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Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z. Integration of spatial and single-cell data across modalities with weakly linked features. Nat Biotechnol 2024; 42:1096-1106. [PMID: 37679544 DOI: 10.1038/s41587-023-01935-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integration methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori 'linked' features. We describe matching X-modality via fuzzy smoothed embedding (MaxFuse), a cross-modal data integration method that, through iterative coembedding, data smoothing and cell matching, uses all information in each modality to obtain high-quality integration even when features are weakly linked. MaxFuse is modality-agnostic and demonstrates high robustness and accuracy in the weak linkage scenario, achieving 20~70% relative improvement over existing methods under key evaluation metrics on benchmarking datasets. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, MaxFuse enabled the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.
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Affiliation(s)
- Shuxiao Chen
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Bokai Zhu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sijia Huang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - John W Hickey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kevin Z Lin
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Nancy R Zhang
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA.
| | - Zongming Ma
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA.
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2
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Aoun M, Coelho A, Krämer A, Saxena A, Sabatier P, Beusch CM, Lönnblom E, Geng M, Do NN, Xu Z, Zhang J, He Y, Romero Castillo L, Abolhassani H, Xu B, Viljanen J, Rorbach J, Fernandez Lahore G, Gjertsson I, Kastbom A, Sjöwall C, Kihlberg J, Zubarev RA, Burkhardt H, Holmdahl R. Antigen-presenting autoreactive B cells activate regulatory T cells and suppress autoimmune arthritis in mice. J Exp Med 2023; 220:e20230101. [PMID: 37695523 PMCID: PMC10494526 DOI: 10.1084/jem.20230101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/31/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
B cells undergo several rounds of selection to eliminate potentially pathogenic autoreactive clones, but in contrast to T cells, evidence of positive selection of autoreactive B cells remains moot. Using unique tetramers, we traced natural autoreactive B cells (C1-B) specific for a defined triple-helical epitope on collagen type-II (COL2), constituting a sizeable fraction of the physiological B cell repertoire in mice, rats, and humans. Adoptive transfer of C1-B suppressed arthritis independently of IL10, separating them from IL10-secreting regulatory B cells. Single-cell sequencing revealed an antigen processing and presentation signature, including induced expression of CD72 and CCR7 as surface markers. C1-B presented COL2 to T cells and induced the expansion of regulatory T cells in a contact-dependent manner. CD72 blockade impeded this effect suggesting a new downstream suppressor mechanism that regulates antigen-specific T cell tolerization. Thus, our results indicate that autoreactive antigen-specific naïve B cells tolerize infiltrating T cells against self-antigens to impede the development of tissue-specific autoimmune inflammation.
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Affiliation(s)
- Mike Aoun
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Ana Coelho
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Alexander Krämer
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Amit Saxena
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Christian Michel Beusch
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Erik Lönnblom
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Manman Geng
- Precision Medicine Institute, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Nhu-Nguyen Do
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- Fraunhofer Institute for Translational Medicine and Pharmacology, and Fraunhofer Cluster of Excellence for Immune-Mediated Diseases, Frankfurt am Main, Germany
| | - Zhongwei Xu
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Jingdian Zhang
- Max Planck Institute Biology of Ageing—Karolinska Institute Laboratory, Karolinska Institute, Solna, Sweden
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Yibo He
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Laura Romero Castillo
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Biosciences and Nutrition, Karolinska Institutet, Karolinska University Hospital, Neo Building, Solna, Sweden
| | - Bingze Xu
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Johan Viljanen
- Department of Chemistry, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Joanna Rorbach
- Max Planck Institute Biology of Ageing—Karolinska Institute Laboratory, Karolinska Institute, Solna, Sweden
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Gonzalo Fernandez Lahore
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Inger Gjertsson
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Alf Kastbom
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Christopher Sjöwall
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Jan Kihlberg
- Department of Chemistry, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Roman A. Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- Department of Pharmacological and Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Harald Burkhardt
- Fraunhofer Institute for Translational Medicine and Pharmacology, and Fraunhofer Cluster of Excellence for Immune-Mediated Diseases, Frankfurt am Main, Germany
- Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
- Precision Medicine Institute, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
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3
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Kozal JS, Lynch HN, Klapacz J, Schoeny RS, Jean PA, Maier A. Mode of action assessment for propylene dichloride as a human carcinogen. Chem Biol Interact 2023; 382:110382. [PMID: 36754223 DOI: 10.1016/j.cbi.2023.110382] [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: 08/02/2022] [Revised: 01/16/2023] [Accepted: 02/04/2023] [Indexed: 02/09/2023]
Abstract
As part of a systematic review of the non-cancer and cancer hazards of propylene dichloride (PDC), with a focus on potential carcinogenicity in workers following inhalation exposures, we determined that a mode of action (MOA)-centric framing of cancer effects was warranted. In our MOA analysis, we systematically reviewed the available mechanistic evidence for PDC-induced carcinogenesis, and we mapped biologically plausible MOA pathways and key events (KEs), as guided by the International Programme on Chemical Safety (IPCS)-MOA framework. For the identified pathways and KEs, biological concordance, essentiality of KEs, concordance of empirical observations among KEs, consistency, and analogy were evaluated. The results of this analysis indicate that multiple biologically plausible pathways may contribute to the cancer MOA for PDC, but that the relevant pathways vary by exposure route and level, tissue type, and species; further, more than one pathway may occur concurrently at high exposure levels. While several important data gaps exist, evidence from in vitro mechanistic studies, in vivo experimental animal studies, and ex vivo human tumor tissue analyses indicates that the predominant MOA pathway likely involves saturation of cytochrome p450 2E1 (CYP2E1)-glutathione (GSH) detoxification (molecular initiating event; MIE), accumulation of CYP2E1-oxidative metabolites, cytotoxicity, chronic tissue damage and inflammation, and ultimately tumor formation. Tumors may occur through several subsets of inflammatory KEs, including inflammation-induced aberrant expression of activation-induced cytidine deaminase (AID), which causes DNA strand breaks and mutations and can lead to tumors with a characteristic mutational signature found in occupational cholangiocarcinoma. Dose concordance analysis showed that low-dose mutagenicity (from any pathway) is not a driving MOA, and that prevention of target tissue damage and inflammation (associated with saturation of CYP2E1-GSH detoxification) is expected to also prevent the cascade of processes responsible for tumor formation.
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Affiliation(s)
| | | | - Joanna Klapacz
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, MI, 48674, USA
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4
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Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z. Integration of spatial and single-cell data across modalities with weak linkage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523851. [PMID: 36711792 PMCID: PMC9882150 DOI: 10.1101/2023.01.12.523851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
single-cell sequencing methods have enabled the profiling of multiple types of molecular readouts at cellular resolution, and recent developments in spatial barcoding, in situ hybridization, and in situ sequencing allow such molecular readouts to retain their spatial context. Since no technology can provide complete characterization across all layers of biological modalities within the same cell, there is pervasive need for computational cross-modal integration (also called diagonal integration) of single-cell and spatial omics data. For current methods, the feasibility of cross-modal integration relies on the existence of highly correlated, a priori "linked" features. When such linked features are few or uninformative, a scenario that we call "weak linkage", existing methods fail. We developed MaxFuse, a cross-modal data integration method that, through iterative co-embedding, data smoothing, and cell matching, leverages all information in each modality to obtain high-quality integration. MaxFuse is modality-agnostic and, through comprehensive benchmarks on single-cell and spatial ground-truth multiome datasets, demonstrates high robustness and accuracy in the weak linkage scenario. A prototypical example of weak linkage is the integration of spatial proteomic data with single-cell sequencing data. On two example analyses of this type, we demonstrate how MaxFuse enables the spatial consolidation of proteomic, transcriptomic and epigenomic information at single-cell resolution on the same tissue section.
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5
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Çakan E, Gunaydin G. Activation induced cytidine deaminase: An old friend with new faces. Front Immunol 2022; 13:965312. [PMID: 36405752 PMCID: PMC9670734 DOI: 10.3389/fimmu.2022.965312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Activation induced cytidine deaminase (AID) protein is a member of APOBEC family. AID converts cytidine to uracil, which is a key step for somatic hypermutation (SHM) and class switch recombination (CSR). AID also plays critical roles in B cell precursor stages, removing polyreactive B cells from immune repertoire. Since the main function of AID is inducing point mutations, dysregulation can lead to increased mutation load, translocations, disturbed genomic integrity, and lymphomagenesis. As such, expression of AID as well as its function is controlled strictly at various molecular steps. Other members of the APOBEC family also play crucial roles during carcinogenesis. Considering all these functions, AID represents a bridge, linking chronic inflammation to carcinogenesis and immune deficiencies to autoimmune manifestations.
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Affiliation(s)
- Elif Çakan
- Hacettepe University School of Medicine, Sihhiye, Ankara, Turkey
| | - Gurcan Gunaydin
- Department of Basic Oncology, Hacettepe University Cancer Institute, Sihhiye, Ankara, Turkey
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6
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Corneth OBJ, Neys SFH, Hendriks RW. Aberrant B Cell Signaling in Autoimmune Diseases. Cells 2022; 11:cells11213391. [PMID: 36359789 PMCID: PMC9654300 DOI: 10.3390/cells11213391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 11/30/2022] Open
Abstract
Aberrant B cell signaling plays a critical in role in various systemic and organ-specific autoimmune diseases. This is supported by genetic evidence by many functional studies in B cells from patients or specific animal models and by the observed efficacy of small-molecule inhibitors. In this review, we first discuss key signal transduction pathways downstream of the B cell receptor (BCR) that ensure that autoreactive B cells are removed from the repertoire or functionally silenced. We provide an overview of aberrant BCR signaling that is associated with inappropriate B cell repertoire selection and activation or survival of peripheral B cell populations and plasma cells, finally leading to autoantibody formation. Next to BCR signaling, abnormalities in other signal transduction pathways have been implicated in autoimmune disease. These include reduced activity of several phosphates that are downstream of co-inhibitory receptors on B cells and increased levels of BAFF and APRIL, which support survival of B cells and plasma cells. Importantly, pathogenic synergy of the BCR and Toll-like receptors (TLR), which can be activated by endogenous ligands, such as self-nucleic acids, has been shown to enhance autoimmunity. Finally, we will briefly discuss therapeutic strategies for autoimmune disease based on interfering with signal transduction in B cells.
