in CSR, while translesion synthesis (TLS) polymerases generate mutations in SHM. REV7, a component of TLS polymerase zeta, is also a downstream effector of 53BP1-RIF1 DSBR pathway. Here, we study the multi-functions of REV7 and find that REV7 is required for the B cell survival upon AID-deamination, which is independent of its roles in DSBR, G2/M transition or REV1-mediated TLS. The cell death in REV7-deficient activated B cells can be fully rescued by AID-deficiency in vivo. We further identify that REV7-depedent TLS across UNG-processed apurinic/apyrimidinic sites is required for cell survival upon AID/APOBEC deamination. This study dissects the multiple roles of Rev7 in antibody diversification, and discovers that TLS is not only required for sequence diversification but also B cell survival upon AID-initiated lesions. REV7 has emerged as a critical regulator of DNA double-strand breaks repair. Here, the authors show that REV7 is crucial for both antibody class switch recombination and somatic hypermutation in activated B cells, in addition to their survival upon AID-deamination.
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Affiliation(s)
- Dingpeng Yang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Sun
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jingjing Chen
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Ying Zhang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuangshuang Fan
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min Huang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yafang Shang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tuantuan Gui
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Liming Sun
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Leng-Siew Yeap
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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39
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Islam H, Kobayashi M, Honjo T. Apurinic/apyrimidinic endonuclease 1 (APE1) is dispensable for activation-induced cytidine deaminase (AID)-dependent somatic hypermutation in the immunoglobulin gene. Int Immunol 2020; 31:543-554. [PMID: 30877298 DOI: 10.1093/intimm/dxz028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates DNA breakage in the variable (V) and switch (S) regions of the immunoglobulin gene, which results in somatic hypermutation (SHM) and class switch recombination (CSR), respectively. Apurinic/apyrimidinic endonuclease 1 (APE1) has been shown to be important for CSR, and is supposed to cleave at abasic sites when AID-dependently deaminated cytidine is removed by uracil DNA glycosylase. However, APE1 is unexpectedly dispensable for SHM in the S region and translocation between immunoglobulin heavy chain (IgH) and c-myc genes in the mouse B lymphoma cell line, CH12F3-2A. This suggested that APE1 is not involved in AID-dependent DNA breakage, but rather, in DNA repair. In order to investigate detailed molecular mechanisms underlying APE1's involvement in CSR and SHM, we measured apurinic/apyrimidinic (AP) sites via aldehyde reactive probe labeling. Results indicated that the frequencies of AP sites in the S regions were not different between APE1-/-/-CH12F3-2A and wild-type CH12F3-2A cells. To carry out similar experiments in SHM of the V region, we generated an APE1 knockout (APE1-/-) human Burkitt's lymphoma cell line, and compared SHM between APE1-proficient and -deficient BL2 lymphoma cells. SHM frequencies in the V regions of APE1-/-BL2 and APE1-proficient cells were also similar. Taken together, we showed that AID does not induce AP sites in the S region of the IgH gene, and that APE1 is not necessary for SHM in the V and S regions; however, it is required for DNA repair following DNA breakage in CSR.
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Affiliation(s)
- Helena Islam
- Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Maki Kobayashi
- Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Tasuku Honjo
- Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
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40
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Liu Y, Yuan X, Li L, Lin L, Zuo X, Cong Y, Li Y. Increased Ileal Immunoglobulin A Production and Immunoglobulin A-Coated Bacteria in Diarrhea-Predominant Irritable Bowel Syndrome. Clin Transl Gastroenterol 2020; 11:e00146. [PMID: 32352710 PMCID: PMC7145038 DOI: 10.14309/ctg.0000000000000146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Immune activation and intestinal microbial dysbiosis could induce diarrhea-predominant irritable bowel syndrome (IBS-D). We examined the roles of ileal immunoglobulin A (IgA) and IgA-coated bacteria in IBS-D pathogenesis. METHODS Peripheral blood, fecal samples, and ileal and cecal biopsies were collected from 32 healthy volunteers and 44 patients with IBS-D. Quantitative reverse transcriptase polymerase chain reaction was used to assess differential gene expression. IgA levels in the blood and fecal samples were quantified by an enzyme-linked immunosorbent assay. IgA cells were assessed by immunofluorescence imaging. Flow-cytometry-based IgA bacterial cell sorting and 16S rRNA gene sequencing (IgA-SEQ) was used to isolate and identify fecal IgA bacteria. RESULTS Fecal IgA, particularly IgA1, was upregulated in patients with IBS-D. IgA class switch and B cell-activating factor-receptor were increased in the terminal ileum of patients. The intestinal microbiota composition was altered in patients compared with that in controls. IgA-SEQ showed that the proportion of fecal IgA-coated bacteria was increased significantly in patients with IBS-D. IgA bacteria in patients with IBS-D showed higher abundances of Escherichia-Shigella, Granulicatella, and Haemophilus compared with healthy controls and IgA bacteria in patients with IBS-D. The Escherichia-Shigella IgA coating index was positively correlated with anxiety and depression. The Escherichia-Shigella relative abundance, luminal IgA activity, and some altered IgA-coated bacteria were positively associated with the clinical manifestations of IBS-D. DISCUSSION Microbial dysbiosis may promote the terminal ileal mucosa to produce higher levels of IgA, increasing the proportion of IgA-coated bacteria by activating IgA class switching, which might regulate local inflammation and clinical manifestations in IBS-D. IgA may mediate the effects of microbial dysbiosis on the pathogenesis of IBS-D.
