1
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Leeman-Neill RJ, Bhagat G, Basu U. AID in non-Hodgkin B-cell lymphomas: The consequences of on- and off-target activity. Adv Immunol 2024; 161:127-164. [PMID: 38763700 DOI: 10.1016/bs.ai.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Activation induced cytidine deaminase (AID) is a key element of the adaptive immune system, required for immunoglobulin isotype switching and affinity maturation of B-cells as they undergo the germinal center (GC) reaction in peripheral lymphoid tissue. The inherent DNA damaging activity of this enzyme can also have off-target effects in B-cells, producing lymphomagenic chromosomal translocations that are characteristic features of various classes of non-Hodgkin B-cell lymphoma (B-NHL), and generating oncogenic mutations, so-called aberrant somatic hypermutation (aSHM). Additionally, AID has been found to affect gene expression through demethylation as well as altered interactions between gene regulatory elements. These changes have been most thoroughly studied in B-NHL arising from GC B-cells. Here, we describe the most common classes of GC-derived B-NHL and explore the consequences of on- and off-target AID activity in B and plasma cell neoplasms. The relationships between AID expression, including effects of infection and other exposures/agents, mutagenic activity and lymphoma biology are also discussed.
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States; Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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2
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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3
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Rokan A, Hernandez JC, Nitiyanandan R, Lin ZY, Chen CL, Machida T, Li M, Khanuja J, Chen ML, Tahara SM, Siddiqi I, Machida K. Gut-derived Endotoxin-TLR4 Signaling Drives MYC-Ig Translocation to Promote Lymphoproliferation through c-JUN and STAT3 Activation. Mol Cancer Res 2023; 21:155-169. [PMID: 36287175 PMCID: PMC9898117 DOI: 10.1158/1541-7786.mcr-19-1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 09/14/2020] [Accepted: 10/19/2022] [Indexed: 02/06/2023]
Abstract
Synergism between obesity and virus infection promotes the development of B-cell lymphoma. In this study, we tested whether obesity-associated endotoxin release induced activation-induced cytidine deaminase (AID). TLR4 activation in turn caused c-JUN-dependent and STAT3-dependent translocations of MYC loci to suppress transactivation of CD95/FAS. We used viral nucleocapside Core transgenic (Tg) mice fed alcohol Western diet to determine whether oncogenesis arising from obesity and chronic virus infection occurred through TLR4-c-JUN-STAT3 pathways. Our results showed B cell-specific, c-Jun and/or Stat3 disruption reduced the incidence of splenomegaly in these mice. AID-dependent t(8;14) translocation was observed between the Ig promoter and MYC loci. Comparison with human B cells showed MYC-immunoglobulin (Ig) translocations after virus infection with lipopolysaccharide stimulation. Accordingly, human patients with lymphoma with virus infections and obesity showed a 40% incidence of MYC-Ig translocations. Thus, obesity and virus infection promote AID-mediated translocation between the Ig promoter and MYC through the TLR4-c-JUN axis, resulting in lymphoproliferation. Taken together, preventative treatment targeting either c-JUN and/or STAT3 may be effective strategies to prevent tumor development. IMPLICATIONS Obesity increases gut-derived endotoxin which induces Toll-like receptor-mediated MYC-Ig translocation via c-JUN-STAT3, leading to lymphoproliferation.