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7
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LAPTM5 mediates immature B cell apoptosis and B cell tolerance by regulating the WWP2-PTEN-AKT pathway. Proc Natl Acad Sci U S A 2022; 119:e2205629119. [PMID: 36037365 PMCID: PMC9457450 DOI: 10.1073/pnas.2205629119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Elimination of autoreactive developing B cells is an important mechanism to prevent autoantibody production. However, how B cell receptor (BCR) signaling triggers apoptosis of immature B cells remains poorly understood. We show that BCR stimulation up-regulates the expression of the lysosomal-associated transmembrane protein 5 (LAPTM5), which in turn triggers apoptosis of immature B cells through two pathways. LAPTM5 causes BCR internalization, resulting in decreased phosphorylation of SYK and ERK. In addition, LAPTM5 targets the E3 ubiquitin ligase WWP2 for lysosomal degradation, resulting in the accumulation of its substrate PTEN. Elevated PTEN levels suppress AKT phosphorylation, leading to increased FOXO1 expression and up-regulation of the cell cycle inhibitor p27Kip1 and the proapoptotic molecule BIM. In vivo, LAPTM5 is involved in the elimination of autoreactive B cells and its deficiency exacerbates autoantibody production. Our results reveal a previously unidentified mechanism that contributes to immature B cell apoptosis and B cell tolerance.
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8
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Bao K, Zhang J, Scherl A, Ziai J, Hadadianpour A, Xu D, Dela Cruz C, Liu J, Liang Y, Tam L, Corzo CA, Roose-Girma M, Warming S, Modrusan Z, Lee WP, Hoi KH, Zarrin AA. Activation-Induced Cytidine Deaminase Impacts the Primary Antibody Repertoire in Naive Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2632-2642. [PMID: 35675956 DOI: 10.4049/jimmunol.2101193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Genetic and environmental cues shape the evolution of the B cell Ig repertoire. Activation-induced cytidine deaminase (AID) is essential to generating Ig diversity through isotype class switching and somatic mutations, which then directly influence clonal selection. Impaired B cell development in AID-knockout mice has made it difficult to study Ig diversification in an aging repertoire. Therefore, in this report, we used a novel inducible AID-knockout mouse model and discovered that deleting AID in adult mice caused spontaneous germinal center formation. Deep sequencing of the IgH repertoire revealed that Ab diversification begins early in life and evolves over time. Our data suggest that activated B cells form germinal centers at steady state and facilitate continuous diversification of the B cell repertoire. In support, we identified shared B cell lineages that were class switched and showed age-dependent rates of mutation. Our data provide novel context to the genesis of the B cell repertoire that may benefit the understanding of autoimmunity and the strength of an immune response to infection.
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Affiliation(s)
| | - Juan Zhang
- Research, Genentech, South San Francisco, CA; and
| | | | - James Ziai
- Research, Genentech, South San Francisco, CA; and
| | | | - Daqi Xu
- Research, Genentech, South San Francisco, CA; and
| | | | - John Liu
- Research, Genentech, South San Francisco, CA; and
| | - Yuxin Liang
- Research, Genentech, South San Francisco, CA; and
| | - Lucinda Tam
- Research, Genentech, South San Francisco, CA; and
| | | | | | | | | | - Wyne P Lee
- Research, Genentech, South San Francisco, CA; and
| | - Kam Hon Hoi
- Research, Genentech, South San Francisco, CA; and
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9
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Kuraoka M, Yeh CH, Bajic G, Kotaki R, Song S, Windsor I, Harrison SC, Kelsoe G. Recall of B cell memory depends on relative locations of prime and boost immunization. Sci Immunol 2022; 7:eabn5311. [PMID: 35522723 PMCID: PMC9169233 DOI: 10.1126/sciimmunol.abn5311] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Immunization or microbial infection can establish long-term B cell memory not only systemically but also locally. Evidence has suggested that local B cell memory contributes to early local plasmacytic responses after secondary challenge. However, it is unclear whether locality of immunization plays any role in memory B cell participation in recall germinal centers (GCs), which is essential for updating their B cell antigen receptors (BCRs). Using single B cell culture and fate mapping, we have characterized BCR repertoires in recall GCs after boost immunizations at sites local or distal to the priming. Local boosts with homologous antigen recruit the progeny of primary GC B cells to recall GCs more efficiently than do distal boosts. Recall GCs elicited by local boosts contain significantly more B cells with elevated levels of immunoglobulin (Ig) mutation and higher avidity BCRs. This local preference is unaffected by blocking CD40:CD154 interaction to terminate active, GC responses. Local boosts with heterologous antigens elicit secondary GCs with B cell populations enriched for cross-reactivity to the prime and boost antigens; in contrast, cross-reactive GC B cells are rare after distal boosts. Our results suggest that local B cell memory is retained in the form of memory B cells, GC B cells, and GC phenotype B cells that are independent of organized GC structures and that these persistent "primed B cells" contribute to recall GC responses at local sites. Our findings indicate the importance of locality in humoral immunity and inform serial vaccination strategies for evolving viruses.
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Affiliation(s)
| | - Chen-Hao Yeh
- Department of Immunology, Duke University, Durham, NC, USA
| | - Goran Bajic
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ryutaro Kotaki
- Department of Immunology, Duke University, Durham, NC, USA
| | - Shengli Song
- Department of Immunology, Duke University, Durham, NC, USA
| | - Ian Windsor
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
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10
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Sterrenberg JN, Folkerts ML, Rangel V, Lee SE, Pannunzio NR. Diversity upon diversity: linking DNA double-strand break repair to blood cancer health disparities. Trends Cancer 2022; 8:328-343. [PMID: 35094960 PMCID: PMC9248772 DOI: 10.1016/j.trecan.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/20/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
Chromosomal translocations arising from aberrant repair of multiple DNA double-strand breaks (DSBs) are a defining characteristic of many cancers. DSBs are an essential part of physiological processes in antibody-producing B cells. The B cell environment is poised to generate genome instability leading to translocations relevant to the pathology of blood cancers. These are a diverse set of cancers, but limited data from under-represented groups have pointed to health disparities associated with each. We focus on the DSBs that occur in developing B cells and propose the most likely mechanism behind the formation of translocations. We also highlight specific cancers in which these rearrangements occur and address the growing concern of health disparities associated with them.
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11
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Liu D, Lieber MR. The mechanisms of human lymphoid chromosomal translocations and their medical relevance. Crit Rev Biochem Mol Biol 2021; 57:227-243. [PMID: 34875186 DOI: 10.1080/10409238.2021.2004576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of expression of AID can introduce long-lived T:G mismatch lesions at 20-600 bp fragile zones. Second, the V(D)J recombination process can occasionally fail to rejoin coding ends, and this failure may permit an opportunity for Artemis:DNA-dependent kinase catalytic subunit (DNA-PKcs) to convert the T:G mismatch sites at the fragile zones into double-strand breaks. The 20-600 bp fragile zones must be, at least transiently, in a single-stranded DNA (ssDNA) state for the first step to occur, because AID only acts on ssDNA. Here we discuss the key DNA sequence features that lead to AID action at a fragile zone, which are (a) the proximity and density of strings of cytosine nucleotides (C-strings) that cause a B/A-intermediate DNA conformation; (b) overlapping AID hotspots that contain a methyl CpG (WRCG), which AID converts to a long-lived T:G mismatch; and (c) transcription, which, though not essential, favors increased ssDNA in the fragile zone. We also summarize chromosomal features of the focal fragile zones in lymphoid malignancies and discuss the clinical relevance of understanding the translocation mechanisms. Many of the key principles covered here are also relevant to chromosomal translocations in non-lymphoid somatic cells as well.
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Affiliation(s)
- Di Liu
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael R Lieber
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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12
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Chen JW, Schickel JN, Tsakiris N, Sng J, Arbogast F, Bouis D, Parisi D, Gera R, Boeckers JM, Delmotte FR, Veselits M, Schuetz C, Jacobsen EM, Posovszky C, Schulz AS, Schwarz K, Clark MR, Menard L, Meffre E. Positive and negative selection shape the human naïve B cell repertoire. J Clin Invest 2021; 132:150985. [PMID: 34813502 PMCID: PMC8759783 DOI: 10.1172/jci150985] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
Although negative selection of developing B cells in the periphery is well described, yet poorly understood, evidence of naive B cell positive selection remains elusive. Using 2 humanized mouse models, we demonstrate that there was strong skewing of the expressed immunoglobulin repertoire upon transit into the peripheral naive B cell pool. This positive selection of expanded naive B cells in humanized mice resembled that observed in healthy human donors and was independent of autologous thymic tissue. In contrast, negative selection of autoreactive B cells required thymus-derived Tregs and MHC class II–restricted self-antigen presentation by B cells. Indeed, both defective MHC class II expression on B cells of patients with rare bare lymphocyte syndrome and prevention of self-antigen presentation via HLA-DM inhibition in humanized mice resulted in the production of autoreactive naive B cells. These latter observations suggest that Tregs repressed autoreactive naive B cells continuously produced by the bone marrow. Thus, a model emerged, in which both positive and negative selection shaped the human naive B cell repertoire and that each process was mediated by fundamentally different molecular and cellular mechanisms.
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Affiliation(s)
- Jeff W Chen
- Department of Immunobiology, Yale University, New Haven, United States of America
| | | | - Nikolaos Tsakiris
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Joel Sng
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Florent Arbogast
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Delphine Bouis
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Daniele Parisi
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Ruchi Gera
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Joshua M Boeckers
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Fabien R Delmotte
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Margaret Veselits
- Department of Medicine, University of Chicago, Chicago, United States of America
| | - Catharina Schuetz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Eva-Maria Jacobsen
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Carsten Posovszky
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Ansgar S Schulz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Klaus Schwarz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, Germany
| | - Marcus R Clark
- Department of Medicine, University of Chicago, Chicago, United States of America
| | - Laurence Menard
- Department of Immunobiology, Yale University, New Haven, United States of America
| | - Eric Meffre
- Department of Immunobiology, Yale University, New Haven, United States of America
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13
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Nguyen HTT, Guevarra RB, Magez S, Radwanska M. Single-cell transcriptome profiling and the use of AID deficient mice reveal that B cell activation combined with antibody class switch recombination and somatic hypermutation do not benefit the control of experimental trypanosomosis. PLoS Pathog 2021; 17:e1010026. [PMID: 34762705 PMCID: PMC8610246 DOI: 10.1371/journal.ppat.1010026] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 11/23/2021] [Accepted: 10/11/2021] [Indexed: 01/02/2023] Open
Abstract
Salivarian trypanosomes are extracellular protozoan parasites causing infections in a wide range of mammalian hosts, with Trypanosoma evansi having the widest geographic distribution, reaching territories far outside Africa and occasionally even Europe. Besides causing the animal diseases, T. evansi can cause atypical Human Trypanosomosis. The success of this parasite is attributed to its capacity to evade and disable the mammalian defense response. To unravel the latter, we applied here for the first time a scRNA-seq analysis on splenocytes from trypanosome infected mice, at two time points during infection, i.e. just after control of the first parasitemia peak (day 14) and a late chronic time point during infection (day 42). This analysis was combined with flow cytometry and ELISA, revealing that T. evansi induces prompt activation of splenic IgM+CD1d+ Marginal Zone and IgMIntIgD+ Follicular B cells, coinciding with an increase in plasma IgG2c Ab levels. Despite the absence of follicles, a rapid accumulation of Aicda+ GC-like B cells followed first parasitemia peak clearance, accompanied by the occurrence of Xbp1+ expressing CD138+ plasma B cells and Tbx21+ atypical CD11c+ memory B cells. Ablation of immature CD93+ bone marrow and Vpreb3+Ly6d+Ighm+ expressing transitional spleen B cells prevented mature peripheral B cell replenishment. Interestingly, AID-/- mice that lack the capacity to mount anti-parasite IgG responses, exhibited a superior defense level against T. evansi infections. Here, elevated natural IgMs were able to exert in vivo and in vitro trypanocidal activity. Hence, we conclude that in immune competent mice, trypanosomosis associated B cell activation and switched IgG production is rapidly induced by T. evansi, facilitating an escape from the detrimental natural IgM killing activity, and resulting in increased host susceptibility. This unique role of IgM and its anti-trypanosome activity are discussed in the context of the dilemma this causes for the future development of anti-trypanosome vaccines.