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Affiliation(s)
- Yi Liu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Department of Gastroenterology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xunyi Yuan
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Lin Lin
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yingzi Cong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan, Shandong, China
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41
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Efficient Acquisition of Fully Human Antibody Genes against Self-Proteins by Sorting Single B Cells Stimulated with Vaccines Based on Nitrated T Helper Cell Epitopes. J Immunol Res 2020; 2019:7914326. [PMID: 32083142 PMCID: PMC7012236 DOI: 10.1155/2019/7914326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/07/2019] [Indexed: 11/19/2022] Open
Abstract
Single B cell antibody technology is a method for isolating antigen-specific B cells from human peripheral blood and obtaining antibody genes in developing antibody drugs. However, owing to immune tolerance to autoantigen, human autoantigen-specific B cells are difficult to acquire by conventional single B cell technology. In this study, we constructed a nitrated T-cell epitope named NitraTh by incorporating p-nitrophenylalanine into a universal T helper epitope. NitraTh had enhanced ability to activate CD4+ T cells and can be recognized by CD4+ T cells with different HLA class II haplotypes. This NitraTh can also break immune tolerance to autoantigens, such as human epidermal growth factor receptor 2 (HER2) and cannabinoid receptor 1, and induce strong specific IgM+ B cell responses in vitro. HER2-NitraTh vaccine can also stimulate the generation of HER2-specific IgG+ B cells in human immune system mice, which was established by cotransplanting lymphocytes and autologous dendritic cells in immunodeficient mice. We obtained 30 fully human IgG antibody genes by sorting single B cells from the human immune system mice immunized with HER2-NitraTh vaccine. The analysis of antibody genes showed that sorted B cells underwent the extensive somatic mutation of the antibody genes. We randomly selected eight genes for cloning, six of which expressed antibodies that can bind to HER2. Hence, we provided a convenient and effective method in acquiring fully human antibody genes against self-proteins, which can be used in developing therapeutic antibody drugs.
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42
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Medina A, Jiménez C, Sarasquete ME, González M, Chillón MC, Balanzategui A, Prieto-Conde I, García-Álvarez M, Puig N, González-Calle V, Alcoceba M, Cuenca I, Barrio S, Escalante F, Gutiérrez NC, Gironella M, Hernández MT, Sureda A, Oriol A, Bladé J, Lahuerta JJ, San Miguel JF, Mateos MV, Martínez-López J, Calasanz MJ, García-Sanz R. Molecular profiling of immunoglobulin heavy-chain gene rearrangements unveils new potential prognostic markers for multiple myeloma patients. Blood Cancer J 2020; 10:14. [PMID: 32029700 PMCID: PMC7004993 DOI: 10.1038/s41408-020-0283-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 01/09/2023] Open
Abstract
Multiple myeloma is a heterogeneous disease whose pathogenesis has not been completely elucidated. Although B-cell receptors play a crucial role in myeloma pathogenesis, the impact of clonal immunoglobulin heavy-chain features in the outcome has not been extensively explored. Here we present the characterization of complete heavy-chain gene rearrangements in 413 myeloma patients treated in Spanish trials, including 113 patients characterized by next-generation sequencing. Compared to the normal B-cell repertoire, gene selection was biased in myeloma, with significant overrepresentation of IGHV3, IGHD2 and IGHD3, as well as IGHJ4 gene groups. Hypermutation was high in our patients (median: 8.8%). Interestingly, regarding patients who are not candidates for transplantation, a high hypermutation rate (≥7%) and the use of IGHD2 and IGHD3 groups were associated with improved prognostic features and longer survival rates in the univariate analyses. Multivariate analysis revealed prolonged progression-free survival rates for patients using IGHD2/IGHD3 groups (HR: 0.552, 95% CI: 0.361-0.845, p = 0.006), as well as prolonged overall survival rates for patients with hypermutation ≥7% (HR: 0.291, 95% CI: 0.137-0.618, p = 0.001). Our results provide new insights into the molecular characterization of multiple myeloma, highlighting the need to evaluate some of these clonal rearrangement characteristics as new potential prognostic markers.
