1
|
Rocca R, Polerà N, Juli G, Grillone K, Maruca A, Di Martino MT, Artese A, Amato J, Pagano B, Randazzo A, Tagliaferri P, Tassone P, Alcaro S. Hit identification of novel small molecules interfering with MALAT1 triplex by a structure-based virtual screening. Arch Pharm (Weinheim) 2023; 356:e2300134. [PMID: 37309243 DOI: 10.1002/ardp.202300134] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 06/14/2023]
Abstract
Nowadays, RNA is an attractive target for the design of new small molecules with different pharmacological activities. Among several RNA molecules, long noncoding RNAs (lncRNAs) are extensively reported to be involved in cancer pathogenesis. In particular, the overexpression of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays an important role in the development of multiple myeloma (MM). Starting from the crystallographic structure of the triple-helical stability element at the 3'-end of MALAT1, we performed a structure-based virtual screening of a large commercial database, previously filtered according to the drug-like properties. After a thermodynamic analysis, we selected five compounds for the in vitro assays. Compound M5, characterized by a diazaindene scaffold, emerged as the most promising molecule enabling the destabilization of the MALAT1 triplex structure and antiproliferative activity on in vitro models of MM. M5 is proposed as a lead compound to be further optimized for improving its affinity toward MALAT1.
Collapse
Affiliation(s)
- Roberta Rocca
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
| | - Nicoletta Polerà
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Annalisa Maruca
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Anna Artese
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Pietrosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Stefano Alcaro
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| |
Collapse
|
2
|
Watanabe G, Lieber MR. The flexible and iterative steps within the NHEJ pathway. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:105-119. [PMID: 37150451 PMCID: PMC10205690 DOI: 10.1016/j.pbiomolbio.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Cellular and biochemical studies of nonhomologous DNA end joining (NHEJ) have long established that nuclease and polymerase action are necessary for the repair of a very large fraction of naturally-arising double-strand breaks (DSBs). This conclusion is derived from NHEJ studies ranging from yeast to humans and all genetically-tractable model organisms. Biochemical models derived from recent real-time and structural studies have yet to incorporate physical space or timing for DNA end processing. In real-time single molecule FRET (smFRET) studies, we analyzed NHEJ synapsis of DNA ends in a defined biochemical system. We described a Flexible Synapsis (FS) state in which the DNA ends were in proximity via only Ku and XRCC4:DNA ligase 4 (X4L4), and in an orientation that would not yet permit ligation until base pairing between one or more nucleotides of microhomology (MH) occurred, thereby allowing an in-line Close Synapsis (CS) state. If no MH was achievable, then XLF was critical for ligation. Neither FS or CS required DNA-PKcs, unless Artemis activation was necessary to permit local resection and subsequent base pairing between the two DNA ends being joined. Here we conjecture on possible 3D configurations for this FS state, which would spatially accommodate the nuclease and polymerase processing steps in an iterative manner. The FS model permits repeated attempts at ligation of at least one strand at the DSB after each round of nuclease or polymerase action. In addition to activation of Artemis, other possible roles for DNA-PKcs are discussed.
Collapse
Affiliation(s)
- Go Watanabe
- Departments of Pathology, Biochemistry, Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), University of Southern California, Los Angeles, CA, 90089-9176, USA
| | - Michael R Lieber
- Departments of Pathology, Biochemistry, Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), University of Southern California, Los Angeles, CA, 90089-9176, USA.
| |
Collapse
|
3
|
Hu YZ, Li Q, Wang PF, Li XP, Hu ZL. Multiple functions and regulatory network of miR-150 in B lymphocyte-related diseases. Front Oncol 2023; 13:1140813. [PMID: 37182123 PMCID: PMC10172652 DOI: 10.3389/fonc.2023.1140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
MicroRNAs (miRNAs) play vital roles in the post-transcriptional regulation of gene expression. Previous studies have shown that miR-150 is a crucial regulator of B cell proliferation, differentiation, metabolism, and apoptosis. miR-150 regulates the immune homeostasis during the development of obesity and is aberrantly expressed in multiple B-cell-related malignant tumors. Additionally, the altered expression of MIR-150 is a diagnostic biomarker of various autoimmune diseases. Furthermore, exosome-derived miR-150 is considered as prognostic tool in B cell lymphoma, autoimmune diseases and immune-mediated disorders, suggesting miR-150 plays a vital role in disease onset and progression. In this review, we summarized the miR-150-dependent regulation of B cell function in B cell-related immune diseases.
Collapse
Affiliation(s)
- Yue-Zi Hu
- Clinical Laboratory, The Second Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Qiao Li
- Department of Anesthesiology, The Second Affiliated Xiangya Hospital, Central South University, Changsha, China
| | - Peng-Fei Wang
- Department of Anesthesiology, The Second Affiliated Xiangya Hospital, Central South University, Changsha, China
| | - Xue-Ping Li
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Zhao-Lan Hu
- Department of Anesthesiology, The Second Affiliated Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zhao-Lan Hu,
| |
Collapse
|
4
|
Crouch S, Painter D, Barrans SL, Roman E, Beer PA, Cooke SL, Glover P, Van Hoppe SJ, Webster N, Lacy SE, Ruiz C, Campbell PJ, Hodson DJ, Patmore R, Burton C, Smith A, Tooze RM. Molecular subclusters of follicular lymphoma: a report from the United Kingdom's Haematological Malignancy Research Network. Blood Adv 2022; 6:5716-5731. [PMID: 35363872 PMCID: PMC9619185 DOI: 10.1182/bloodadvances.2021005284] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 03/06/2022] [Indexed: 11/20/2022] Open
Abstract
Follicular lymphoma (FL) is morphologically and clinically diverse, with mutations in epigenetic regulators alongside t(14;18) identified as disease-initiating events. Identification of additional mutational entities confirms this cancer's heterogeneity, but whether mutational data can be resolved into mechanistically distinct subsets remains an open question. Targeted sequencing was applied to an unselected population-based FL cohort (n = 548) with full clinical follow-up (n = 538), which included 96 diffuse large B-cell lymphoma (DLBCL) transformations. We investigated whether molecular subclusters of FL can be identified and whether mutational data provide predictive information relating to transformation. DNA extracted from FL samples was sequenced with a 293-gene panel representing genes frequently mutated in DLBCL and FL. Three clusters were resolved using mutational data alone, independent of translocation status: FL_aSHM, with high burden of aberrant somatic hypermutation (aSHM) targets; FL_STAT6, with high STAT6 & CREBBP mutation and low aSHM; and FL_Com, with the absence of features of other subtypes and enriched KMT2D mutation. Analysis of mutation signatures demonstrated differential enrichment of predicted mutation signatures between subgroups and a dominant preference in the FL_aSHM subgroup for G(C>T)T and G(C>T)C transitions consistent with previously defined aSHM-like patterns. Of transformed cases with paired samples, 17 of 26 had evidence of branching evolution. Poorer overall survival (OS) in the aSHM group (P = .04) was associated with older age; however, overall tumor genetics provided limited information to predict individual patient risk. Our approach identifies 3 molecular subclusters of FL linked to differences in underlying mechanistic pathways. These clusters, which may be further resolved by the inclusion of translocation status and wider mutation profiles, have implications for understanding pathogenesis as well as improving treatment strategies in the future.
Collapse
Affiliation(s)
- Simon Crouch
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Daniel Painter
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Sharon L. Barrans
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Eve Roman
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Philip A. Beer
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Susanna L. Cooke
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Paul Glover
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Suzan J.L. Van Hoppe
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Nichola Webster
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Stuart E. Lacy
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Camilo Ruiz
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Daniel J. Hodson
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Russell Patmore
- Queen’s Centre for Oncology and Haematology, Castle Hill Hospital, Cottingham, United Kingdom
| | - Cathy Burton
- Haematological Malignancy Diagnostic Service, St. James’s Institute of Oncology, Leeds, United Kingdom
| | - Alexandra Smith
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, United Kingdom
| | - Reuben M. Tooze
- Section of Experimental Haematology, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
5
|
Siu JHY, Pitcher MJ, Tull TJ, Velounias RL, Guesdon W, Montorsi L, Mahbubani KT, Ellis R, Dhami P, Todd K, Kadolsky UD, Kleeman M, D'Cruz DP, Saeb-Parsy K, Bemark M, Pettigrew GJ, Spencer J. Two subsets of human marginal zone B cells resolved by global analysis of lymphoid tissues and blood. Sci Immunol 2022; 7:eabm9060. [PMID: 35302862 DOI: 10.1126/sciimmunol.abm9060] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
B cells generate antibodies that are essential for immune protection, but their subgroups are poorly defined. Here, we perform undirected deep profiling of B cells in matched human lymphoid tissues from deceased transplant organ donors and blood. In addition to identifying unanticipated features of tissue-based B cell differentiation, we resolve two subsets of marginal zone B (MZB) cells differing in cell surface and transcriptomic profiles, clonal relationships to other subsets, enrichment of genes in the NOTCH pathway, distribution bias within splenic marginal zone microenvironment, and immunoglobulin repertoire diversity and hypermutation frequency. Each subset is present in spleen, gut-associated lymphoid tissue, mesenteric lymph nodes, and blood. MZB cells and the lineage from which they are derived are depleted in lupus nephritis. Here, we show that this depletion is of only one MZB subset. The other remains unchanged as a proportion of total B cells compared with health. Thus, it is important to factor MZB cell heterogeneity into studies of human B cell responses and pathology.