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Affiliation(s)
- Hang Thi Thu Nguyen
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Robin B. Guevarra
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
| | - Stefan Magez
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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14
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Finney J, Kelsoe G. Continuous Culture of Mouse Primary B Lymphocytes by Forced Expression of Bach2. THE JOURNAL OF IMMUNOLOGY 2021; 207:1478-1492. [PMID: 34389622 DOI: 10.4049/jimmunol.2100172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/01/2021] [Indexed: 12/26/2022]
Abstract
Stable, long-term culture of primary B lymphocytes has many potential scientific and medical applications, but remains an elusive feat. A major obstacle to long-term culture is that in vitro mitogens quickly drive B cells to differentiate into short-lived plasma cells (PCs). PC differentiation is governed by opposing teams of transcription factors: Pax5, Bach2, and Bcl6 suppress PC commitment, whereas IFN regulatory factor 4 and Blimp1 promote it. To determine whether transcriptional programming could prolong B cell culture by blocking PC commitment, we generated mouse primary B cells harboring gain- or loss-of-function in the key transcription factors, continuously stimulated these cells with CD154 and IL-21, and determined growth potential and phenotypes in vitro. We found that transgenic expression of Bach2 prohibits PC commitment and endows B cells with extraordinary growth potential in response to external proliferation and survival cues. Long-term Bach2-transgenic B cell lines have genetically stable BCRs [i.e., do not acquire V(D)J mutations], express high levels of MHC class II and molecules for costimulation of T cells, and transduce intracellular signals when incubated with BCR ligands. Silencing the Bach2 transgene in an established transgenic cell line causes the cells to secrete large quantities of Ig. This system has potential applications in mAb production, BCR signaling studies, Ag presentation to T cells, and ex vivo clonal expansion for adoptive cell transfer. Additionally, our results provide insight into molecular control over activated B cell fate and suggest that forced Bach2 expression in vivo may augment germinal center B cell or memory B cell differentiation at the expense of PC commitment.
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Affiliation(s)
- Joel Finney
- Department of Immunology, Duke University, Durham, NC; and
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC; and .,Human Vaccine Institute, Duke University, Durham, NC
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15
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Liu D, Loh YHE, Hsieh CL, Lieber MR. Mechanistic basis for chromosomal translocations at the E2A gene and its broader relevance to human B cell malignancies. Cell Rep 2021; 36:109387. [PMID: 34260910 PMCID: PMC8327686 DOI: 10.1016/j.celrep.2021.109387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
Analysis of translocation breakpoints in human B cell malignancies reveals that DNA double-strand breaks at oncogenes most frequently occur at CpG sites located within 20-600 bp fragile zones and depend on activation-induced deaminase (AID). AID requires single-stranded DNA (ssDNA) to act, but it has been unclear why or how this region transiently acquires a ssDNA state. Here, we demonstrate the ssDNA state in the 23 bp E2A fragile zone using several methods, including native bisulfite DNA structural analysis in live human pre-B cells. AID deamination within the E2A fragile zone does not require but is increased upon transcription. High C-string density, nascent RNA tails, and direct DNA sequence repeats prolong the ssDNA state of the E2A fragile zone and increase AID deamination at overlapping AID hotspots that contain the CpG sites at which breaks occur in patients. These features provide key insights into lymphoid fragile zones generally.
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Affiliation(s)
- Di Liu
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Yong-Hwee Eddie Loh
- USC Libraries Bioinformatics Services, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Chih-Lin Hsieh
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Michael R Lieber
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA.
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16
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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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17
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Do Transgenerational Epigenetic Inheritance and Immune System Development Share Common Epigenetic Processes? J Dev Biol 2021; 9:jdb9020020. [PMID: 34065783 PMCID: PMC8162332 DOI: 10.3390/jdb9020020] [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: 04/01/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modifications regulate gene expression for development, immune response, disease, and other processes. A major role of epigenetics is to control the dynamics of chromatin structure, i.e., the condensed packaging of DNA around histone proteins in eukaryotic nuclei. Key epigenetic factors include enzymes for histone modifications and DNA methylation, non-coding RNAs, and prions. Epigenetic modifications are heritable but during embryonic development, most parental epigenetic marks are erased and reset. Interestingly, some epigenetic modifications, that may be resulting from immune response to stimuli, can escape remodeling and transmit to subsequent generations who are not exposed to those stimuli. This phenomenon is called transgenerational epigenetic inheritance if the epigenetic phenotype persists beyond the third generation in female germlines and second generation in male germlines. Although its primary function is likely immune response for survival, its role in the development and functioning of the immune system is not extensively explored, despite studies reporting transgenerational inheritance of stress-induced epigenetic modifications resulting in immune disorders. Hence, this review draws from studies on transgenerational epigenetic inheritance, immune system development and function, high-throughput epigenetics tools to study those phenomena, and relevant clinical trials, to focus on their significance and deeper understanding for future research, therapeutic developments, and various applications.
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18
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Prasad R, Yen TJ, Bellacosa A. Active DNA demethylation-The epigenetic gatekeeper of development, immunity, and cancer. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10033. [PMID: 36618446 PMCID: PMC9744510 DOI: 10.1002/ggn2.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/11/2023]
Abstract
DNA methylation is a critical process in the regulation of gene expression with dramatic effects in development and continually expanding roles in oncogenesis. 5-Methylcytosine was once considered to be an inherited and stably repressive epigenetic mark, which can be only removed by passive dilution during multiple rounds of DNA replication. However, in the past two decades, physiologically controlled DNA demethylation and deamination processes have been identified, thereby revealing the function of cytosine methylation as a highly regulated and complex state-not simply a static, inherited signature or binary on-off switch. Alongside these fundamental discoveries, clinical studies over the past decade have revealed the dramatic consequences of aberrant DNA demethylation. In this review we discuss DNA demethylation and deamination in the context of 5-methylcytosine as critical processes for physiological and physiopathological transitions within three states-development, immune maturation, and oncogenic transformation; and we describe the expanding role of DNA demethylating drugs as therapeutic agents in cancer.
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Affiliation(s)
- Rahul Prasad
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Timothy J. Yen
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
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19
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Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Di Noia JM. The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID. NAR Cancer 2021; 2:zcaa019. [PMID: 33554121 PMCID: PMC7848951 DOI: 10.1093/narcan/zcaa019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
In B lymphocytes, the uracil N-glycosylase (UNG) excises genomic uracils made by activation-induced deaminase (AID), thus underpinning antibody gene diversification and oncogenic chromosomal translocations, but also initiating faithful DNA repair. Ung−/− mice develop B-cell lymphoma (BCL). However, since UNG has anti- and pro-oncogenic activities, its tumor suppressor relevance is unclear. Moreover, how the constant DNA damage and repair caused by the AID and UNG interplay affects B-cell fitness and thereby the dynamics of cell populations in vivo is unknown. Here, we show that UNG specifically protects the fitness of germinal center B cells, which express AID, and not of any other B-cell subset, coincident with AID-induced telomere damage activating p53-dependent checkpoints. Consistent with AID expression being detrimental in UNG-deficient B cells, Ung−/− mice develop BCL originating from activated B cells but lose AID expression in the established tumor. Accordingly, we find that UNG is rarely lost in human BCL. The fitness preservation activity of UNG contingent to AID expression was confirmed in a B-cell leukemia model. Hence, UNG, typically considered a tumor suppressor, acquires tumor-enabling activity in cancer cell populations that express AID by protecting cell fitness.
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Affiliation(s)
- Shiva Safavi
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Ariane Larouche
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Anne-Marie Patenaude
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Kiersten Dionne
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Felix Dingler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Seong-Kwi Kang
- ITR Laboratories Canada, Inc., 19601 Clark Graham Ave, Baie-D'Urfe, QC H9X 3T1, Canada
| | - Yan Liu
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Nathalie Johnson
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Josée Hébert
- Department of Medicine, Université de Montréal, C.P. 6128, Montreal, QC H3C 3J7, Canada
| | - Ramiro E Verdun
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | | | - Francisco Vega
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | - Hilde Nilsen
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
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20
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Kuhny M, Forbes LR, Çakan E, Vega-Loza A, Kostiuk V, Dinesh RK, Glauzy S, Stray-Pedersen A, Pezzi AE, Hanson IC, Vargas-Hernandez A, Xu ML, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Chinn IK, Schatz DG, Orange JS, Meffre E. Disease-associated CTNNBL1 mutation impairs somatic hypermutation by decreasing nuclear AID. J Clin Invest 2021; 130:4411-4422. [PMID: 32484799 DOI: 10.1172/jci131297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 05/13/2020] [Indexed: 01/02/2023] Open
Abstract
Patients with common variable immunodeficiency associated with autoimmune cytopenia (CVID+AIC) generate few isotype-switched B cells with severely decreased frequencies of somatic hypermutations (SHMs), but their underlying molecular defects remain poorly characterized. We identified a CVID+AIC patient who displays a rare homozygous missense M466V mutation in β-catenin-like protein 1 (CTNNBL1). Because CTNNBL1 binds activation-induced cytidine deaminase (AID) that catalyzes SHM, we tested AID interactions with the CTNNBL1 M466V variant. We found that the M466V mutation interfered with the association of CTNNBL1 with AID, resulting in decreased AID in the nuclei of patient EBV-transformed B cell lines and of CTNNBL1 466V/V Ramos B cells engineered to express only CTNNBL1 M466V using CRISPR/Cas9 technology. As a consequence, the scarce IgG+ memory B cells from the CTNNBL1 466V/V patient showed a low SHM frequency that averaged 6.7 mutations compared with about 18 mutations per clone in healthy-donor counterparts. In addition, CTNNBL1 466V/V Ramos B cells displayed a decreased incidence of SHM that was reduced by half compared with parental WT Ramos B cells, demonstrating that the CTNNBL1 M466V mutation is responsible for defective SHM induction. We conclude that CTNNBL1 plays an important role in regulating AID-dependent antibody diversification in humans.