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Affiliation(s)
- Alejandro Medina
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - Cristina Jiménez
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - M Eugenia Sarasquete
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain.
| | - Marcos González
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - M Carmen Chillón
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - Ana Balanzategui
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - Isabel Prieto-Conde
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - María García-Álvarez
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - Noemí Puig
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - Verónica González-Calle
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | - Miguel Alcoceba
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | | | | | | | - Norma C Gutiérrez
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | | | | | - Anna Sureda
- Hospital Duran i Reynals, Institut Català d'Oncología (ICO), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Albert Oriol
- Hospital Germans Trias i Pujol, Institut Català d'Oncología (ICO), Institut Josep Carreras, Badalona, Spain
| | - Joan Bladé
- Hospital Clínic i Provincial, Institut de Investicacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Jesús F San Miguel
- Clínica Universidad de Navarra (CUN), Centro de Investigación Médica Aplicada, IDISNA, CIBERONC, Pamplona, Spain
| | - María-Victoria Mateos
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
| | | | - María-José Calasanz
- Clínica Universidad de Navarra (CUN), Centro de Investigación Médica Aplicada, IDISNA, CIBERONC, Pamplona, Spain
| | - Ramón García-Sanz
- Hospital Universitario de Salamanca (HUSAL), IBSAL, IBMCC (USAL-CSIC), CIBERONC, Salamanca, Spain
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43
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Kassab MA, Yu LL, Yu X. Targeting dePARylation for cancer therapy. Cell Biosci 2020; 10:7. [PMID: 32010441 PMCID: PMC6988220 DOI: 10.1186/s13578-020-0375-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) mediated by poly ADP-ribose polymerases (PARPs) plays a key role in DNA damage repair. Suppression of PARylation by PARP inhibitors impairs DNA damage repair and induces apoptosis of tumor cells with repair defects. Thus, PARP inhibitors have been approved by the US FDA for various types of cancer treatment. However, recent studies suggest that dePARylation also plays a key role in DNA damage repair. Instead of antagonizing PARylation, dePARylation acts as a downstream step of PARylation in DNA damage repair. Moreover, several types of dePARylation inhibitors have been developed and examined in the preclinical studies for cancer treatment. In this review, we will discuss the recent progress on the role of dePARylation in DNA damage repair and cancer suppression. We expect that targeting dePARylation could be a promising approach for cancer chemotherapy in the future.
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Affiliation(s)
- Muzaffer Ahmad Kassab
- 1Department of Cancer Genetics & Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
| | - Lily L Yu
- Westridge School, 324 Madeline Dr., Pasadena, CA 91105 USA
| | - Xiaochun Yu
- 1Department of Cancer Genetics & Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA 91010 USA
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44
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Pasqualucci L. Molecular pathogenesis of germinal center-derived B cell lymphomas. Immunol Rev 2019; 288:240-261. [PMID: 30874347 DOI: 10.1111/imr.12745] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
B cell lymphomas comprise a heterogeneous group of genetically, biologically, and clinically distinct neoplasms that, in most cases, originate from the clonal expansion of B cells in the germinal center (GC). In recent years, the advent of novel genomics technologies has revolutionized our understanding of the molecular pathogenesis of lymphoid malignancies as a multistep process that requires the progressive accumulation of multiple genetic and epigenetic alterations. A common theme that emerged from these studies is the ability of lymphoma cells to co-opt the same biological programs and signal transduction networks that operate during the normal GC reaction, and misuse them for their own survival advantage. This review summarizes recent progress in the understanding of the genetic and epigenetic mechanisms that drive the malignant transformation of GC B cells. These insights provide a conceptual framework for the identification of cellular pathways that may be explored for precision medicine approaches.