Collapse
Affiliation(s)
- Jacqueline H Y Siu
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Michael J Pitcher
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Thomas J Tull
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Rebekah L Velounias
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - William Guesdon
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Lucia Montorsi
- School of Cancer Sciences, King's College London, Guy's Campus, London, UK.,Cancer Systems Biology Laboratory, Francis Crick Institute, London, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Richard Ellis
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Pawan Dhami
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Katrina Todd
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Ulrich D Kadolsky
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Michelle Kleeman
- NIHR Guy's and St Thomas' Biomedical Research Centre, Guy's and St Thomas NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - David P D'Cruz
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE 405 30 Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Gavin J Pettigrew
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Jo Spencer
- School of Immunology and Microbial Sciences, King's College London, Guy's Campus, London SE1 9RT, UK
| |
Collapse
|
6
|
Fernandes M, Marques H, Teixeira AL, Medeiros R. ceRNA Network of lncRNA/miRNA as Circulating Prognostic Biomarkers in Non-Hodgkin Lymphomas: Bioinformatic Analysis and Assessment of Their Prognostic Value in an NHL Cohort. Int J Mol Sci 2021; 23:ijms23010201. [PMID: 35008626 PMCID: PMC8745130 DOI: 10.3390/ijms23010201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
Research has been focusing on identifying novel biomarkers to better stratify non-Hodgkin lymphoma patients based on prognosis. Studies have demonstrated that lncRNAs act as miRNA sponges, creating ceRNA networks to regulate mRNA expression, and its deregulation is associated with lymphoma development. This study aimed to identify novel circulating prognostic biomarkers based on miRNA/lncRNA-associated ceRNA network for NHL. Herein, bioinformatic analysis was performed to construct ceRNA networks for hsa-miR-150-5p and hsa-miR335-5p. Then, the prognostic value of the miRNA–lncRNA pairs’ plasma levels was assessed in a cohort of 113 NHL patients. Bioinformatic analysis identified MALAT1 and NEAT1 as hsa-miR-150-5p and has-miR-335-5p sponges, respectively. Plasma hsa-miR-150-5p/MALAT1 and hsa-miR335-5p/NEAT1 levels were significantly associated with more aggressive and advanced disease. The overall survival and progression-free survival analysis indicated that hsa-miR-150-5p/MALAT1 and hsa-miR335-5p/NEAT1 pairs’ plasma levels were remarkably associated with NHL patients’ prognosis, being independent prognostic factors in a multivariate Cox analysis. Low levels of hsa-miR-150-5p and hsa-miR-335-5p combined with high levels of the respective lncRNA pair were associated with poor prognosis of NHL patients. Overall, the analysis of ceRNA network expression levels may be a useful prognostic biomarker for NHL patients and could identify patients who could benefit from more intensive treatments.
Collapse
MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cohort Studies
- Computational Biology
- Disease-Free Survival
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Lymphoma, Non-Hodgkin/blood
- Lymphoma, Non-Hodgkin/genetics
- MicroRNAs/blood
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Prognosis
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Risk Factors
Collapse
Affiliation(s)
- Mara Fernandes
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal;
- ICVS/3B’s—PT Government Associate Laboratory, 4805-017 Braga/Guimarães, Portugal
- Department of Oncology, Hospital de Braga, 4710-243 Braga, Portugal
- CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
| | - Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of Fernando Pessoa University (UFP), 4249-004 Porto, Portugal
- Correspondence: ; Tel.: +351-225-084-000 (ext. 5414)
| |
Collapse
|
7
|
Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.
Collapse
Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
| |
Collapse
|
8
|
Li Y, Gao L, Zhang C, Meng J. LncRNA SNHG3 Promotes Proliferation and Metastasis of Non-Small-Cell Lung Cancer Cells Through miR-515-5p/SUMO2 Axis. Technol Cancer Res Treat 2021; 20:15330338211019376. [PMID: 34032148 PMCID: PMC8155750 DOI: 10.1177/15330338211019376] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is a global disease and a major cause of cancer-related mortality worldwide. Accumulated studies have confirmed the essential role of long non-coding RNAs (lncRNAs) in the occurrence and development of cancers. Meanwhile, there have been reports concerning the role of Small Nucleolar RNA Host Gene 3 (SNHG3) in various cancers. However, there are so far few studies on the function and mechanism of SNHG3 in lung cancer. In the present study, SNHG3 was found to be highly expressed in lung cancer tissues and cells. Downregulation of SNHG3 could inhibit cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) process. In addition, SNHG3 was found to have the ability to bind to miR-515-5p. Furthermore, Small Ubiquitin Like Modifier 2 (SUMO2) was identified to be the downstream target of miR-515-5p, which was negatively correlated with miR-515-5p expression. SNHG3 could positively regulate SUMO2 expression by sponging miR-515-5p. In addition, the rescue experiment showed that simultaneous transfection of miR-515-5p or SUMO2 siRNA could reverse the effect of SNHG3 expression on cell proliferation and metastasis. Collectively, our study demonstrates that SNHG3 can act on miR-515-5p in the form of competitive endogenous RNA (ceRNA) to regulate SUMO2 positively and thus affect the proliferation and metastasis of NSCLC cells. Findings in our study support that SNHG3/miR-515-5p/SUMO2 regulatory axis may become a potential therapeutic target for lung cancer.
Collapse
Affiliation(s)
- Yongqun Li
- Department of Respiratory Medicine, The Sixth Medical Center of PLA
General Hospital, Beijing, China
| | - Lipin Gao
- Department of Hematology, The Sixth Medical Center of PLA General
Hospital, Beijing, China
| | - Caiyun Zhang
- Department of Respiratory Medicine, The Sixth Medical Center of PLA
General Hospital, Beijing, China
| | - Jiguang Meng
- Department of Respiratory Medicine, The Sixth Medical Center of PLA
General Hospital, Beijing, China
| |
Collapse
|
9
|
Wang WJ, Li LY, Cui JW. Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis. Epigenetics Chromatin 2020; 13:49. [PMID: 33168103 PMCID: PMC7654176 DOI: 10.1186/s13072-020-00371-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
With the rapid development of next-generation sequencing technology, chromosome structural variation has gradually gained increased clinical significance in tumorigenesis. However, the molecular mechanism(s) underlying this structural variation remain poorly understood. A search of the literature shows that a three-dimensional chromatin state plays a vital role in inducing structural variation and in the gene expression profiles in tumorigenesis. Structural variants may result in changes in copy number or deletions of coding sequences, as well as the perturbation of structural chromatin features, especially topological domains, and disruption of interactions between genes and their regulatory elements. This review focuses recent work aiming at elucidating how structural variations develop and misregulate oncogenes and tumor suppressors, to provide general insights into tumor formation mechanisms and to provide potential targets for future anticancer therapies.
Collapse
Affiliation(s)
- Wen-Jun Wang
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
| | - Ling-Yu Li
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
| | - Jiu-Wei Cui
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
| |
Collapse
|
10
|
Xu B, Mei J, Ji W, Bian Z, Jiao J, Sun J, Shao J. LncRNA SNHG3, a potential oncogene in human cancers. Cancer Cell Int 2020; 20:536. [PMID: 33292213 PMCID: PMC7640707 DOI: 10.1186/s12935-020-01608-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are composed of > 200 nucleotides; they lack the ability to encode proteins but play important roles in a variety of human tumors. A large number of studies have shown that dysregulated expression of lncRNAs is related to tumor oncogenesis and progression. Emerging evidence shows that SNHG3 is a novel oncogenic lncRNA that is abnormally expressed in various tumors, including osteosarcoma, liver cancer, lung cancer, etc. SNHG3 primarily competes as a competitive endogenous RNA (ceRNA) that targets tumor suppressor microRNAs (miRNAs) and ceRNA mechanisms that regulate biological processes of tumors. In addition, abnormal expression of SNHG3 is significantly correlated with patient clinical features. Upregulation of SNHG3 contributes to biological functions, including tumor cell proliferation, migration, invasion and EMT. Therefore, SNHG3 may represent a potential diagnostic and prognostic biomarker, as well as a novel therapeutic target.