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Affiliation(s)
- Marcel Kuhny
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lisa R Forbes
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA
| | - Elif Çakan
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrea Vega-Loza
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Valentyna Kostiuk
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Salomé Glauzy
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Asbjorg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Institute of Clinical Medicine and.,Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Ashley E Pezzi
- Department of Dermatology, Baylor College of Medicine, Houston, Texas, USA
| | - I Celine Hanson
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Alexander Vargas-Hernandez
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA
| | - Mina LuQuing Xu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ivan K Chinn
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA.,Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jordan S Orange
- Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York-Presbyterian Morgan Stanley Children's Hospital, New York, New York, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Section of Rheumatology, Allergy, and Clinical Immunology, Yale University School of Medicine, New Haven, Connecticut, USA
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21
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Nojima T, Reynolds AE, Kitamura D, Kelsoe G, Kuraoka M. Tracing Self-Reactive B Cells in Normal Mice. THE JOURNAL OF IMMUNOLOGY 2020; 205:90-101. [PMID: 32414809 DOI: 10.4049/jimmunol.1901015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 04/22/2020] [Indexed: 12/20/2022]
Abstract
BCR transgenic mice dominate studies of B cell tolerance; consequently, tolerance in normal mice expressing diverse sets of autoreactive B cells is poorly characterized. We have used single B cell cultures to trace self-reactivity in BCR repertoires across the first and second tolerance checkpoints and in tolerized B cell compartments of normal mice. This approach reveals affinity "setpoints" that define each checkpoint and a subset of tolerized, autoreactive B cells that is long-lived. In normal mice, the numbers of B cells avidly specific for DNA fall significantly as small pre-B become immature and transitional-1 B cells, revealing the first tolerance checkpoint. By contrast, DNA reactivity does not significantly change when immature and transitional-1 B cells become mature follicular B cells, showing that the second checkpoint does not reduce DNA reactivity. In the spleen, autoreactivity was high in transitional-3 (T3) B cells, CD93+IgM-/loIgDhi anergic B cells, and a CD93- anergic subset. Whereas splenic T3 and CD93+ anergic B cells are short-lived, CD93-IgM-/loIgDhi B cells have half-lives comparable to mature follicular B cells. B cell-specific deletion of proapoptotic genes, Bak and Bax, resulted in increased CD93-IgM-/loIgDhi B cell numbers but not T3 B cell numbers, suggesting that apoptosis regulates differently persistent and ephemeral autoreactive B cells. The self-reactivity and longevity of CD93-IgM-/loIgDhi B cells and their capacity to proliferate and differentiate into plasmacytes in response to CD40 activation in vitro lead us to propose that this persistent, self-reactive compartment may be the origin of systemic autoimmunity and a potential target for vaccines to elicit protective Abs cross-reactive with self-antigens.
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Affiliation(s)
- Takuya Nojima
- Department of Immunology, Duke University, Durham, NC 27710
| | | | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan; and
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710.,Duke Human Vaccine Institute, Duke University, Durham, NC 27710
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22
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Mitsunaga EM, Snyder MP. Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing. Mol Cell Proteomics 2020; 19:278-293. [PMID: 31767621 PMCID: PMC7000125 DOI: 10.1074/mcp.ra119.001633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Human antibody response studies are largely restricted to periods of high immune activity (e.g. vaccination). To comprehensively understand the healthy B cell immune repertoire and how this changes over time and through natural infection, we conducted immune repertoire RNA sequencing on flow cytometry-sorted B cell subsets to profile a single individual's antibodies over 11 months through two periods of natural viral infection. We found that 1) a baseline of healthy variable (V) gene usage in antibodies exists and is stable over time, but antibodies in memory cells consistently have a different usage profile relative to earlier B cell stages; 2) a single complementarity-determining region 3 (CDR3) is potentially generated from more than one VJ gene combination; and 3) IgG and IgA antibody transcripts are found at low levels in early human B cell development, suggesting that class switching may occur earlier than previously realized. These findings provide insight into immune repertoire stability, response to natural infections, and human B cell development.
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Affiliation(s)
- Erin M Mitsunaga
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305.
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23
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Chen J, Li N, Yin Y, Zheng N, Min M, Lin B, Zhang L, Long X, Zhang Y, Cai Z, Zhai S, Qin J, Wang X. Methyltransferase Nsd2 Ensures Germinal Center Selection by Promoting Adhesive Interactions between B Cells and Follicular Dendritic Cells. Cell Rep 2019; 25:3393-3404.e6. [PMID: 30566865 DOI: 10.1016/j.celrep.2018.11.096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/23/2018] [Accepted: 11/28/2018] [Indexed: 01/23/2023] Open
Abstract
Antibody affinity maturation, which is an antigen-based selection process for B cells, occurs in germinal centers (GCs). GCB cells must efficiently recognize, acquire, and present antigens from follicular dendritic cells (FDCs) to receive positive selection signals from T helper cells. Previous studies showed that GCB cells undergo adhesive interactions with FDCs, but the regulatory mechanisms underlying the cell adhesions and their functional relevance remain unclear. Here, we identified H3K36me2 methyltransferase Nsd2 as a critical regulator of GCB cell-FDC adhesion. Nsd2 deletion modestly reduced GC responses but strongly impaired B cell affinity maturation. Mechanistically, Nsd2 directly regulated expression of multiple actin polymerization-related genes in GCB cells. Nsd2 loss reduced B cell adhesion to FDC-expressed adhesion molecules, thus affecting both B cell receptor (BCR) signaling and antigen acquisition. Overall, Nsd2 coordinates GCB positive selection by enhancing both BCR signaling and T cell help.
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Affiliation(s)
- Jingjing Chen
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Ni Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yuye Yin
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Nan Zheng
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Min Min
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Bichun Lin
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Le Zhang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Xuehui Long
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Yang Zhang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Zhenming Cai
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Sulan Zhai
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Road, Nanjing, Jiangsu 211166, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
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24
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Finney J, Yang G, Kuraoka M, Song S, Nojima T, Verkoczy L, Kitamura D, Haynes BF, Kelsoe G. Cross-Reactivity to Kynureninase Tolerizes B Cells That Express the HIV-1 Broadly Neutralizing Antibody 2F5. THE JOURNAL OF IMMUNOLOGY 2019; 203:3268-3281. [PMID: 31732530 DOI: 10.4049/jimmunol.1900069] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/11/2019] [Indexed: 11/19/2022]
Abstract
2F5 is an HIV-1 broadly neutralizing Ab that also binds the autoantigens kynureninase (KYNU) and anionic lipids. Generation of 2F5-like Abs is proscribed by immune tolerance, but it is unclear which autospecificity is responsible. We sampled the BCR repertoire of 2F5 knock-in mice before and after the first and second tolerance checkpoints. Nearly all small pre-B (precheckpoint) and 35-70% of anergic peripheral B cells (postcheckpoint) expressed the 2F5 BCR and maintained KYNU, lipid, and HIV-1 gp41 reactivity. In contrast, all postcheckpoint mature follicular (MF) B cells had undergone L chain editing that purged KYNU and gp41 binding but left lipid reactivity largely intact. We conclude that specificity for KYNU is the primary driver of tolerization of 2F5-expressing B cells. The MF and anergic B cell populations favored distinct collections of editor L chains; surprisingly, however, MF and anergic B cells also frequently expressed identical BCRs. These results imply that BCR autoreactivity is the primary determinant of whether a developing B cell enters the MF or anergic compartments, with a secondary role for stochastic factors that slightly mix the two pools. Our study provides mechanistic insights into how immunological tolerance impairs humoral responses to HIV-1 and supports activation of anergic B cells as a potential method for HIV-1 vaccination.
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Affiliation(s)
- Joel Finney
- Department of Immunology, Duke University, Durham, NC 27710
| | - Guang Yang
- Department of Immunology, Duke University, Durham, NC 27710
| | | | - Shengli Song
- Department of Immunology, Duke University, Durham, NC 27710
| | - Takuya Nojima
- Department of Immunology, Duke University, Durham, NC 27710
| | | | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan; and
| | - Barton F Haynes
- Department of Immunology, Duke University, Durham, NC 27710.,Human Vaccine Institute, Duke University, Durham, NC 27710
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710; .,Human Vaccine Institute, Duke University, Durham, NC 27710
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25
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Meffre E, O'Connor KC. Impaired B‐cell tolerance checkpoints promote the development of autoimmune diseases and pathogenic autoantibodies. Immunol Rev 2019; 292:90-101. [DOI: 10.1111/imr.12821] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Eric Meffre
- Department of Immunobiology Yale University School of Medicine New Haven CT USA
- Section of Rheumatology, Allergy, and Clinical Immunology Yale University School of Medicine New Haven CT USA
| | - Kevin C. O'Connor
- Department of Immunobiology Yale University School of Medicine New Haven CT USA
- Department of Neurology Yale University School of Medicine New Haven CT USA
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26
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Finney J, Watanabe A, Kelsoe G, Kuraoka M. Minding the gap: The impact of B-cell tolerance on the microbial antibody repertoire. Immunol Rev 2019; 292:24-36. [PMID: 31559648 PMCID: PMC6935408 DOI: 10.1111/imr.12805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 09/02/2019] [Indexed: 12/19/2022]
Abstract
B lymphocytes must respond to vast numbers of foreign antigens, including those of microbial pathogens. To do so, developing B cells use combinatorial joining of V-, D-, and J-gene segments to generate an extraordinarily diverse repertoire of B-cell antigen receptors (BCRs). Unsurprisingly, a large fraction of this initial BCR repertoire reacts to self-antigens, and these "forbidden" B cells are culled by immunological tolerance from mature B-cell populations. While culling of autoreactive BCRs mitigates the risk of autoimmunity, it also opens gaps in the BCR repertoire, which are exploited by pathogens that mimic the forbidden self-epitopes. Consequently, immunological tolerance, necessary for averting autoimmune disease, also acts to limit effective microbial immunity. In this brief review, we recount the evidence for the linkage of tolerance and impaired microbial immunity, consider the implications of this linkage for vaccine development, and discuss modulating tolerance as a potential strategy for strengthening humoral immune responses.