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Affiliation(s)
- Laura Pasqualucci
- Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York City, New York
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45
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Robaina MC, Mazzoccoli L, Klumb CE. Germinal Centre B Cell Functions and Lymphomagenesis: Circuits Involving MYC and MicroRNAs. Cells 2019; 8:E1365. [PMID: 31683676 PMCID: PMC6912346 DOI: 10.3390/cells8111365] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/30/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The transcription factor MYC regulates several biological cellular processes, and its target gene network comprises approximately 15% of all human genes, including microRNAs (miRNAs), that also contribute to MYC regulatory activity. Although miRNAs are emerging as key regulators of immune functions, the specific roles of miRNAs in the regulation/dysregulation of germinal centre B-cells and B-cell lymphomas are still being uncovered. The regulatory network that integrates MYC, target genes and miRNAs is a field of intense study, highlighting potential pathways to be explored in the context of future clinical approaches. METHODS The scientific literature that is indexed in PUBMED was consulted for publications involving MYC and miRNAs with validated bioinformatics analyses or experimental protocols. Additionally, seminal studies on germinal centre B-cell functions and lymphomagenesis were reported. CONCLUSIONS This review summarizes the interactions between MYC and miRNAs through regulatory loops and circuits involving target genes in germinal centre B-cell lymphomas with MYC alterations. Moreover, we provide an overview of the understanding of the regulatory networks between MYC and miRNAs, highlighting the potential implication of this approach for the comprehension of germinal centre B-cell lymphoma pathogenesis. Therefore, circuits involving MYC, target genes and miRNAs provide novel insight into lymphomagenesis that could be useful for new improved therapeutic strategies.
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Affiliation(s)
- Marcela Cristina Robaina
- Programa de Pesquisa em Hemato-Oncologia Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, CEP: 20230-130, Brazil.
| | - Luciano Mazzoccoli
- Programa de Pesquisa em Hemato-Oncologia Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, CEP: 20230-130, Brazil.
| | - Claudete Esteves Klumb
- Programa de Pesquisa em Hemato-Oncologia Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, CEP: 20230-130, Brazil.
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Morande PE, Sivina M, Uriepero A, Seija N, Berca C, Fresia P, Landoni AI, Di Noia JM, Burger JA, Oppezzo P. Ibrutinib therapy downregulates AID enzyme and proliferative fractions in chronic lymphocytic leukemia. Blood 2019; 133:2056-2068. [PMID: 30814061 PMCID: PMC7022232 DOI: 10.1182/blood-2018-09-876292] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates somatic hypermutation and class switch recombination of the immunoglobulin genes. As a trade-off for its physiological function, AID also contributes to tumor development through its mutagenic activity. In chronic lymphocytic leukemia (CLL), AID is overexpressed in the proliferative fractions (PFs) of the malignant B lymphocytes, and its anomalous expression has been associated with a clinical poor outcome. Recent preclinical data suggested that ibrutinib and idelalisib, 2 clinically approved kinase inhibitors, increase AID expression and genomic instability in normal and neoplastic B cells. These results raise concerns about a potential mutagenic risk in patients receiving long-term therapy. To corroborate these findings in the clinical setting, we analyzed AID expression and PFs in a CLL cohort before and during ibrutinib treatment. We found that ibrutinib decreases the CLL PFs and, interestingly, also reduces AID expression, which correlates with dampened AKT and Janus Kinase 1 signaling. Moreover, although ibrutinib increases AID expression in a CLL cell line, it is unable to do so in primary CLL samples. Our results uncover a differential response to ibrutinib between cell lines and the CLL clone and imply that ibrutinib could differ from idelalisib in their potential to induce AID in treated patients. Possible reasons for the discrepancy between preclinical and clinical findings, and their effect on treatment safety, are discussed.