Collapse
Affiliation(s)
- Bin Xu
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, P. R. China
| | - Wei Ji
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Zheng Bian
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jiantong Jiao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jun Sun
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China.
| | - Junfei Shao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China.
| |
Collapse
|
11
|
Jaiswal A, Singh AK, Tamrakar A, Kodgire P. Unfolding the Role of Splicing Factors and RNA Debranching in AID Mediated Antibody Diversification. Int Rev Immunol 2020; 40:289-306. [PMID: 32924658 DOI: 10.1080/08830185.2020.1815725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Activated B-cells diversify their antibody repertoire via somatic hypermutation (SHM) and class switch recombination (CSR). SHM is restricted to the variable region, whereas, CSR is confined to the constant region of immunoglobulin (Ig) genes. Activation-induced cytidine deaminase (AID) is a crucial player in the diversification of antibodies in the activated B-cell. AID catalyzes the deamination of cytidine (C) into uracil (U) at Ig genes. Subsequently, low fidelity repair of U:G mismatches may lead to mutations. Transcription is essential for the AID action, as it provides a transient single-strand DNA substrate. Since splicing is a co-transcriptional event, various splicing factors or regulators influence the transcription. Numerous splicing factors are known to regulate the AID targeting, function, Ig transcription, and AID splicing, which eventually influence antibody diversification processes. Splicing regulator SRSF1-3, a splicing isoform of serine arginine-rich splicing factor (SRSF1), and CTNNBL1, a spliceosome interacting factor, interact with AID and play a critical role in SHM. Likewise, a splicing regulator polypyrimidine tract binding protein-2 (PTBP2) and the debranching enzyme (DBR1) debranches primary switch transcripts which later forms G-quadruplex structures, and the S region guide RNAs direct AID to S region DNA. Moreover, AID shows several alternate splicing isoforms, like AID devoid of exon-4 (AIDΔE4) that is expressed in various pathological conditions. Interestingly, RBM5, a splicing regulator, is responsible for the skipping of AID exon 4. In this review, we discuss the role and significance of splicing factors in the AID mediated antibody diversification.
Collapse
Affiliation(s)
- Ankit Jaiswal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Amit Kumar Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Anubhav Tamrakar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Prashant Kodgire
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| |
Collapse
|
12
|
Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL. Leukemia 2020; 34:2722-2735. [PMID: 32576963 DOI: 10.1038/s41375-020-0919-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/20/2022]
Abstract
Mutations in genes encoding subunits of the SWI/SNF chromatin remodeling complex are frequently found in different human cancers. While the tumor suppressor function of this complex is widely established in solid tumors, its role in hematologic malignancies is largely unknown. Recurrent point mutations in BCL7A gene, encoding a subunit of the SWI/SNF complex, have been reported in diffuse large B-cell lymphoma (DLBCL), but their functional impact remains to be elucidated. Here we show that BCL7A often undergoes biallelic inactivation, including a previously unnoticed mutational hotspot in the splice donor site of intron one. The splice site mutations render a truncated BCL7A protein, lacking a portion of the amino-terminal domain. Moreover, restoration of wild-type BCL7A expression elicits a tumor suppressor-like phenotype in vitro and in vivo. In contrast, splice site mutations block the tumor suppressor function of BCL7A by preventing its binding to the SWI/SNF complex. We also show that BCL7A restoration induces transcriptomic changes in genes involved in B-cell activation. In addition, we report that SWI/SNF complex subunits harbor mutations in more than half of patients with germinal center B-cell (GCB)-DLBCL. Overall, this work demonstrates the tumor suppressor function of BCL7A in DLBCL, and highlights that the SWI/SNF complex plays a relevant role in DLBCL pathogenesis.
Collapse
|
13
|
Zhang J, Dong B, Hao J, Yi S, Cai W, Luo Z. LncRNA Snhg3 contributes to dysfunction of cerebral microvascular cells in intracerebral hemorrhage rats by activating the TWEAK/Fn14/STAT3 pathway. Life Sci 2019; 237:116929. [PMID: 31610210 DOI: 10.1016/j.lfs.2019.116929] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 12/22/2022]
Abstract
LncRNA small nucleolar RNA host gene 3 (Snhg3) has been involved in cell proliferation and migration in malignant cells. However, its role in regulating functions of non-malignant cells has been hardly reported. Here, we found Snhg3 expression was sharply induced in primary brain microvascular endothelial cells (BMVECs) treated with oxygen-and-glucose-deprivation (OGD) plus hemin, an in vitro model of intracerebral hemorrhage (ICH). Downregulation of Snhg3 by siRNA transfection improved cell proliferation and migration abilities and reduced cell apoptosis and monolayer permeability in BMVECs under treatment with OGD plus hemin. Snhg3 overexpression suppressed cell proliferation and migration and increased cell apoptosis and monolayer permeability under normal condition. In ICH rats, downregulation of Snhg3 by siRNA injection improved behavioral and histological manifestations, including number of right turns, limb placement score, integrity of blood-brain barrier (BBB), brain water content and cell apoptosis in vivo. In the mechanism exploration, we found that, TWEAK and Snhg3 displayed a positive correlation with each other. Snhg3 overexpression increased expression of TWEAK protein and its receptor Fn14, that were also induced by OGD plus hemin, activating the downstream neuroinflammatory pathway STAT3 and enhancing the secretion of MMP-2/9. Finally, the TWEAK-siRNA, the Fn14 inhibitor ATA and the STAT3 blocker AG490 were respectively used to treat BMVECs under treatment with OGD plus hemin. Our results showed either TWEAK downregulation, Fn14 inhibition, or STAT3 blockade, could rescue Snhg3-induced impairment of BMVEC functions. In conclusion, the lncRNA Snhg3 contributes to dysfunction of cerebral microvascular cells in ICH rats by activating the TWEAK/Fn14/STAT3 pathway.
Collapse
Affiliation(s)
- Jie Zhang
- Department of Anesthesiology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shannxi province, PR China
| | - Buhuai Dong
- Department of Anesthesiology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shannxi province, PR China
| | - Jianhong Hao
- Department of Anesthesiology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shannxi province, PR China
| | - Shuangqiang Yi
- Department of Anesthesiology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shannxi province, PR China
| | - Wenbo Cai
- Department of Anesthesiology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shannxi province, PR China
| | - Zhenguo Luo
- Department of Anesthesiology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shannxi province, PR China.
| |
Collapse
|
14
|
Epigenetic regulation of histone H3 in the process of hepatocellular tumorigenesis. Biosci Rep 2019; 39:BSR20191815. [PMID: 31320544 PMCID: PMC6680372 DOI: 10.1042/bsr20191815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022] Open
Abstract
Better understanding of epigenetic regulation of hepatocellular carcinoma (HCC) will help us to cure this most common malignant liver cancer worldwide. The underlying mechanisms of HCC tumorigenesis are genomic aberrations regulated by genetic and epigenetic modifications. Histone H3 lysine modifications regulate histone structure and modulate transcriptional factor binding with target gene promoters. Targetting genes include VASH2, fatty acids synthase, RIZ1, FBP1, MPP1/3, YAP, which affect tumorigenesis, metabolisms, angiogenesis, and metastasis. Signal pathway studies demonstrate that the HGF-MET-MLL axis, phosphatase and tensin homolog (PTEN)-PI3K-Akt axis; WNT-β-catenin signal pathway is involved in histone H3 modification. A variety of factors such as virus infection, reactive oxygen species, food-borne toxins, irradiation, or non-coding RNA cause hepatocellular DNA damage or modification. Dysfunctional DNA repair mechanisms, including those at the epigenetic level are also major causes of HCC tumorigenesis. The development of therapies based on epigenetic regulatory mechanisms has great potential to advance the care of HCC patients in the future.
Collapse
|
15
|
Zhang L, Dong X, Lee M, Maslov AY, Wang T, Vijg J. Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan. Proc Natl Acad Sci U S A 2019; 116:9014-9019. [PMID: 30992375 PMCID: PMC6500118 DOI: 10.1073/pnas.1902510116] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell-specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461;
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
| |
Collapse
|
16
|
Al Ismail A, Husain A, Kobayashi M, Honjo T, Begum NA. Depletion of recombination-specific cofactors by the C-terminal mutant of the activation-induced cytidine deaminase causes the dominant negative effect on class switch recombination. Int Immunol 2019; 29:525-537. [PMID: 29136157 DOI: 10.1093/intimm/dxx061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for class-switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin genes. Studies on in vitro mutagenized AID as well as its mutations in human patients with hyper-IgM (HIGM)-syndrome type II revealed that C-terminal AID mutations were defective in CSR whereas their DNA cleavage and SHM activities remained intact. The C-terminal mutants of AID were speculated to exert the dominant negative effect on wild-type (WT) AID whereas its mechanism remains unknown. We generated the JP41 (R190X) mutation in one allele and a null mutation on the other allele in a mouse B cell line (CH12F3-2A) using CRISPR/Cas9 genome-editing tools and studied the effect of JP41 expression on the function of exogenously introduced WT AID fused with estrogen receptor (AIDER) in AIDJP41/∆/AIDER CH12F3-2A cells. We found that JP41 expression strongly suppressed not only CSR but also Igh/c-Myc chromosomal translocations by AIDER. We showed that the dominant negative effect is not evident at the DNA cleavage step but obvious at both deletional and inversional recombination steps. We also confirmed the dominant negative effect of other C-terminal mutants, JP8Bdel (R183X) and P20 (34-aa insertion at residue 182) in AID-deficient spleen B cells. Finally, we showed that the expression of JP41 reduced the binding of AIDER with its cofactors (hnRNP L, SERBP1 and hnRNP U). Together, these data indicate that dominant negative effect of JP41 on CSR is likely due to the depletion of the CSR-specific RNA-binding proteins from WT AID.