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Affiliation(s)
- Joel Finney
- Department of Immunology, Duke University, Durham, NC, USA
| | - Akiko Watanabe
- Department of Immunology, Duke University, Durham, NC, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC, USA
- Duke University Human Vaccine Institute, Duke University, Durham, NC, USA
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27
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Myles A, Sanz I, Cancro MP. T-bet + B cells: A common denominator in protective and autoreactive antibody responses? Curr Opin Immunol 2019; 57:40-45. [PMID: 30784957 DOI: 10.1016/j.coi.2019.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/02/2019] [Accepted: 01/16/2019] [Indexed: 12/15/2022]
Abstract
T-bet+ B cells have emerged as a key component of the humoral immune response in both infections and autoimmune disorders, with many of their phenotypic and functional attributes conserved between mice and humans. They are protective (infections) and pathogenic (autoimmunity), although the associated commonalities and differences remain unclear. Heterogeneity within this pool, in terms of origin, fate and function may underlie these divergent roles. Their significance is context-dependent- they may constitute a persistent effector memory cell pool, or products of recent primary responses. In both cases however, T-bet+ cells likely represent antigen-experienced progenitors of antibody-secreting cells with multipotent properties. Given their key contributions to both immunity and disease, T-bet+ B cells are an attractive target for vaccination and therapeutic strategies.
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Affiliation(s)
- Arpita Myles
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael P Cancro
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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28
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Rodríguez Bustos H, Espinoza-Navarro O, Castro ME. Effect of classical conditioning over immature and mature B lymphocytes regulation. Microsc Res Tech 2018; 81:1451-1455. [PMID: 30365190 DOI: 10.1002/jemt.23112] [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: 09/21/2017] [Revised: 06/11/2018] [Accepted: 07/23/2018] [Indexed: 11/09/2022]
Abstract
Classical conditioning (CC) with a sweet flavored is useful for experimental models of immune response. The objective this work was analyze spleen cell response on the differentiation of B-lymphocytes associated with the CC with sweet flavored in adult rats. Twelve adult male rats were divided (n = 3) in Group 1 (control); Group 2 without conditioned stimulus (WCS) received only water; Group 3 receiving only water with salt; Group 4 (experimental) with CS of sweet flavored and salty flavored afterwards. In every work group, all animals were subjected to the unconditioned stimulus (US) treated by 10 mg/kg body weight of cyclophosphamide injected intraperitoneally (i.p.). Subsequently an immunological challenge with sheep red blood cells i.p. was applied. Spleen samples were obtained 15 days after using euthanasia with 1% sodium thiopental i.p. The evaluation B lymphocyte (immature and mature) was performed by immunohistochemistry using specific antibodies against CD20 and against CD37, and revealed with HRP/DAB. The results show in every work group significant increases of CD20+ and CD37+ cell densities in the red pulp of the spleen of male adult rats from different groups of the experimental design. We concluded that the immunomodulatory response under CC might facilitate a less aggressive and more physiological immunological response against immunosuppression. RESEARCH HIGHLIGHTS: The immune response can be reinforced by classical conditioning. The sweet taste allows to positively condition the immune response. B lymphocytes actively participate in the immune response and classical conditioning.
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Affiliation(s)
- Héctor Rodríguez Bustos
- Laboratory of Morphology, Anatomy and Development of Biology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Omar Espinoza-Navarro
- Laboratory of Morphology, Anatomy and Development of Biology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - María Eugenia Castro
- Laboratory of Morphology, Anatomy and Development of Biology, Faculty of Medicine, University of Chile, Santiago, Chile
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29
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Le Gallou S, Zhou Z, Thai LH, Fritzen R, de Los Aires AV, Mégret J, Yu P, Kitamura D, Bille E, Tros F, Nassif X, Charbit A, Weller S, Weill JC, Reynaud CA. A splenic IgM memory subset with antibacterial specificities is sustained from persistent mucosal responses. J Exp Med 2018; 215:2035-2053. [PMID: 29959173 PMCID: PMC6080908 DOI: 10.1084/jem.20180977] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/08/2018] [Accepted: 06/18/2018] [Indexed: 12/12/2022] Open
Abstract
Le Gallou et al. use an AID fate-mapping model to identify an IgM memory population in the spleen of unimmunized mice, originating from persistent gut immune responses and endowed with cross-reactivity against bacteria. To what extent immune responses against the gut flora are compartmentalized within mucosal tissues in homeostatic conditions remains a much-debated issue. We describe here, based on an inducible AID fate-mapping mouse model, that systemic memory B cell subsets, including mainly IgM+ B cells in spleen, together with IgA+ plasma cells in spleen and bone marrow, are generated in mice in the absence of deliberate immunization. While the IgA component appears dependent on the gut flora, IgM memory B cells are still generated in germ-free mice, albeit to a reduced extent. Clonal relationships and renewal kinetics after anti-CD20 treatment reveal that this long-lasting splenic population is mainly sustained by output of B cell clones persisting in mucosal germinal centers. IgM-secreting hybridomas established from splenic IgM memory B cells showed reactivity against various bacterial isolates and endogenous retroviruses. Ongoing activation of B cells in gut-associated lymphoid tissues thus generates a diversified systemic compartment showing long-lasting clonal persistence and protective capacity against systemic bacterial infections.
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Affiliation(s)
- Simon Le Gallou
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Zhicheng Zhou
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Lan-Huong Thai
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Remi Fritzen
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Alba Verge de Los Aires
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jérôme Mégret
- Flow Cytometry Core Facility, Structure Fédérative de Recherche Necker, Institut National de la Santé et de la Recherche Médicale US24-Centre National de la Recherche Scientifique UMS 3633, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Philipp Yu
- Institute of Immunology, Philipps-Universität Marburg, Marburg, Germany
| | - Daisuke Kitamura
- Division of Molecular Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Emmanuelle Bille
- Team "Pathogeny of Systemic Infections", Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Service de Microbiologie, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Fabiola Tros
- Team "Pathogeny of Systemic Infections", Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Xavier Nassif
- Team "Pathogeny of Systemic Infections", Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Service de Microbiologie, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alain Charbit
- Team "Pathogeny of Systemic Infections", Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Sandra Weller
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jean-Claude Weill
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Claude-Agnès Reynaud
- Team "Development of the Immune System," Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151-Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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30
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Pandya KD, Palomo-Caturla I, Walker JA, K Sandilya V, Zhong Z, Alugupalli KR. An Unmutated IgM Response to the Vi Polysaccharide of Salmonella Typhi Contributes to Protective Immunity in a Murine Model of Typhoid. THE JOURNAL OF IMMUNOLOGY 2018; 200:4078-4084. [PMID: 29743315 DOI: 10.4049/jimmunol.1701348] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/16/2018] [Indexed: 11/19/2022]
Abstract
T cell-dependent B cell responses typically develop in germinal centers. Abs generated during such responses are isotype switched and have a high affinity to the Ag because of somatic hypermutation of Ab genes. B cell responses to purified polysaccharides are T cell independent and do not result in the formation of bona fide germinal centers, and the dominant Ab isotype produced during such responses is IgM with very few or no somatic mutations. Activation-induced cytidine deaminase (AID) is required for both somatic hypermutation and Ig isotype switching in humans and mice. To test the extent to which unmutated polysaccharide-specific IgM confers protective immunity, we immunized wildtype and AID-/- mice with either heat-killed Salmonella enterica serovar Typhi (S. Typhi) or purified Vi polysaccharide (ViPS). We found that wildtype and AID-/- mice immunized with heat-killed S. Typhi generated similar anti-ViPS IgM responses. As expected, wildtype, but not AID-/- mice generated ViPS-specific IgG. However, the differences in the Ab-dependent killing of S. Typhi mediated by the classical pathway of complement activation were not statistically significant. In ViPS-immunized wildtype and AID-/- mice, the ViPS-specific IgM levels and S. Typhi bactericidal Ab titers at 7 but not at 28 d postimmunization were also comparable. To test the protective immunity conferred by these immunizations, mice were challenged with a chimeric S. Typhimurium strain expressing ViPS. Compared with their naive counterparts, immunized wildtype and AID-/- mice exhibited significantly reduced bacterial burden regardless of the route of infection. These data indicate that an unmutated IgM response to ViPS contributes to protective immunity to S. Typhi.
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Affiliation(s)
- Kalgi D Pandya
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107; and
| | - Isabel Palomo-Caturla
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107; and
| | - Justin A Walker
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107; and
| | - Vijay K Sandilya
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107; and
| | - Zhijiu Zhong
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107
| | - Kishore R Alugupalli
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107; and .,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107
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31
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Hao F, Tian M, Feng Y, Quan C, Chen Y, Chen S, Wei M. Abrogation of Lupus Nephritis in Somatic Hypermutation-Deficient MRL/lpr Mice. THE JOURNAL OF IMMUNOLOGY 2018; 200:3905-3912. [PMID: 29728506 DOI: 10.4049/jimmunol.1800115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/31/2018] [Indexed: 01/31/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease posing threats to multiple organs in the human body. As a typical manifestation of SLE, lupus nephritis is characterized by a series of pathological changes in glomerulus as well as accumulation of pathogenic autoreactive IgG with complement in the kidney that dramatically disrupts renal functions. Activation-induced deaminase (AID), which governs both somatic hypermutation (SHM) and class-switch recombination (CSR), has been shown to be essential for the regulation of SLE. However, the relative contributions of SHM and CSR to SLE pathology have not been determined. Based on the available AIDG23S mice, we successfully established an AIDG23S MRL/lpr mouse model, in which SHM is specifically abolished, although CSR is largely unaffected. We found that the abrogation of SHM effectively alleviated SLE-associated histopathological alterations, such as expansion of the mesangial matrix and thickening of the basement membrane of Bowman's capsule as well as infiltration of inflammatory cells. Compared with SLE mice, AIDG23S MRL/lpr mice exhibited decreased proteinuria, blood urea nitrogen, and creatinine, indicating that the loss of SHM contributed to the recovery of renal functions. As a consequence, the life span of those SHM-deficient MRL/lpr mice was extended. Together, we provide direct evidence pinpointing a vital role of SHM in the control of SLE development.