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Affiliation(s)
- Pablo Elías Morande
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariela Sivina
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Angimar Uriepero
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Noé Seija
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Catalina Berca
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Fresia
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Ana Inés Landoni
- Hospital Maciel, Administración de los Servicios de Salud del Estado, Ministerio de Salud, Montevideo, Uruguay
| | - Javier M Di Noia
- Division of Immunity and Viral Infections, Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada; and
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jan A Burger
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
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Repository corticotropin injection reverses critical elements of the TLR9/B cell receptor activation response in human B cells in vitro. Clin Immunol 2019; 201:70-78. [DOI: 10.1016/j.clim.2019.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/29/2019] [Accepted: 02/20/2019] [Indexed: 12/25/2022]
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48
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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Up-regulation of activation-induced cytidine deaminase and its strong expression in extra-germinal centres in IgG4-related disease. Sci Rep 2019; 9:761. [PMID: 30679751 PMCID: PMC6346144 DOI: 10.1038/s41598-018-37404-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/05/2018] [Indexed: 12/24/2022] Open
Abstract
Immunoglobulin (Ig) G4-related disease (IgG4-RD) is a systemic disorder involving benign mass formation due to fibrosis and intense lymphoplasmacytosis; the chronic inflammation associated with the disease might also contribute to oncogenesis. Activation-induced cytidine deaminase (AID), normally expressed in germinal centre activated B-cells, is an enzyme that edits DNA/RNA and induces somatic hypermutation and Ig class switching. AID expression is strictly controlled under physiological conditions; however, chronic inflammation and some infectious agents induce its up-regulation. AID is overexpressed in various cancers and may be important in chronic inflammation-associated oncogenesis. We examined AID expression in IgG4-related sialadenitis (n = 14), sialolithiasis (non-specific inflammation, n = 13), and normal submandibular glands (n = 13) using immunohistochemistry and quantitative real-time polymerase chain reaction (qPCR). Immunohistochemistry revealed significantly more AID-expressing cells in IgG4-related sialadenitis than in sialolithiasis or normal submandibular gland samples (P = 0.02 and P < 0.01, respectively); qPCR yielded similar results. Thus, AID was significantly more up-regulated and had higher expression in extra-germinal centres in IgG4-RD than in non-specific inflammation or normal conditions. This report suggests that IgG4-RD has several specific causes of AID up-regulation in addition to inflammation. Furthermore, chronic inflammation-associated AID-mediated oncogenesis is possible in IgG4-RD.
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Wu L, Fu S, Yin X, Leng W, Guo Z, Wang A, Ye J. Affinity maturation occurs in channel catfish (Ictalurus punctaus) following immunization with a T-cell dependent antigen. FISH & SHELLFISH IMMUNOLOGY 2019; 84:781-786. [PMID: 30393175 DOI: 10.1016/j.fsi.2018.10.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/13/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Affinity maturation of the antibody response, a process of antibody affinity increasing over response, is one of the key features of the mammalian immune system. However, the process is incompletely understood in teleost, including channel catfish (Ictalurus punctaus). In this study, IgM affinity maturation in channel catfish was investigated by estimating the kinetics of antibody affinity using ELISA and ELISPOT assays. Fish were immunized with a T-cell dependent antigen (TNP-KLH), and individual serum IgM antibody titers and affinities, and IgM+ antibody-secreting cells (ASCs) in peripheral blood were analyzed over a period of 14 weeks. A detectable serum anti-TNP response developed by 2-weeks post-immunization, and the maximal antibody production was observed by 6-weeks post-immunization. The average affinity of anti-TNP serum antibody increased consistently and reached the maximum by 10-weeks post-immunization. The increase of antibody affinity beyond the point of optimal antibody titer revealed that the affinity maturation of IgM antibody response occurred in channel catfish. Dissection of dynamics of individual affinity subpopulations indicated that a significant proportion of low affinity subpopulations appeared at early response, and high affinity subpopulations appeared predominantly at later, resulting in a 100-fold increase in affinity over response. Additional, TNP+ IgM+ ASCs was detected by 2-weeks post-immunization and achieved the maximal number by 6-weeks post-immunization. Using an inhibition ELISPOT assay, the findings of a consistent increase in the average affinity of secreted IgM antibody by peripheral blood ASCs, as the immune response progressed, confirmed the occurrence of the affinity maturation. Taken together, the results of this study indicated that affinity maturation occurred in channel catfish following immunization with a TD antigen TNP-KLH.
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Affiliation(s)
- Liting Wu
- School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China
| | - Shengli Fu
- School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China
| | - Xiaoxue Yin
- School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China
| | - Wenna Leng
- School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China
| | - Zheng Guo
- School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China
| | - Anli Wang
- School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China
| | - Jianmin Ye
- School of Life Sciences, South China Normal University, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangzhou, 510631, PR China.
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