Collapse
Affiliation(s)
- Azza Al Ismail
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Afzal Husain
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Maki Kobayashi
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| |
Collapse
|
17
|
Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun 2018; 9:4001. [PMID: 30275490 PMCID: PMC6167379 DOI: 10.1038/s41467-018-06354-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/31/2018] [Indexed: 11/26/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3′ UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics. The driver mutations for the two main molecular subgroups of diffuse large B-cell lymphoma (DLBCL) are poorly defined. Here, an integrative genomics analysis identifies 3′ UTR NFKBIZ mutations within the activated B-cell DLBCL subgroup and small FCGR2B amplifications in the germinal centre B-cell DLBCL subgroup.
Collapse
|
18
|
Yuan J, Zhang S, Zhang Y. Nrf1 is paved as a new strategic avenue to prevent and treat cancer, neurodegenerative and other diseases. Toxicol Appl Pharmacol 2018; 360:273-283. [PMID: 30267745 DOI: 10.1016/j.taap.2018.09.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
Abstract
Transcription factor Nrf1 acts as a unique vital player in maintaining cellular homeostasis and organ integrity during normal development and growth throughout the life process. Loss-of-function of Nrf1 results in severe oxidative stress, genomic instability, embryonic lethality, developmental disorders, and adult diseases such as non-alcoholic steatohepatitis, hepatocellular carcinoma, diabetes and neurogenerative diseases. Thereby, Nrf1 is critically implicated in a variety of important physio-pathological processes by governing robust target genes in order to reinforce antioxidant, detoxification and cytoprotective responses to cellular stress. Notably, there also exists a proteasomal 'bounce-back' response mediated by Nrf1, insofar as to enhance the drug resistance to proteasomal inhibitors in clinical treatment of neuroblastoma, multiple myeloma and triple-negative breast cancers. Recently, several drugs or chemicals are found or re-found in new ways to block the proteasomal compensatory process through inhibiting the multistep processing of Nrf1. Conversely, activation of Nrf1 induced by some drugs or chemicals leads to cytoprotection from cell apoptosis and promotes cell viability. This is the start of constructive and meaningful studies, approaching to explore the mechanism(s) by which Nrf1 is activated to protect neurons and other cells from malignant and degenerative diseases. Overall, Nrf1 has appealed attentions as a new attractive therapeutic strategy for human diseases including cancers.
Collapse
Affiliation(s)
- Jianxin Yuan
- Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China
| | - Shuwei Zhang
- Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China
| | - Yiguo Zhang
- Laboratory of Cell Biochemistry and Topogenetic Regulation, College of Bioengineering and Faculty of Sciences, Chongqing University, No. 174 Shazheng Street, Shapingba District, Chongqing 400044, China.
| |
Collapse
|
19
|
Hu Y, Lin J, Fang H, Fang J, Li C, Chen W, Liu S, Ondrejka S, Gong Z, Reu F, Maciejewski J, Yi Q, Zhao JJ. Targeting the MALAT1/PARP1/LIG3 complex induces DNA damage and apoptosis in multiple myeloma. Leukemia 2018; 32:2250-2262. [PMID: 29632340 PMCID: PMC6151178 DOI: 10.1038/s41375-018-0104-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 02/12/2018] [Accepted: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Metastasis-associated lung adenocarcinoma transcript 1(MALAT1) is a highly conserved long non-coding RNA (lncRNA). Overexpression of MALAT1 has been demonstrated to related to poor prognosis of multiple myeloma(MM) patients. Here, we demonstrated that MALAT1 plays important roles in MM DNA repair and cell death. We found bone marrow plasma cells from patients with monoclonal gammopathy of undetermined significance (MGUS) and MM express elevated MALAT1 and involve in alternative-non-homozygous end joining (A-NHEJ) pathway by binding to PARP1 and LIG3, two key components of the A-NHEJ protein complex. Degradation of the MALAT1 RNA by RNase H using antisense gapmer DNA oligos in MM cells stimulated poly-ADP-ribosylation of nuclear proteins, defected the DNA repair pathway, and further provoked apoptotic pathways. Anti-MALAT1 therapy combined with PARP1 inhibitor or proteasome inhibitor in MM cells showed a synergistic effect in vitro. Furthermore, using novel single wall carbon nanotube (SWCNT) conjugated with anti-MALAT1 oligos, we successfully knocked down MALAT1 RNA in cultured MM cell lines and xenograft murine models. Most importantly, anti-MALAT1 therapy induced DNA damage and cell apoptosis in vivo, indicating that MALAT1 could serve as a potential novel therapeutic target for MM treatment.
Collapse
Affiliation(s)
- Yi Hu
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jianhong Lin
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Hua Fang
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Oncology, Fu Xing Hospital, Capital Medical University, Beijing, 100038, China
| | - Jing Fang
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Chen Li
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,College of Food Science and Technology, Agricultural University of Hebei, Baoding, Hebei, 071000, China
| | - Wei Chen
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Ultrasound, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Shuang Liu
- Department of Pathology, Norman Bethune International Peace Hospital, Shijiazhuang, Hebei, 050082, China
| | - Sarah Ondrejka
- Department of Laboratory Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Zihua Gong
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Frederic Reu
- Department of Translational Hematology & Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jaroslaw Maciejewski
- Department of Translational Hematology & Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Qing Yi
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jian-Jun Zhao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
| |
Collapse
|
20
|
Amodio N, Stamato MA, Juli G, Morelli E, Fulciniti M, Manzoni M, Taiana E, Agnelli L, Cantafio MEG, Romeo E, Raimondi L, Caracciolo D, Zuccalà V, Rossi M, Neri A, Munshi NC, Tagliaferri P, Tassone P. Drugging the lncRNA MALAT1 via LNA gapmeR ASO inhibits gene expression of proteasome subunits and triggers anti-multiple myeloma activity. Leukemia 2018; 32:1948-1957. [PMID: 29487387 PMCID: PMC6127082 DOI: 10.1038/s41375-018-0067-3] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/21/2018] [Accepted: 01/25/2018] [Indexed: 12/27/2022]
Abstract
The biological role and therapeutic potential of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) are still to be investigated. Here, we studied the functional significance and the druggability of the oncogenic lncRNA MALAT1 in MM. Targeting MALAT1 by novel LNA-gapmeR antisense oligonucleotide antagonized MM cell proliferation and triggered apoptosis both in vitro and in vivo in a murine xenograft model of human MM. Of note, antagonism of MALAT1 downmodulated the two major transcriptional activators of proteasome subunit genes, namely NRF1 and NRF2, and resulted in reduced trypsin, chymotrypsin and caspase-like proteasome activities and in accumulation of polyubiquitinated proteins. NRF1 and NRF2 decrease upon MALAT1 targeting was due to transcriptional activation of their negative regulator KEAP1, and resulted in reduced expression of anti-oxidant genes and increased ROS levels. In turn, NRF1 promoted MALAT1 expression thus establishing a positive feedback loop. Our findings demonstrate a crucial role of MALAT1 in the regulation of the proteasome machinery, and provide proof-of-concept that its targeting is a novel powerful option for the treatment of MM.
Collapse
Affiliation(s)
- Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Maria Angelica Stamato
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Eugenio Morelli
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Mariateresa Fulciniti
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martina Manzoni
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Taiana
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Agnelli
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Enrica Romeo
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Lavinia Raimondi
- Laboratory of Tissue Engineering, Rizzoli Orthopedic Institute, Palermo, Italy
| | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | | | - Marco Rossi
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Nikhil C Munshi
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,VA Boston Healthcare System, West Roxbury, Boston, MA, USA
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy. .,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
| |
Collapse
|
21
|
Gothe HJ, Minneker V, Roukos V. Dynamics of Double-Strand Breaks: Implications for the Formation of Chromosome Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:27-38. [PMID: 29956289 DOI: 10.1007/978-981-13-0593-1_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Illegitimate joining of chromosome breaks can lead to the formation of chromosome translocations, a catastrophic type of genome rearrangements that often plays key roles in tumorigenesis. Emerging evidence suggests that the mobility of broken DNA loci can be an important determinant in partner search and clustering of individual breaks, events that can influence translocation frequency. We summarize here the recent literature on the mechanisms that regulate chromatin movement, focusing on studies exploring the motion properties of double-strand breaks in the context of chromatin, the functional consequences for DNA repair, and the formation of chromosome fusions.