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Affiliation(s)
- Fengqi Hao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, People's Republic of China.,School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130022, People's Republic of China; and
| | - Miaomiao Tian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Yunpeng Feng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Chao Quan
- Ministry of Education Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing, 210061, People's Republic of China
| | - Yixi Chen
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Shuai Chen
- Ministry of Education Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing, 210061, People's Republic of China
| | - Min Wei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, People's Republic of China;
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32
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Ott JA, Castro CD, Deiss TC, Ohta Y, Flajnik MF, Criscitiello MF. Somatic hypermutation of T cell receptor α chain contributes to selection in nurse shark thymus. eLife 2018; 7:28477. [PMID: 29664399 PMCID: PMC5931798 DOI: 10.7554/elife.28477] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 04/16/2018] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of the T cell receptor (TcR), immunologists have assigned somatic hypermutation (SHM) as a mechanism employed solely by B cells to diversify their antigen receptors. Remarkably, we found SHM acting in the thymus on α chain locus of shark TcR. SHM in developing shark T cells likely is catalyzed by activation-induced cytidine deaminase (AID) and results in both point and tandem mutations that accumulate non-conservative amino acid replacements within complementarity-determining regions (CDRs). Mutation frequency at TcRα was as high as that seen at B cell receptor loci (BcR) in sharks and mammals, and the mechanism of SHM shares unique characteristics first detected at shark BcR loci. Additionally, fluorescence in situ hybridization showed the strongest AID expression in thymic corticomedullary junction and medulla. We suggest that TcRα utilizes SHM to broaden diversification of the primary αβ T cell repertoire in sharks, the first reported use in vertebrates.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Caitlin D Castro
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Texas, United States
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33
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Tan Q, Tai N, Li Y, Pearson J, Pennetti S, Zhou Z, Wong FS, Wen L. Activation-induced cytidine deaminase deficiency accelerates autoimmune diabetes in NOD mice. JCI Insight 2018; 3:95882. [PMID: 29321370 DOI: 10.1172/jci.insight.95882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/05/2017] [Indexed: 01/15/2023] Open
Abstract
B cells play an important role in type 1 diabetes (T1D) development. However, the role of B cell activation-induced cytidine deaminase (AID) in diabetes development is not clear. We hypothesized that AID is important in the immunopathogenesis of T1D. To test this hypothesis, we generated AID-deficient (AID-/-) NOD mice. We found that AID-/-NOD mice developed accelerated T1D, with worse insulitis and high levels of anti-insulin autoantibody in the circulation. Interestingly, neither maternal IgG transferred through placenta, nor IgA transferred through milk affected the accelerated diabetes development. AID-/-NOD mice showed increased activation and proliferation of B and T cells. We found enhanced T-B cell interactions in AID-/-NOD mice, with increased T-bet and IFN-γ expression in CD4+ T cells in the presence of AID-/- B cells. Moreover, excessive lymphoid expansion was observed in AID-/-NOD mice. Importantly, antigen-specific BDC2.5 CD4+ T cells caused more rapid onset of diabetes when cotransferred with AID-/- B cells than when cotransferred with AID+/+ B cells. Thus, our study provides insights into the role of AID in T1D. Our data also suggest that AID is a negative regulator of immune tolerance and ablation of AID can lead to exacerbated islet autoimmunity and accelerated T1D development.
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Affiliation(s)
- Qiyuan Tan
- Institute of Metabolism and Endocrinology, The Second Xiangya Hospital, Key Laboratory of Diabetes Immunology, Ministry of Education, Central South University, National Clinical Research Center for Metabolic Diseases, Changsha,Hunan, China.,Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Endocrinology and Metabolism, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ningwen Tai
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yangyang Li
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Endocrinology, Jilin University, Changchun, China
| | - James Pearson
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sean Pennetti
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,School of Medicine, Quinnipiac University, North Haven, Connecticut, USA
| | - Zhiguang Zhou
- Institute of Metabolism and Endocrinology, The Second Xiangya Hospital, Key Laboratory of Diabetes Immunology, Ministry of Education, Central South University, National Clinical Research Center for Metabolic Diseases, Changsha,Hunan, China
| | - F Susan Wong
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Li Wen
- Institute of Metabolism and Endocrinology, The Second Xiangya Hospital, Key Laboratory of Diabetes Immunology, Ministry of Education, Central South University, National Clinical Research Center for Metabolic Diseases, Changsha,Hunan, China.,Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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35
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Perera J, Zheng Z, Li S, Gudjonson H, Kalinina O, Benichou JIC, Block KE, Louzoun Y, Yin D, Chong AS, Dinner AR, Weigert M, Huang H. Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance. Cell Rep 2017; 17:387-398. [PMID: 27705788 DOI: 10.1016/j.celrep.2016.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 07/20/2016] [Accepted: 09/02/2016] [Indexed: 11/26/2022] Open
Abstract
B cells are unique antigen-presenting cells because their antigen presentation machinery is closely tied to the B cell receptor. Autoreactive thymic B cells can efficiently present cognate self-antigens to mediate CD4+ T cell-negative selection. However, the nature of thymocyte-thymic B cell interaction and how this interaction affects the selection of thymic B cell repertoire and, in turn, the T cell repertoire are not well understood. Here we demonstrate that a large percentage of thymic B cells have undergone class switching intrathymically. Thymic B cell class switching requires cognate interaction with specific T cells. Class-switched thymic B cells have a distinct repertoire compared with unswitched thymic B cells or splenic B cells. Particularly, autoreactive B cell specificities preferentially expand in the thymus by undergoing class switching, and these enriched, class-switched autoreactive thymic B cells play an important role in CD4 T cell tolerance.
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Affiliation(s)
- Jason Perera
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Rheumatology, and Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Zhong Zheng
- Department of Medicine, Section of Rheumatology, and Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Shuyin Li
- Department of Medicine, Section of Rheumatology, and Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Herman Gudjonson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Graduate Program in the Biophysical Sciences, Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Olga Kalinina
- Knapp Center for Lupus and Immunology Research, Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Jennifer I C Benichou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
| | - Katharine E Block
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Rheumatology, and Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Yoram Louzoun
- Department of Mathematics and Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Dengping Yin
- Section of Transplantation, Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Anita S Chong
- Section of Transplantation, Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Aaron R Dinner
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Graduate Program in the Biophysical Sciences, Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Martin Weigert
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Knapp Center for Lupus and Immunology Research, Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Haochu Huang
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Rheumatology, and Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA.
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36
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Kuraoka M, Snowden PB, Nojima T, Verkoczy L, Haynes BF, Kitamura D, Kelsoe G. BCR and Endosomal TLR Signals Synergize to Increase AID Expression and Establish Central B Cell Tolerance. Cell Rep 2017; 18:1627-1635. [PMID: 28199836 DOI: 10.1016/j.celrep.2017.01.050] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/01/2016] [Accepted: 01/19/2017] [Indexed: 12/31/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is required to purge autoreactive immature and transitional-1 (immature/T1) B cells at the first tolerance checkpoint, but how AID selectively removes self-reactive B cells is unclear. We now show that B cell antigen receptor (BCR) and endosomal Toll-like receptor (TLR) signals synergize to elicit high levels of AID expression in immature/T1 B cells. This synergy is restricted to ligands for endocytic TLR and requires phospholipase-D activation, endosomal acidification, and MyD88. The first checkpoint is significantly impaired in AID- or MyD88-deficient mice and in mice doubly heterozygous for AID and MyD88, suggesting interaction of these factors in central B cell tolerance. Moreover, administration of chloroquine, an inhibitor of endosomal acidification, results in a failure to remove autoreactive immature/T1 B cells in mice. We propose that a BCR/TLR pathway coordinately establishes central tolerance by hyper-activating AID in immature/T1 B cells that bind ligands for endosomal TLRs.
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Affiliation(s)
- Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Pilar B Snowden
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Takuya Nojima
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | | | - Barton F Haynes
- Department of Immunology, Duke University, Durham, NC 27710, USA; Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710, USA; Human Vaccine Institute, Duke University, Durham, NC 27710, USA.
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37
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Liu J, Xiong E, Zhu H, Mori H, Yasuda S, Kinoshita K, Tsubata T, Wang JY. Efficient Induction of Ig Gene Hypermutation in Ex Vivo–Activated Primary B Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:3023-3030. [DOI: 10.4049/jimmunol.1700868] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/29/2017] [Indexed: 11/19/2022]
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38
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McDonald G, Medina CO, Pilichowska M, Kearney JF, Shinkura R, Selsing E, Wortis HH, Honjo T, Imanishi-Kari T. Accelerated Systemic Autoimmunity in the Absence of Somatic Hypermutation in 564Igi: A Mouse Model of Systemic Lupus with Knocked-In Heavy and Light Chain Genes. Front Immunol 2017; 8:1094. [PMID: 28955333 PMCID: PMC5601273 DOI: 10.3389/fimmu.2017.01094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/22/2017] [Indexed: 11/18/2022] Open
Abstract
564Igi mice have knocked-in immunoglobulin (Ig) heavy (H) and light (L) chain genes that encode an autoantibody recognizing RNA. Previously, we showed that these mice produce pathogenic IgG autoantibodies when activation-induced deaminase (AID) is expressed in pre-B and immature B cells but not when it is expressed only in mature B cells. AID has two functions; it is necessary for somatic hypermutation (SHM) and class switch recombination (CSR). To determine the role of each of these functions in the generation of pathogenic autoantibodies, we generated 564Igi mice that carry a mutant AID-encoding gene, Aicda (AicdaG23S), which is capable of promoting CSR but not SHM. We found that 564Igi AicdaG23S mice secreted class-switched antibodies (Abs) at levels approximately equal to 564Igi mice. However, compared to 564Igi mice, 564Igi AicdaG23S mice had increased pathogenic IgG Abs and severe systemic lupus erythematosus-like disease, including, glomerulonephritis, and early death. We suggest that in 564Igi mice SHM by AID changes Ig receptors away from self reactivity, thereby mitigating the production of autoantibody, providing a novel mechanism of tolerance.