Collapse
|
22
|
Yu N, Shin S, Choi JR, Kim Y, Lee KA. Concomitant AID Expression and BCL7A Loss Associates With Accelerated Phase Progression and Imatinib Resistance in Chronic Myeloid Leukemia. Ann Lab Med 2016; 37:177-179. [PMID: 28029010 PMCID: PMC5204001 DOI: 10.3343/alm.2017.37.2.177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 08/08/2016] [Accepted: 12/02/2016] [Indexed: 11/24/2022] Open
Affiliation(s)
- Nae Yu
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangnam Sacred Heart Hospital, Seoul, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Kyung A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
| |
Collapse
|
23
|
Wang X, Sehgal L, Jain N, Khashab T, Mathur R, Samaniego F. LncRNA MALAT1 promotes development of mantle cell lymphoma by associating with EZH2. J Transl Med 2016; 14:346. [PMID: 27998273 PMCID: PMC5175387 DOI: 10.1186/s12967-016-1100-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/29/2016] [Indexed: 02/07/2023] Open
Abstract
Background Mantle cell lymphoma (MCL) is considered an aggressive subtype of non-Hodgkin’s lymphoma with variable treatment responses. There is an urgent need to identify novel markers with prognostic and therapeutic value for MCL. Long non-coding RNAs (lncRNAs) have emerged as key regulators in cancers, including MCL. Metastasis-associated lung adenocarcinoma transcript 1(MALAT1), a lncRNA located at pathognomonic translocation site of t (11; 14) of MCL. MALAT1 is known to be overexpressed in solid tumors and hematologic malignancies. However, the pathological role and clinical relevance of MALAT1 in MCL are not completely understood. Methods We quantified MALAT1 in MCL samples (40) and CD19+ B cells by quantitative real time polymerase chain reaction (qRT-PCR) and correlated levels with clinical outcome. We silenced MALAT1 in MCL cell lines and analyzed cells in tumorigenic assays and formation of transcription complexes. Results We found that the expression of MALAT1 was elevated in human MCL tumors and cell lines as compared to normal controls, and the elevated levels of MALAT1 correlated with higher MCL international prognostic index (MIPI) and reduced overall survival. MCL with knockdown of MALAT1 showed impaired cell proliferation, facilitated apoptosis and produced fewer clonogenic foci. The increased expression of p21 and p27 upon MALAT1 knockdown was regulated by enhancer of zeste homolog 2 (EZH2). Moreover, decreased phosphorylation of EZH2 at T350 attenuated the binding to MALAT1. Conclusions Our findings illuminate the oncogenic role of MALAT1, which may serve as a novel biomarker and as a therapeutic target in MCL. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-1100-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xin Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Lalit Sehgal
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
| | - Neeraj Jain
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Tamer Khashab
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.,Department of Internal Medicine, Lankenau Medical Center, Wynnewood, PA, USA
| | - Rohit Mathur
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Felipe Samaniego
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Chou C, Verbaro DJ, Tonc E, Holmgren M, Cella M, Colonna M, Bhattacharya D, Egawa T. The Transcription Factor AP4 Mediates Resolution of Chronic Viral Infection through Amplification of Germinal Center B Cell Responses. Immunity 2016; 45:570-582. [PMID: 27566940 DOI: 10.1016/j.immuni.2016.07.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/09/2016] [Accepted: 07/27/2016] [Indexed: 12/31/2022]
Abstract
B cells diversify and affinity mature their antigen receptor repertoire in germinal centers (GCs). GC B cells receive help signals during transient interaction with T cells, yet it remains unknown how these transient T-B interactions in the light zone sustain the subsequent proliferative program of selected B cells that occurs in the anatomically distant dark zone. Here, we show that the transcription factor AP4 was required for sustained GC B cell proliferation and subsequent establishment of a diverse and protective antibody repertoire. AP4 was induced by c-MYC during the T-B interactions, was maintained by T-cell-derived interleukin-21 (IL-21), and promoted repeated rounds of divisions of selected GC B cells. B-cell-specific deletion of AP4 resulted in reduced GC sizes and reduced somatic hypermutation coupled with a failure to control chronic viral infection. These results indicate that AP4 integrates T-cell-mediated selection and sustained expansion of GC B cells for humoral immunity.
Collapse
Affiliation(s)
- Chun Chou
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Daniel J Verbaro
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Elena Tonc
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Melanie Holmgren
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Deepta Bhattacharya
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| |
Collapse
|
26
|
Abstract
Chromosomal translocations are a hallmark of cancer. Unraveling the molecular mechanism of these rare genetic events requires a clear distinction between correlative and causative risk-determinants, where technical and analytical issues can be excluded. To meet this goal, we performed in-depth analyses of publicly available genome-wide datasets. In contrast to several recent reports, we demonstrate that chromosomal translocation risk is causally unrelated to promoter stalling (Spt5), transcriptional activity, or off-targeting activity of the activation-induced cytidine deaminase. Rather, an open chromatin configuration, which is not promoter-specific, explained the elevated translocation risk of promoter regions. Furthermore, the fact that gene size directly correlates with the translocation risk in mice and human cancers further demonstrated the general irrelevance of promoter-specific activities. Interestingly, a subset of translocations observed in cancer patients likely initiates from double-strand breaks induced by an access-independent process. Together, these unexpected and novel insights are fundamental in understanding the origin of chromosome translocations and, consequently, cancer.
Collapse
|
27
|
Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability. Nat Commun 2016; 7:10549. [PMID: 26842758 PMCID: PMC4742980 DOI: 10.1038/ncomms10549] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/25/2015] [Indexed: 02/07/2023] Open
Abstract
Topoisomerase 1, an enzyme that relieves superhelical tension, is implicated in transcription-associated mutagenesis and genome instability-associated with neurodegenerative diseases as well as activation-induced cytidine deaminase. From proteomic analysis of TOP1-associated proteins, we identify SMARCA4, an ATP-dependent chromatin remodeller; FACT, a histone chaperone; and H3K4me3, a transcriptionally active chromatin marker. Here we show that SMARCA4 knockdown in a B-cell line decreases TOP1 recruitment to chromatin, and leads to increases in Igh/c-Myc chromosomal translocations, variable and switch region mutations and negative superhelicity, all of which are also observed in response to TOP1 knockdown. In contrast, FACT knockdown inhibits association of TOP1 with H3K4me3, and severely reduces DNA cleavage and Igh/c-Myc translocations, without significant effect on TOP1 recruitment to chromatin. We thus propose that SMARCA4 is involved in the TOP1 recruitment to general chromatin, whereas FACT is required for TOP1 binding to H3K4me3 at non-B DNA containing chromatin for the site-specific cleavage. Topoisomerase 1 (TOP1) relieves superhelical tension when DNA strands are unwound during transcription. Here, Husain et al. report that SMARCA4, an ATP-dependent chromatin remodeller, is associated with TOP1 and suppresses transcription-associated genomic instability.
Collapse
|
28
|
Canela A, Stanlie A, Nussenzweig A. Collateral DNA damage produced by genome-editing drones: exception or rule? Mol Cell 2016; 58:565-7. [PMID: 26000841 DOI: 10.1016/j.molcel.2015.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the recent issue of Nature Biotechnology, Frock et al. (2015) developed an elegant technique to capture translocation partners that can be utilized to determine off-target regions of genome-editing endonucleases as well as endogenous mutators at nucleotide resolution.
Collapse
Affiliation(s)
- Andres Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andre Stanlie
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
29
|
Knisbacher BA, Gerber D, Levanon EY. DNA Editing by APOBECs: A Genomic Preserver and Transformer. Trends Genet 2016; 32:16-28. [PMID: 26608778 DOI: 10.1016/j.tig.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Information warfare is not limited to the cyber world because it is waged within our cells as well. The unique AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family comprises proteins that alter DNA sequences by converting deoxycytidines to deoxyuridines through deamination. This C-to-U DNA editing enables them to inhibit parasitic viruses and retrotransposons by disrupting their genomic content. In addition to attacking genomic invaders, APOBECs can target their host genome, which can be beneficial by initiating processes that create antibody diversity needed for the immune system or by accelerating the rate of evolution. AID can also alter gene regulation by removing epigenetic modifications from genomic DNA. However, when uncontrolled, these powerful agents of change can threaten genome stability and eventually lead to cancer.
Collapse
Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel.
| |
Collapse
|
30
|
Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya KR, Pham P, Mak CH, Goodman MF, Rueda D. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nat Commun 2015; 6:10209. [PMID: 26681117 PMCID: PMC4703863 DOI: 10.1038/ncomms10209] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/13/2015] [Indexed: 12/20/2022] Open
Abstract
Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ∼5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer. Activation-induced deoxycytidine deaminase (AID) induces somatic hypermutation and class-switch recombination during transcription of immunoglobulin genes. Here the authors use single-molecule FRET to show that AID translocates together with RNA polymerase and scans within stalled transcription bubbles.
Collapse
Affiliation(s)
- Gayan Senavirathne
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
| | - Jeffrey G Bertram
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Malgorzata Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Kathy R Chaurasiya
- Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Chi H Mak
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Center for Applied Mathematical Science, University of Southern California, Los Angeles, California 90089, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA.,Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
| |
Collapse
|
31
|
Zan H, Casali P. Epigenetics of Peripheral B-Cell Differentiation and the Antibody Response. Front Immunol 2015; 6:631. [PMID: 26697022 PMCID: PMC4677338 DOI: 10.3389/fimmu.2015.00631] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, such as histone post-translational modifications, DNA methylation, and alteration of gene expression by non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are heritable changes that are independent from the genomic DNA sequence. These regulate gene activities and, therefore, cellular functions. Epigenetic modifications act in concert with transcription factors and play critical roles in B cell development and differentiation, thereby modulating antibody responses to foreign- and self-antigens. Upon antigen encounter by mature B cells in the periphery, alterations of these lymphocytes epigenetic landscape are induced by the same stimuli that drive the antibody response. Such alterations instruct B cells to undergo immunoglobulin (Ig) class switch DNA recombination (CSR) and somatic hypermutation (SHM), as well as differentiation to memory B cells or long-lived plasma cells for the immune memory. Inducible histone modifications, together with DNA methylation and miRNAs modulate the transcriptome, particularly the expression of activation-induced cytidine deaminase, which is essential for CSR and SHM, and factors central to plasma cell differentiation, such as B lymphocyte-induced maturation protein-1. These inducible B cell-intrinsic epigenetic marks guide the maturation of antibody responses. Combinatorial histone modifications also function as histone codes to target CSR and, possibly, SHM machinery to the Ig loci by recruiting specific adaptors that can stabilize CSR/SHM factors. In addition, lncRNAs, such as recently reported lncRNA-CSR and an lncRNA generated through transcription of the S region that form G-quadruplex structures, are also important for CSR targeting. Epigenetic dysregulation in B cells, including the aberrant expression of non-coding RNAs and alterations of histone modifications and DNA methylation, can result in aberrant antibody responses to foreign antigens, such as those on microbial pathogens, and generation of pathogenic autoantibodies, IgE in allergic reactions, as well as B cell neoplasia. Epigenetic marks would be attractive targets for new therapeutics for autoimmune and allergic diseases, and B cell malignancies.