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Affiliation(s)
- Gabrielle McDonald
- Department of Integrative Physiology and Pathobiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
| | - Carlos O Medina
- Department of Integrative Physiology and Pathobiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
| | - Monika Pilichowska
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, United States
| | - John F Kearney
- Department of Microbiology, University of Alabama, Birmingham, AL, United States
| | - Reiko Shinkura
- Department of Immunology, Nagahama Institute of Bioscience and Technology, Nagahama, Japan
| | - Erik Selsing
- Department of Integrative Physiology and Pathobiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
| | - Henry H Wortis
- Department of Integrative Physiology and Pathobiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thereza Imanishi-Kari
- Department of Integrative Physiology and Pathobiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
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39
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Auer F, Ingenhag D, Pinkert S, Kracker S, Hacein-Bey-Abina S, Cavazzana M, Gombert M, Martin-Lorenzo A, Lin MH, Vicente-Dueñas C, Sánchez-García I, Borkhardt A, Hauer J. Activation-induced cytidine deaminase prevents pro-B cell acute lymphoblastic leukemia by functioning as a negative regulator in Rag1 deficient pro-B cells. Oncotarget 2017; 8:75797-75807. [PMID: 29100269 PMCID: PMC5652663 DOI: 10.18632/oncotarget.20563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 11/25/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation and class switch recombination in mature B-cells, while AID was also shown to play a role in developing pre-BCR/BCR-positive B-cells of the bone marrow. To further elucidate a potential function of Aid in the bone marrow prior to V(D)J-recombination, we utilized an in vivo model which exerts a B-cell developmental arrest at the pro-B cell stage with low frequencies of pro-B cell acute lymphoblastic leukemia (pro-B ALL) development. Therefore, p19Arf-/-Rag1-/- (AR) mice were crossed with Aid-deficient mice (ARA). Surprisingly, loss of Aid expression in pro-B cells accelerated pro-B ALL incidence from 30% (AR) to 98% (ARA). This effect was Aid dose dependent, since Aid+/- animals of the same background displayed a significantly lower incidence (83%). Furthermore, B-cell-specific Aid up-regulation was observed in Aid-competent pro-B ALLs. Additional whole exome/sanger sequencing of murine pro-B ALLs revealed an accumulation of recurrent somatic Jak3 (p.R653H, p.V670A) and Dnm2 (p.G397R) mutations, which highlights the importance of active IL7R signaling in the pro-B ALL blast cells. These findings were further supported by an enhanced proliferative potential of ARA pro-B cells compared to Aid-competent cells from the same genetic background. In summary, we show that both Aid and Rag1 act as a negative regulators in pro-B cells, preventing pro-B ALL.
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Affiliation(s)
- Franziska Auer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Deborah Ingenhag
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Stefan Pinkert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Sven Kracker
- Université Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM UMR 1163, Human Lymphohematopoiesis Laboratory, Paris, France
| | - Salima Hacein-Bey-Abina
- UTCBS CNRS UMR 8258, INSERM U1022, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Chimie Paris-Tech, Paris, France.,Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, Assistance Publique-Hôpitaux de Paris, Le-Kremlin-Bicêtre, France
| | - Marina Cavazzana
- Université Paris Descartes, Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM UMR 1163, Human Lymphohematopoiesis Laboratory, Paris, France
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Alberto Martin-Lorenzo
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/ Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain.,Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Min-Hui Lin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | | | - Isidro Sánchez-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC/ Universidad de Salamanca, Campus M. de Unamuno s/n, Salamanca, Spain.,Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Duesseldorf, Medical Faculty, Duesseldorf, Germany
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40
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Abstract
Induction of broadly neutralizing antibodies (bNAbs) is a major goal of HIV vaccine development. BNAbs are made during HIV infection by a subset of individuals but currently cannot be induced in the setting of vaccination. Considerable progress has been made recently in understanding host immunologic controls of bNAb induction and maturation in the setting of HIV infection, and point to key roles for both central and peripheral immunologic tolerance mechanisms in limiting bnAb development. Immune tolerance checkpoint inhibition has been transformative in promotion of anti-tumor CD8 T-cell responses in the treatment of certain malignancies. Here, we review the evidence for host controls of bNAb responses, and discuss strategies for the transient modulation of immune responses with vaccines toward the goal of enhancing germinal center B-cell responses to favor bNAb B-cell lineages and to foster their maturation to full neutralization potency.
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Affiliation(s)
- Garnett Kelsoe
- Departments of Immunology and Medicine, Duke University School of Medicine, Duke Human Vaccine Institute, Durham, NC, 27710, USA
| | - Barton F Haynes
- Departments of Immunology and Medicine, Duke University School of Medicine, Duke Human Vaccine Institute, Durham, NC, 27710, USA
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41
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Kaku H, Holodick NE, Tumang JR, Rothstein TL. CD25 + B-1a Cells Express Aicda. Front Immunol 2017; 8:672. [PMID: 28676801 PMCID: PMC5477345 DOI: 10.3389/fimmu.2017.00672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/23/2017] [Indexed: 11/25/2022] Open
Abstract
B-1a cells are innate-like B-lymphocytes producing natural antibodies. Activation-induced cytidine deaminase (AID), a product of the Aicda gene, plays a central role in class-switch recombination and somatic hypermutation in B cells. Although a role for Aicda in B-1a cells has been suggested on the basis of experiments with knock out (KO) mice, whether B-1a cells express Aicda, and if so, which B-1a cell subpopulation expresses Aicda, remains unknown. Here, we demonstrate that B-1 cells express Aicda, but at a level below that expressed by germinal center (GC) B cells. We previously reported that B-1a cells can be subdivided based on CD25 expression. We show here that B-1a cell Aicda expression is concentrated in the CD25+ B-1a cell subpopulation. These results suggest the possibility that previous studies of memory B cells identified on the basis of Aicda expression may have inadvertently included an unknown number of CD25+ B-1a cells. Although B-1a cells develop normally in the absence of Aicda, a competitive reconstitution assay reveals enhanced vigor for AID KO B-1a cell bone marrow (BM) progenitors, as compared with wild-type BM B-1 cell progenitors. These results suggest that AID inhibits the development of B-1a cells from BM B-1 cell progenitors in a competitive environment.
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Affiliation(s)
- Hiroaki Kaku
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Nichol E Holodick
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY, United States
| | | | - Thomas L Rothstein
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY, United States.,Department of Medicine, The Hofstra Northwell School of Medicine, Manhasset, NY, United States.,Department of Molecular Medicine, The Hofstra Northwell School of Medicine, Manhasset, NY, United States
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42
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Ratiu JJ, Racine JJ, Hasham MG, Wang Q, Branca JA, Chapman HD, Zhu J, Donghia N, Philip V, Schott WH, Wasserfall C, Atkinson MA, Mills KD, Leeth CM, Serreze DV. Genetic and Small Molecule Disruption of the AID/RAD51 Axis Similarly Protects Nonobese Diabetic Mice from Type 1 Diabetes through Expansion of Regulatory B Lymphocytes. THE JOURNAL OF IMMUNOLOGY 2017; 198:4255-4267. [PMID: 28461573 DOI: 10.4049/jimmunol.1700024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/04/2017] [Indexed: 11/19/2022]
Abstract
B lymphocytes play a key role in type 1 diabetes (T1D) development by serving as a subset of APCs preferentially supporting the expansion of autoreactive pathogenic T cells. As a result of their pathogenic importance, B lymphocyte-targeted therapies have received considerable interest as potential T1D interventions. Unfortunately, the B lymphocyte-directed T1D interventions tested to date failed to halt β cell demise. IgG autoantibodies marking humans at future risk for T1D indicate that B lymphocytes producing them have undergone the affinity-maturation processes of class switch recombination and, possibly, somatic hypermutation. This study found that CRISPR/Cas9-mediated ablation of the activation-induced cytidine deaminase gene required for class switch recombination/somatic hypermutation induction inhibits T1D development in the NOD mouse model. The activation-induced cytidine deaminase protein induces genome-wide DNA breaks that, if not repaired through RAD51-mediated homologous recombination, result in B lymphocyte death. Treatment with the RAD51 inhibitor 4,4'-diisothiocyanatostilbene-2, 2'-disulfonic acid also strongly inhibited T1D development in NOD mice. The genetic and small molecule-targeting approaches expanded CD73+ B lymphocytes that exert regulatory activity suppressing diabetogenic T cell responses. Hence, an initial CRISPR/Cas9-mediated genetic modification approach has identified the AID/RAD51 axis as a target for a potentially clinically translatable pharmacological approach that can block T1D development by converting B lymphocytes to a disease-inhibitory CD73+ regulatory state.
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Affiliation(s)
| | | | | | - Qiming Wang
- The Jackson Laboratory, Bar Harbor, ME 04609.,Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111
| | | | | | - Jing Zhu
- Department of Animal and Poultry Sciences, Virginia Polytechnic and State University, Blacksburg, VA 24061
| | | | | | | | - Clive Wasserfall
- Department of Pathology, University of Florida, Gainesville, FL 32610; and
| | - Mark A Atkinson
- Department of Pathology, University of Florida, Gainesville, FL 32610; and
| | | | - Caroline M Leeth
- Department of Animal and Poultry Sciences, Virginia Polytechnic and State University, Blacksburg, VA 24061;
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43
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Abstract
Immune tolerance hinders the potentially destructive responses of lymphocytes to host tissues. Tolerance is regulated at the stage of immature B cell development (central tolerance) by clonal deletion, involving apoptosis, and by receptor editing, which reprogrammes the specificity of B cells through secondary recombination of antibody genes. Recent mechanistic studies have begun to elucidate how these divergent mechanisms are controlled. Single-cell antibody cloning has revealed defects of B cell central tolerance in human autoimmune diseases and in several human immunodeficiency diseases caused by single gene mutations, which indicates the relevance of B cell tolerance to disease and suggests possible genetic pathways that regulate tolerance.
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44
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Wilmore JR, Maue AC, Rochford R. Plasmodium chabaudi infection induces AID expression in transitional and marginal zone B cells. IMMUNITY INFLAMMATION AND DISEASE 2016; 4:497-505. [PMID: 27980783 PMCID: PMC5134720 DOI: 10.1002/iid3.134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/31/2016] [Accepted: 09/30/2016] [Indexed: 11/25/2022]
Abstract
Introduction Endemic Burkitt's lymphoma (eBL) is associated with Epstein–Barr virus and repeated malaria infections. A defining feature of eBL is the translocation of the c‐myc oncogene to the control of the immunoglobulin promoter. Activation‐induced cytidine deaminase (AID) has been shown to be critical for this translocation. Malaria infection induces AID in germinal center B cells, but whether malaria infection more broadly affects AID activation in extrafollicular B cells is unknown. Methods We either stimulated purified B cells from AID‐green fluorescence protein (GFP) reporter mice or infected AID‐GFP mice with Plasmodium chabaudi, AID fluorescence was monitored in B cell subsets by flow cytometry. Results In vitro analysis of B cells from these mice revealed that CpG (a Toll‐like receptor 9 ligand) was a potent inducer of AID in both mature and immature B cell subsets. Infection of AID‐GFP mice with Plasmodium chabaudi demonstrated that AID expression occurs in transitional and marginal zone B cells during acute malaria infection. Transitional B cells were also capable of differentiating into antibody secreting cells when stimulated in vitro with CpG when isolated from a P. chabaudi‐infected mouse. Conclusions These data suggest that P. chabaudi is capable of inducing AID expression in B cell subsets that do not participate in the germinal center reaction, suggesting an alternative role for malaria in the etiology of eBL.