Collapse
Affiliation(s)
- Hong Zan
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| | - Paolo Casali
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| |
Collapse
|
32
|
AID-associated DNA repair pathways regulate malignant transformation in a murine model of BCL6-driven diffuse large B-cell lymphoma. Blood 2015; 127:102-12. [PMID: 26385350 DOI: 10.1182/blood-2015-02-628164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 09/08/2015] [Indexed: 12/27/2022] Open
Abstract
Somatic hypermutation and class-switch recombination of the immunoglobulin (Ig) genes occur in germinal center (GC) B cells and are initiated through deamination of cytidine to uracil by activation-induced cytidine deaminase (AID). Resulting uracil-guanine mismatches are processed by uracil DNA glycosylase (UNG)-mediated base-excision repair and MSH2-mediated mismatch repair (MMR) to yield mutations and DNA strand lesions. Although off-target AID activity also contributes to oncogenic point mutations and chromosome translocations associated with GC and post-GC B-cell lymphomas, the role of downstream AID-associated DNA repair pathways in the pathogenesis of lymphoma is unknown. Here, we show that simultaneous deficiency of UNG and MSH2 or MSH2 alone causes genomic instability and a shorter latency to the development of BCL6-driven diffuse large B-cell lymphoma (DLBCL) in a murine model. The additional development of several BCL6-independent malignancies in these mice underscores the critical role of MMR in maintaining general genomic stability. In contrast, absence of UNG alone is highly protective and prevents the development of BCL6-driven DLBCL. We further demonstrate that clonal and nonclonal mutations arise within non-Ig AID target genes in the combined absence of UNG and MSH2 and that DNA strand lesions arise in an UNG-dependent manner but are offset by MSH2. These findings lend insight into a complex interplay whereby potentially deleterious UNG activity and general genomic instability are opposed by the protective influence of MSH2, producing a net protective effect that promotes immune diversification while simultaneously attenuating malignant transformation of GC B cells.
Collapse
|
33
|
Identification of DNA cleavage- and recombination-specific hnRNP cofactors for activation-induced cytidine deaminase. Proc Natl Acad Sci U S A 2015; 112:5791-6. [PMID: 25902538 DOI: 10.1073/pnas.1506167112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for antibody class switch recombination (CSR) and somatic hypermutation (SHM). AID originally was postulated to function as an RNA-editing enzyme, based on its strong homology with apolipoprotein B mRNA-editing enzyme, catalytic polypeptide 1 (APOBEC1), the enzyme that edits apolipoprotein B-100 mRNA in the presence of the APOBEC cofactor APOBEC1 complementation factor/APOBEC complementation factor (A1CF/ACF). Because A1CF is structurally similar to heterogeneous nuclear ribonucleoproteins (hnRNPs), we investigated the involvement of several well-known hnRNPs in AID function by using siRNA knockdown and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated disruption. We found that hnRNP K deficiency inhibited DNA cleavage and thereby induced both CSR and SHM, whereas hnRNP L deficiency inhibited only CSR and somewhat enhanced SHM. Interestingly, both hnRNPs exhibited RNA-dependent interactions with AID, and mutant forms of these proteins containing deletions in the RNA-recognition motif failed to rescue CSR. Thus, our study suggests that hnRNP K and hnRNP L may serve as A1CF-like cofactors in AID-mediated CSR and SHM.
Collapse
|
34
|
Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR, Resch W, Liang G, Tang Z, Mathé E, Benner C, Dubois W, Nelson S, Vian L, Oliveira TY, Jankovic M, Hakim O, Gazumyan A, Pavri R, Awasthi P, Song B, Liu G, Chen L, Zhu S, Feigenbaum L, Staudt L, Murre C, Ruan Y, Robbiani DF, Pan-Hammarström Q, Nussenzweig MC, Casellas R. B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity. Cell 2014; 159:1524-37. [PMID: 25483777 DOI: 10.1016/j.cell.2014.11.013] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 09/26/2014] [Accepted: 10/30/2014] [Indexed: 02/07/2023]
Abstract
The antibody gene mutator activation-induced cytidine deaminase (AID) promiscuously damages oncogenes, leading to chromosomal translocations and tumorigenesis. Why nonimmunoglobulin loci are susceptible to AID activity is unknown. Here, we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the genome but are predominantly grouped within super-enhancers and regulatory clusters. Unexpectedly, in these domains, AID deaminates active promoters and eRNA(+) enhancers interconnected in some instances over megabases of linear chromatin. Using genome editing, we demonstrate that 3D-linked targets cooperate to recruit AID-mediated breaks. Furthermore, a comparison of hypermutation in mouse B cells, AID-induced kataegis in human lymphomas, and translocations in MEFs reveals that AID damages different genes in different cell types. Yet, in all cases, the targets are predominantly associated with topological complex, highly transcribed super-enhancers, demonstrating that these compartments are key mediators of AID recruitment.
Collapse
Affiliation(s)
- Jason Qian
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marei Dose
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA.
| | | | | | - Wolfgang Resch
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Genqing Liang
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Zhonghui Tang
- Department of Genetic and Development Biology, Jackson Laboratory for Genomic Medicine, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Ewy Mathé
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Christopher Benner
- The Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wendy Dubois
- Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Laura Vian
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Ofir Hakim
- Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Rushad Pavri
- Institute of Molecular Pathology (IMP), Vienna BioCenter, Doktor Bohr Gasse 7, Vienna 1030, Austria
| | - Parirokh Awasthi
- Science Applications International Corporation/Frederick, NCI-Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
| | - Bin Song
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Geng Liu
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Longyun Chen
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Shida Zhu
- Beijing Genomics Institute, Shenzhen, Shenzhen 518083, China
| | - Lionel Feigenbaum
- Science Applications International Corporation/Frederick, NCI-Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
| | - Louis Staudt
- Metabolism Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Cornelis Murre
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yijun Ruan
- Department of Genetic and Development Biology, Jackson Laboratory for Genomic Medicine, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Pan-Hammarström
- Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, 14186 Stockholm, Sweden
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; HHMI, The Rockefeller University, New York, NY 10065, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
35
|
Stanlie A, Yousif A, Akiyama H, Honjo T, Begum N. Chromatin Reader Brd4 Functions in Ig Class Switching as a Repair Complex Adaptor of Nonhomologous End-Joining. Mol Cell 2014; 55:97-110. [DOI: 10.1016/j.molcel.2014.05.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/20/2014] [Accepted: 04/28/2014] [Indexed: 12/29/2022]
|
36
|
Abstract
Chromosome translocations are catastrophic genomic events and often play key roles in tumorigenesis. Yet the biogenesis of chromosome translocations is remarkably poorly understood. Recent work has delineated several distinct mechanistic steps in the formation of translocations, and it has become apparent that non-random spatial genome organization, DNA repair pathways and chromatin features, including histone marks and the dynamic motion of broken chromatin, are critical for determining translocation frequency and partner selection.
Collapse
Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, Bethesda, Maryland 20892, USA
| |
Collapse
|
37
|
Fear DJ. Mechanisms regulating the targeting and activity of activation induced cytidine deaminase. Curr Opin Immunol 2014; 25:619-28. [PMID: 24209594 DOI: 10.1016/j.coi.2013.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 05/23/2013] [Indexed: 01/03/2023]
Abstract
Activation induced cytidine deaminase (AID) plays a central role in the vertebrate adaptive immune response, initiating immunoglobulin (Ig) somatic hypermutation (SHM) and class-switch recombination (CSR). AID converts deoxycytosine (dC) in the DNA to deoxyuridine (dU), causing a DNA base-pairing mismatch. How this mismatch is recognised and resolved determines whether the site will undergo mutation, recombination or high-fidelity repair. Although AID action is essential for antibody diversification it is also known to act upon many non-Ig genes where it can cause tumourigenic mutations and translocations. Although much is known about the pathways of Ig diversification, there is still very little known about the mechanisms that target AID to its sites of action and regulate the different repair processes that can participate at these sites.