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Affiliation(s)
- Joel R Wilmore
- Department of Microbiology and Immunology SUNY Upstate Medical University Syracuse New York USA
| | - Alexander C Maue
- Department of Microbiology and Immunology SUNY Upstate Medical University Syracuse New York USA
| | - Rosemary Rochford
- Department of Microbiology and ImmunologySUNY Upstate Medical UniversitySyracuseNew YorkUSA; Department of Immunology and MicrobiologyUniversity of ColoradoAuroraColoradoUSA
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45
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Abstract
The AID/APOBEC family enzymes convert cytosines in single-stranded DNA to uracils, causing base substitutions and strand breaks. They are induced by cytokines produced during the body's inflammatory response to infections, and they help combat infections through diverse mechanisms. AID is essential for the maturation of antibodies and causes mutations and deletions in antibody genes through somatic hypermutation (SHM) and class-switch recombination (CSR) processes. One member of the APOBEC family, APOBEC1, edits mRNA for a protein involved in lipid transport. Members of the APOBEC3 subfamily in humans (APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H) inhibit infections of viruses such as HIV-1, HBV, and HCV, and retrotransposition of endogenous retroelements through mutagenic and nonmutagenic mechanisms. There is emerging consensus that these enzymes can cause mutations in the cellular genome at replication forks or within transcription bubbles depending on the physiological state of the cell and the phase of the cell cycle during which they are expressed. We describe here the state of knowledge about the structures of these enzymes, regulation of their expression, and both the advantageous and deleterious consequences of their expression, including carcinogenesis. We highlight similarities among them and present a holistic view of their regulation and function.
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Affiliation(s)
- Sachini U Siriwardena
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Kang Chen
- Department of Obstetrics and Gynecology, Wayne State University , Detroit, Michigan 48201, United States
- Mucosal Immunology Studies Team, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
- Department of Immunology and Microbiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
- Department of Immunology and Microbiology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
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46
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Cantaert T, Schickel JN, Bannock JM, Ng YS, Massad C, Delmotte FR, Yamakawa N, Glauzy S, Chamberlain N, Kinnunen T, Menard L, Lavoie A, Walter JE, Notarangelo LD, Bruneau J, Al-Herz W, Kilic SS, Ochs HD, Cunningham-Rundles C, van der Burg M, Kuijpers TW, Kracker S, Kaneko H, Sekinaka Y, Nonoyama S, Durandy A, Meffre E. Decreased somatic hypermutation induces an impaired peripheral B cell tolerance checkpoint. J Clin Invest 2016; 126:4289-4302. [PMID: 27701145 DOI: 10.1172/jci84645] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 08/30/2016] [Indexed: 12/28/2022] Open
Abstract
Patients with mutations in AICDA, which encodes activation-induced cytidine deaminase (AID), display an impaired peripheral B cell tolerance. AID mediates class-switch recombination (CSR) and somatic hypermutation (SHM) in B cells, but the mechanism by which AID prevents the accumulation of autoreactive B cells in blood is unclear. Here, we analyzed B cell tolerance in AID-deficient patients, patients with autosomal dominant AID mutations (AD-AID), asymptomatic AICDA heterozygotes (AID+/-), and patients with uracil N-glycosylase (UNG) deficiency, which impairs CSR but not SHM. The low frequency of autoreactive mature naive B cells in UNG-deficient patients resembled that of healthy subjects, revealing that impaired CSR does not interfere with the peripheral B cell tolerance checkpoint. In contrast, we observed decreased frequencies of SHM in memory B cells from AD-AID patients and AID+/- subjects, who were unable to prevent the accumulation of autoreactive mature naive B cells. In addition, the individuals with AICDA mutations, but not UNG-deficient patients, displayed Tregs with defective suppressive capacity that correlated with increases in circulating T follicular helper cells and enhanced cytokine production. We conclude that SHM, but not CSR, regulates peripheral B cell tolerance through the production of mutated antibodies that clear antigens and prevent sustained interleukin secretions that interfere with Treg function.
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47
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Li S, Liu W, Li Y, Zhao S, Liu C, Hu M, Yue W, Liu Y, Wang Y, Yang R, Xiang R, Liu F. Contribution of secondary Igkappa rearrangement to primary immunoglobulin repertoire diversification. Mol Immunol 2016; 78:193-206. [PMID: 27665270 DOI: 10.1016/j.molimm.2016.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 09/01/2016] [Accepted: 09/06/2016] [Indexed: 10/21/2022]
Abstract
Abs reactive to DNA and DNA/histone complexes are a distinguished characteristic of primary immunoglobulin repertoires in autoimmune B6.MRL-Faslpr and MRL/MpJ-Faslpr mice. These mice are defective in Fas receptor, which is critical for the apoptosis of autoreactive B cells by an extrinsic pathway. In the present study, we explored the possibility that bone marrow small pre-B and immature B cells from adult B6.MRL-Faslpr mice and MRL/MpJ-Faslpr mice respectively, which contain autoreactive B-cell antigen receptors (BCR) and manifest autoimmune syndromes, exhibit enhanced receptor editing patterns. Indeed, FASlpr pre B and immature B cells were shown to possess more ongoing replacements of non-productive (nP) than productive (P) primary VκJκ rearrangements. Significantly, the P vs nP ratios of these replaced primary rearrangements were 1:2, thus indicating that κ light-chain production appears not to inhibit secondary rearrangements. In addition, we identified multiple atypical rearrangements, such as Vκ cRS (cryptic recombination signals) cleavages. These results suggest that the onset of light chain secondary rearrangements persists similarly as a non-selected mode and independent of BCR autoreactivity during certain developmental windows of bone marrow B cells in lupus-prone mice and control, and leads us to propose the function of secondary, de novo Igκ rearrangements to increase BCR diversity.
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Affiliation(s)
- Shufang Li
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Wei Liu
- Tianjin Entry-Exit Inspection and Quarantine Bureau, Tianjin 300308, China
| | - Yinghui Li
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Shaorong Zhao
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Can Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Mengyun Hu
- Collage of Life Science, Nankai University, Tianjin, 300071, China
| | - Wei Yue
- Department of Neurology, Huanhu Hospital, Tianjin 300060, China
| | - Yanhua Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yue Wang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Rongcun Yang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Rong Xiang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China.
| | - Feifei Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China.
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48
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Azizi G, Abolhassani H, Asgardoon MH, Alinia T, Yazdani R, Mohammadi J, Rezaei N, Ochs HD, Aghamohammadi A. Autoimmunity in common variable immunodeficiency: epidemiology, pathophysiology and management. Expert Rev Clin Immunol 2016; 13:101-115. [DOI: 10.1080/1744666x.2016.1224664] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Gholamreza Azizi
- Department of Laboratory Medicine, Imam Hassan Mojtaba Hospital, Alborz University of Medical Sciences, Karaj, Iran
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Primary Immunodeficiency Diseases Network (PIDNet), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Mohammad Hosein Asgardoon
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Iranian Student Society for Immunodeficiencies, Student’s Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tina Alinia
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Yazdani
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Javad Mohammadi
- Department of Biomedical Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hans D. Ochs
- Seattle Children’s Research Institute and Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Primary Immunodeficiency Diseases Network (PIDNet), Universal Scientific Education and Research Network (USERN), Tehran, Iran
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49
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AID/APOBEC-network reconstruction identifies pathways associated with survival in ovarian cancer. BMC Genomics 2016; 17:643. [PMID: 27527602 PMCID: PMC4986275 DOI: 10.1186/s12864-016-3001-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/08/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Building up of pathway-/disease-relevant signatures provides a persuasive tool for understanding the functional relevance of gene alterations and gene network associations in multifactorial human diseases. Ovarian cancer is a highly complex heterogeneous malignancy in respect of tumor anatomy, tumor microenvironment including pro-/antitumor immunity and inflammation; still, it is generally treated as single disease. Thus, further approaches to investigate novel aspects of ovarian cancer pathogenesis aiming to provide a personalized strategy to clinical decision making are of high priority. Herein we assessed the contribution of the AID/APOBEC family and their associated genes given the remarkable ability of AID and APOBECs to edit DNA/RNA, and as such, providing tools for genetic and epigenetic alterations potentially leading to reprogramming of tumor cells, stroma and immune cells. RESULTS We structured the study by three consecutive analytical modules, which include the multigene-based expression profiling in a cohort of patients with primary serous ovarian cancer using a self-created AID/APOBEC-associated gene signature, building up of multivariable survival models with high predictive accuracy and nomination of top-ranked candidate/target genes according to their prognostic impact, and systems biology-based reconstruction of the AID/APOBEC-driven disease-relevant mechanisms using transcriptomics data from ovarian cancer samples. We demonstrated that inclusion of the AID/APOBEC signature-based variables significantly improves the clinicopathological variables-based survival prognostication allowing significant patient stratification. Furthermore, several of the profiling-derived variables such as ID3, PTPRC/CD45, AID, APOBEC3G, and ID2 exceed the prognostic impact of some clinicopathological variables. We next extended the signature-/modeling-based knowledge by extracting top genes co-regulated with target molecules in ovarian cancer tissues and dissected potential networks/pathways/regulators contributing to pathomechanisms. We thereby revealed that the AID/APOBEC-related network in ovarian cancer is particularly associated with remodeling/fibrotic pathways, altered immune response, and autoimmune disorders with inflammatory background. CONCLUSIONS The herein study is, to our knowledge, the first one linking expression of entire AID/APOBECs and interacting genes with clinical outcome with respect to survival of cancer patients. Overall, data propose a novel AID/APOBEC-derived survival model for patient risk assessment and reconstitute mapping to molecular pathways. The established study algorithm can be applied further for any biologically relevant signature and any type of diseased tissue.
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50
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Abstract
Analysis of chromosomal translocation sequence locations in human lymphomas has provided valuable clues about the mechanism of the translocations and when they occur. Biochemical analyses on the mechanisms of DNA breakage and rejoining permit formulation of detailed models of the human chromosomal translocation process in lymphoid neoplasms. Most human lymphomas are derived from B cells in which a DNA break at an oncogene is initiated by activation-induced deaminase (AID). The partner locus in many cases is located at one of the antigen receptor loci, and this break is generated by the recombination activating gene (RAG) complex or by AID. After breakage, the joining process typically occurs by non-homologous DNA end-joining (NHEJ). Some of the insights into this mechanism also apply to translocations that occur in non-lymphoid neoplasms.
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Affiliation(s)
- Michael R Lieber
- USC Norris Comprehensive Cancer Center, Room 5428, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, MC9176, Los Angeles, California 90089-9176, USA
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