Collapse
|
38
|
Abstract
Hepatocellular carcinoma (HCC) is a major cause of cancer death, and its development is influenced by the status of inflammation and oxidative stress in the liver. Although oxidative stress might induce genetic changes and play a role in HCC development, many epigenetic alterations have also been reported in this type of tumor, suggesting the importance of epigenetic instability in hepatocarcinogenesis. Epigenetic instability results in 2 types of DNA alterations: hypermethylation of the promoter of tumor suppressor genes (TSGs), and hypomethylation of nonpromoter CpG, such as repetitive elements and satellite DNA. The former causes transcriptional inactivation of TSGs, while the latter reportedly induces chromosomal instability and an abnormal activation of oncogenes as well as mobile genetic elements. Oxidative stress could induce epigenetic instability and inactivate TSGs through the recruitment of the polycomb repressive complex to the promoter sequence carrying DNA damage induced by oxidation. Inflammatory cytokines from immune cells also reportedly induce expression of several histone and DNA modulators. On the other hand, DNA oxidation could lead to activation of DNA repair pathways and affect the binding of methyl cytosine-binding protein to DNA, which could cause DNA hypomethylation. The decrease of the level of methyl group donors also contributes to the alteration in the methylation status. These mechanisms should act in concert and induce epigenetic instability, leading to HCC.
Collapse
Affiliation(s)
- Naoshi Nishida
- Department of Gastroenterology and Hepatology, Kinki University School of Medicine, Osakasayama, Japan
| | | |
Collapse
|
39
|
Nallar SC, Kalvakolanu DV. Regulation of snoRNAs in cancer: close encounters with interferon. J Interferon Cytokine Res 2013; 33:189-98. [PMID: 23570385 DOI: 10.1089/jir.2012.0106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interferon (IFN) family of cytokines regulates many cellular processes, such as transcription, translation, post-translational modifications, and protein degradation. IFNs induce growth inhibition and/or cell death, depending on the cell type, by employing different proteins. This review describes a novel growth-suppressive pathway employed by IFNs that affects rRNA levels. Maturation of rRNA involves numerous noncoding small regulatory RNA-guided processes. These regulatory RNAs, called small nucleolar RNA (snoRNAs), function as a ribonucleoprotein particle (RNP) in the nucleolus. The biogenesis of snoRNPs is dependent on core protein and assembly factors. Our laboratory recently isolated a growth-suppressive protein gene associated with retinoid-IFN-induced mortality (GRIM)-1 using a genetic screen. IFN-inducible GRIM-1 (SHQ1) is an assembly factor that controls one arm of the snoRNP machinery. GRIM-1 inhibits sno/scaRNP formation to induce growth suppression via reduction in mature rRNA levels. Loss of GRIM-1 observed in certain cancers implicates it to be a novel tumor suppressor. Certain snoRNAs have been reported to act as either oncogenes or tumor suppressors in vitro. Recent studies have shown that certain sno/scaRNAs are further processed into micro RNA-like molecules to control translation of protein-coding RNAs. We present a model as to how these small regulatory RNAs influence cell growth and a potential role for GRIM-1 in this process.
Collapse
Affiliation(s)
- Shreeram C Nallar
- Department of Microbiology & Immunology, Greenebaum Cancer Center, University of Maryland School of Medicine , Baltimore, MD 21201, USA
| | | |
Collapse
|
40
|
Kim SK, Nasu A, Komori J, Shimizu T, Matsumoto Y, Minaki Y, Kohno K, Shimizu K, Uemoto S, Chiba T, Marusawa H. A model of liver carcinogenesis originating from hepatic progenitor cells with accumulation of genetic alterations. Int J Cancer 2013; 134:1067-76. [PMID: 23959426 DOI: 10.1002/ijc.28445] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 08/07/2013] [Indexed: 02/06/2023]
Abstract
Activation-induced cytidine deaminase (AID) contributes to inflammation-associated carcinogenesis through its mutagenic activity. In our study, by taking advantage of the ability of AID to induce genetic aberrations, we investigated whether liver cancer originates from hepatic stem/progenitor cells that accumulate stepwise genetic alterations. For this purpose, hepatic progenitor cells enriched from the fetal liver of AID transgenic (Tg) mice were transplanted into recipient "toxin-receptor mediated conditional cell knockout" (TRECK) mice, which have enhanced liver regeneration activity under the condition of diphtheria toxin treatment. Whole exome sequencing was used to determine the landscape of the accumulated genetic alterations in the transplanted progenitor cells during tumorigenesis. Liver tumors developed in 7 of 11 (63.6%) recipient TRECK mice receiving enriched hepatic progenitor cells from AID Tg mice, while no tumorigenesis was observed in TRECK mice receiving hepatic progenitor cells of wild-type mice. Histologic examination revealed that the tumors showed characteristics of hepatocellular carcinoma and partial features of cholangiocarcinoma with expression of the AID transgene. Whole exome sequencing revealed that several dozen genes acquired single nucleotide variants in tumor tissues originating from the transplanted hepatic progenitor cells of AID Tg mice. Microarray analyses revealed that the majority of the mutations (>80%) were present in actively transcribed genes in the liver-lineage cells. These findings provided the evidence suggesting that accumulation of genetic alterations in fetal hepatic progenitor cells progressed to liver cancers, and the selection of mutagenesis depends on active transcription in the liver-lineage cells.
Collapse
Affiliation(s)
- Soo Ki Kim
- Department of Gastroenterology and Hepatology, Graduate School of MedicineKyoto University, Kyoto, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Affiliation(s)
- Masatoshi Aida
- Department of Immunology and Genetic Medicine; Graduate School of Medicine; Kyoto University; Kyoto, Japan
| | | |
Collapse
|
42
|
Abstract
Fusion genes that are caused by chromosome translocations have been recognized for several decades as drivers of deregulated cell growth in certain types of cancer. In recent years, oncogenic fusion genes have been found in many haematological and solid tumours, demonstrating that translocations are a common cause of malignancy. Sequencing approaches have now confirmed that numerous, non-clonal translocations are a typical feature of cancer cells. These chromosome rearrangements are often highly complex and contain DNA sequence from multiple genomic sites. The factors and pathways that promote translocations are becoming clearer, with non-homologous end-joining implicated as a key source of genomic rearrangements.
Collapse
Affiliation(s)
- Samuel F Bunting
- Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA.
| | | |
Collapse
|
43
|
Accumulation of the FACT complex, as well as histone H3.3, serves as a target marker for somatic hypermutation. Proc Natl Acad Sci U S A 2013; 110:7784-9. [PMID: 23610419 DOI: 10.1073/pnas.1305859110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Somatic hypermutation (SHM) requires not only the expression of activation-induced cytidine deaminase, but also transcription in the target regions. However, how transcription guides activation-induced cytidine deaminase in targeting SHM to the Ig genes is not fully understood. Here, we found that the "facilitates chromatin transcription" (FACT) complex promotes SHM by RNAi screening of transcription elongation factors. Furthermore, FACT and histone H3.3, a hallmark of transcription-coupled histone turnover, are enriched at the V(D)J region, 5' flanking sequence of the Sμ switch region and the light chain Jκ 5 segment region in the Ig loci. The regions with the most abundant deposition of FACT and H3.3 were also the most efficient targets of SHM. These results demonstrate the importance of histone-exchanging dynamics at the chromatin of SHM targets, especially in Ig genes.
Collapse
|
44
|
Huong LT, Kobayashi M, Nakata M, Shioi G, Miyachi H, Honjo T, Nagaoka H. In vivo analysis of Aicda gene regulation: a critical balance between upstream enhancers and intronic silencers governs appropriate expression. PLoS One 2013; 8:e61433. [PMID: 23613851 PMCID: PMC3628980 DOI: 10.1371/journal.pone.0061433] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 03/08/2013] [Indexed: 12/12/2022] Open
Abstract
The Aicda gene encodes activation-induced cytidine deaminase (AID). Aicda is strongly transcribed in activated B cells to diversify immunoglobulin genes, but expressed at low levels in various other cells in response to physiological or pathological stimuli. AID’s mutagenic nature has been shown to be involved in tumor development. Here, we used a transgenic strategy with bacterial artificial chromosomes (BACs) to examine the in vivo functions of Aicda regulatory elements, which cluster in two regions: in the first intron (region 2), and approximately 8-kb upstream of the transcription start site (region 4). Deleting either of these regions completely abolished the expression of Aicda-BAC reporters, demonstrating these elements’ critical roles. Furthermore, we found that selectively deleting two C/EBP-binding sites in region 4 inactivated the enhancer activity of the region despite the presence of intact NF-κB-, STAT6- and Smad-binding sites. On the other hand, selectively deleting E2F- and c-Myb-binding sites in region 2 increased the frequency of germinal-center B cells in which the Aicda promoter was active, indicating that E2F and c-Myb act as silencers in vivo. Interestingly, the silencer deletion did not cause ectopic activation of the Aicda promoter, indicating that Aicda activation requires enhancer-specific stimulation. In summary, precise regulation of the Aicda promoter appears to depend on a coordinated balance of activities between enhancer and silencer elements.
Collapse
Affiliation(s)
- Le Thi Huong
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Maki Kobayashi
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mikiyo Nakata
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Go Shioi
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, Kobe, Japan
| | - Hitoshi Miyachi
- Reproductive Engineering Team, Institute of Virus Research, Kyoto University, Kyoto, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hitoshi Nagaoka
- Department of Molecular Pathobiochemistry, Gifu University Graduate School of Medicine, Gifu, Japan
- * E-mail:
| |
Collapse
|
45
|
Roukos V, Burman B, Misteli T. The cellular etiology of chromosome translocations. Curr Opin Cell Biol 2013; 25:357-64. [PMID: 23498663 DOI: 10.1016/j.ceb.2013.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 01/26/2023]
Abstract
Chromosome translocations are the most severe form of genome defect. Translocations represent the end product of a series of cellular mistakes and they form after cells suffer multiple DNA double strand breaks (DSBs), which evade the surveillance mechanisms that usually eliminate them. Rather than being accurately repaired, translocating DSBs are misjoined to form aberrant fusion chromosomes. Although translocations have been extensively characterized using cytological methods and their pathological relevance in cancer and numerous other diseases is well established, how translocations form in the context of the intact cell nucleus is poorly understood. A combination of imaging approaches and biochemical methods to probe genome architecture and chromatin structure suggest that the spatial organization of the genome and features of chromatin, including sequence properties, higher order chromatin structure and histone modifications, are key determinants of translocation formation.
Collapse
|
46
|
Rocha PP, Skok JA. The origin of recurrent translocations in recombining lymphocytes: a balance between break frequency and nuclear proximity. Curr Opin Cell Biol 2013; 25:365-71. [PMID: 23478218 DOI: 10.1016/j.ceb.2013.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/13/2013] [Accepted: 02/16/2013] [Indexed: 02/05/2023]
Abstract
Translocations occur through the aberrant joining of large stretches of non-contiguous chromosomal regions. The substrates for these illegitimate rearrangements can arise as a result of damage incurred during normal cellular processes, such as transcription and replication, or through the action of genotoxic agents. In lymphocytes many translocations bear signs of having originated from abnormalities introduced during programmed recombination. Although recombination is tightly controlled at different levels, mistakes can occur leading to cytogenetic anomalies that include deletions, insertions, amplifications and translocations, which are an underlying cause of leukemias and lymphomas. In this review we focus on recent studies that provide insight into the origins of translocations that arise during the two lymphocyte specific programmed recombination events: V(D)J and class switch recombination (CSR).
Collapse
Affiliation(s)
- Pedro P Rocha
- Department of Pathology, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA
| | | |
Collapse
|
47
|
BCL6 breaks occur at different AID sequence motifs in Ig-BCL6 and non-Ig-BCL6 rearrangements. Blood 2013; 121:4551-4. [PMID: 23476051 DOI: 10.1182/blood-2012-10-464958] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BCL6 translocations are common in B-cell lymphomas and frequently have chromosomal breaks in immunoglobulin heavy chain (IgH) switch regions, suggesting that they occur during class-switch recombination. We analyze 120 BCL6 translocation breakpoints clustered in a 2156-bp segment of BCL6 intron 1, including 62 breakpoints (52%) joined to IgH, 12 (10%) joined to Ig light chains, and 46 (38%) joined to non-Ig partners. The BCL6 breaks in Ig-BCL6 translocations prefer known activation-induced cytosine deaminase (AID) hotspots such as WGCW and WRC (W = A/T, R = A/G), whereas BCL6 breaks in non-Ig rearrangements occur at CpG/CGC sites in addition to WGCW. Unlike previously identified CpG breaks in pro-B/pre-B-cell translocations, the BCL6 breaks do not show evidence of recombination activating gene or terminal deoxynucleotidyl transferase activity. Both WGCW/WRC and CpG/CGC breaks at BCL6 are most likely initiated by AID in germinal center B-cells, and their differential use suggests subtle mechanistic differences between Ig-BCL6 and non-Ig-BCL6 rearrangements.
Collapse
|
48
|
Fillatreau S, Six A, Magadan S, Castro R, Sunyer JO, Boudinot P. The astonishing diversity of Ig classes and B cell repertoires in teleost fish. Front Immunol 2013; 4:28. [PMID: 23408183 PMCID: PMC3570791 DOI: 10.3389/fimmu.2013.00028] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 01/24/2013] [Indexed: 12/17/2022] Open
Abstract
With lymphoid tissue anatomy different than mammals, and diverse adaptations to all aquatic environments, fish constitute a fascinating group of vertebrate to study the biology of B cell repertoires in a comparative perspective. Fish B lymphocytes express immunoglobulin (Ig) on their surface and secrete antigen-specific antibodies in response to immune challenges. Three antibody classes have been identified in fish, namely IgM, IgD, and IgT, while IgG, IgA, and IgE are absent. IgM and IgD have been found in all fish species analyzed, and thus seem to be primordial antibody classes. IgM and IgD are normally co-expressed from the same mRNA through alternative splicing, as in mammals. Tetrameric IgM is the main antibody class found in serum. Some species of fish also have IgT, which seems to exist only in fish and is specialized in mucosal immunity. IgM/IgD and IgT are expressed by two different sub-populations of B cells. The tools available to investigate B cell responses at the cellular level in fish are limited, but the progress of fish genomics has started to unravel a rich diversity of IgH and immunoglobulin light chain locus organization, which might be related to the succession of genome remodelings that occurred during fish evolution. Moreover, the development of deep sequencing techniques has allowed the investigation of the global features of the expressed fish B cell repertoires in zebrafish and rainbow trout, in steady state or after infection. This review provides a description of the organization of fish Ig loci, with a particular emphasis on their heterogeneity between species, and presents recent data on the structure of the expressed Ig repertoire in healthy and infected fish.
Collapse
Affiliation(s)
- Simon Fillatreau
- Deutsches Rheuma-Forschungszentrum, Leibniz Institute Berlin, Germany
| | | | | | | | | | | |
Collapse
|
49
|
Barlow J, Faryabi RB, Callen E, Wong N, Malhowski A, Chen HT, Gutierez-Cruz G, Sun HW, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A. Identification of early replicating fragile sites that contribute to genome instability. Cell 2013; 152:620-32. [PMID: 23352430 PMCID: PMC3629730 DOI: 10.1016/j.cell.2013.01.006] [Citation(s) in RCA: 318] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 12/10/2012] [Accepted: 01/02/2013] [Indexed: 12/20/2022]
Abstract
DNA double-strand breaks (DSBs) in B lymphocytes arise stochastically during replication or as a result of targeted DNA damage by activation-induced cytidine deaminase (AID). Here we identify recurrent, early replicating, and AID-independent DNA lesions, termed early replication fragile sites (ERFSs), by genome-wide localization of DNA repair proteins in B cells subjected to replication stress. ERFSs colocalize with highly expressed gene clusters and are enriched for repetitive elements and CpG dinucleotides. Although distinct from late-replicating common fragile sites (CFS), the stability of ERFSs and CFSs is similarly dependent on the replication-stress response kinase ATR. ERFSs break spontaneously during replication, but their fragility is increased by hydroxyurea, ATR inhibition, or deregulated c-Myc expression. Moreover, greater than 50% of recurrent amplifications/deletions in human diffuse large B cell lymphoma map to ERFSs. In summary, we have identified a source of spontaneous DNA lesions that drives instability at preferred genomic sites.
Collapse
Affiliation(s)
- Jacqueline Barlow
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Robert B. Faryabi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Amy Malhowski
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Hua Tang Chen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| | - Gustavo Gutierez-Cruz
- Laboratory of Muscle Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH Bethesda MD 20892
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH Bethesda MD 20892
| | - Peter McKinnon
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - George Wright
- Metabolism Branch Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | - Rafael Casellas
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH Bethesda MD 20892
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Louis Staudt
- Metabolism Branch Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda MD 20892
| |
Collapse
|
50
|
Jaszczur M, Bertram JG, Pham P, Scharff MD, Goodman MF. AID and Apobec3G haphazard deamination and mutational diversity. Cell Mol Life Sci 2012. [PMID: 23178850 DOI: 10.1007/s00018-012-1212-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activation-induced deoxycytidine deaminase (AID) and Apobec 3G (Apo3G) cause mutational diversity by initiating mutations on regions of single-stranded (ss) DNA. Expressed in B cells, AID deaminates C → U in actively transcribed immunoglobulin (Ig) variable and switch regions to initiate the somatic hypermutation (SHM) and class switch recombination (CSR) that are essential for antibody diversity. Apo3G expressed in T cells catalyzes C deaminations on reverse transcribed cDNA causing HIV-1 retroviral inactivation. When operating properly, AID- and Apo3G-initiated mutations boost human fitness. Yet, both enzymes are potentially powerful somatic cell "mutators". Loss of regulated expression and proper genome targeting can cause human cancer. Here, we review well-established biological roles of AID and Apo3G. We provide a synopsis of AID partnering proteins during SHM and CSR, and describe how an Apo2 crystal structure provides "surrogate" insight for AID and Apo3G biochemical behavior. However, large gaps remain in our understanding of how dC deaminases search ssDNA to identify trinucleotide motifs to deaminate. We discuss two recent methods to analyze ssDNA scanning and deamination. Apo3G scanning and deamination is visualized in real-time using single-molecule FRET, and AID deamination efficiencies are determined with a random walk analysis. AID and Apo3G encounter many candidate deamination sites while scanning ssDNA. Generating mutational diversity is a principal aim of AID and an important ancillary property of Apo3G. Success seems likely to involve hit and miss deamination motif targeting, biased strongly toward miss.
Collapse
Affiliation(s)
- Malgorzata Jaszczur
- Departments of Biological Sciences and Chemistry, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089-2910, USA
| | | | | | | | | |
Collapse
|