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Affiliation(s)
- Ahmed Rokan
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA,Department of Medical Laboratory Sciences (MLS), Prince Sattam Bin Abdulaziz University (PSAU)
| | - Juan Carlos Hernandez
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA,California State University Channel Islands, Los Angeles, CA
| | - Rajeshwar Nitiyanandan
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Zi-Ying Lin
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Chia-Lin Chen
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Tatsuya Machida
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Meng Li
- Norris Medical Library, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Jasleen Khanuja
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Mo Li Chen
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Stanley M. Tahara
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Imran Siddiqi
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Keigo Machida
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA,Southern California Research Center for ALPD and Cirrhosis, Los Angeles, CA,Correspondence: , 2011 Zonal Avenue, HMR503C, Los Angeles, CA 90089, Phone: +1-323-442-2692, Fax: +1-323-442-2091
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4
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Paranjape AM, Desai SS, Nishana M, Roy U, Nilavar NM, Mondal A, Kumari R, Radha G, Katapadi VK, Choudhary B, Raghavan SC. Nonamer dependent RAG cleavage at CpGs can explain mechanism of chromosomal translocations associated to lymphoid cancers. PLoS Genet 2022; 18:e1010421. [PMID: 36228010 PMCID: PMC9595545 DOI: 10.1371/journal.pgen.1010421] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/25/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
Chromosomal translocations are considered as one of the major causes of lymphoid cancers. RAG complex, which is responsible for V(D)J recombination, can also cleave non-B DNA structures and cryptic RSSs in the genome leading to chromosomal translocations. The mechanism and factors regulating the illegitimate function of RAGs resulting in oncogenesis are largely unknown. Upon in silico analysis of 3760 chromosomal translocations from lymphoid cancer patients, we find that 93% of the translocation breakpoints possess adjacent cryptic nonamers (RAG binding sequences), of which 77% had CpGs in proximity. As a proof of principle, we show that RAGs can efficiently bind to cryptic nonamers present at multiple fragile regions and cleave at adjacent mismatches generated to mimic the deamination of CpGs. ChIP studies reveal that RAGs can indeed recognize these fragile sites on a chromatin context inside the cell. Finally, we show that AID, the cytidine deaminase, plays a significant role during the generation of mismatches at CpGs and reconstitute the process of RAG-dependent generation of DNA breaks both in vitro and inside the cells. Thus, we propose a novel mechanism for generation of chromosomal translocation, where RAGs bind to the cryptic nonamer sequences and direct cleavage at adjacent mismatch generated due to deamination of meCpGs or cytosines.
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Affiliation(s)
- Amita M. Paranjape
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sagar S. Desai
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mayilaadumveettil Nishana
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Namrata M. Nilavar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Amrita Mondal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Gudapureddy Radha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
- * E-mail: (BC); (SCR)
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
- * E-mail: (BC); (SCR)
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5
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Bal S, Kumar SK, Fonseca R, Gay F, Hungria VTM, Dogan A, Costa LJ. Multiple myeloma with t(11;14): unique biology and evolving landscape. Am J Cancer Res 2022; 12:2950-2965. [PMID: 35968339 PMCID: PMC9360221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023] Open
Abstract
Multiple myeloma is characterized by heterogeneity in clinical presentation, response to treatment, and importantly, patient outcomes. The translocation of chromosomes 11 and 14 [t(11;14)(q13;32)], hereafter referred to as t(11;14), is the most common primary translocation event in multiple myeloma, occurring in approximately 16%-24% of patients. Multiple myeloma harboring t(11;14) represents a unique disease subset as t(11;14)-positive myeloma cells exhibit biological features that are distinct from t(11;14)-negative myeloma cells, including overexpression of cyclin D1, higher levels of the antiapoptotic protein BCL-2, and the frequent expression of the B-cell lineage protein CD20. Additionally, t(11;14) is associated with less common clinical features, such as immunoglobulin M and light chain disease. With the evolution of the treatment landscape, the prognostic significance of t(11;14) multiple myeloma remains debatable. However, it is clear that t(11;14) multiple myeloma represents a distinct subset and a rare opportunity for targeted therapy with BCL-2 inhibition. In this review, we first describe the underlying biology of t(11;14) multiple myeloma cells, then summarize the body of literature evaluating the prognosis of patients with t(11;14) multiple myeloma, and finally discuss therapeutic implications.
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Affiliation(s)
- Susan Bal
- Department of Medicine, Division of Hematology Oncology, O’Neal Comprehensive Cancer Center, The University of Alabama at BirminghamBirmingham, AL, USA
| | - Shaji K Kumar
- Division of Hematology, Mayo ClinicRochester, MN, USA
| | - Rafael Fonseca
- Division of Hematology and Oncology, Mayo ClinicPhoenix, AZ, USA
| | - Francesca Gay
- Clinical Trial Unit, Division of Hematology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, University of TorinoTorino TO, Italy
| | | | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer CenterNew York, NY, USA
| | - Luciano J Costa
- Department of Medicine, Division of Hematology Oncology, O’Neal Comprehensive Cancer Center, The University of Alabama at BirminghamBirmingham, AL, USA
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6
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Sterrenberg JN, Folkerts ML, Rangel V, Lee SE, Pannunzio NR. Diversity upon diversity: linking DNA double-strand break repair to blood cancer health disparities. Trends Cancer 2022; 8:328-343. [PMID: 35094960 PMCID: PMC9248772 DOI: 10.1016/j.trecan.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/20/2021] [Accepted: 01/03/2022] [Indexed: 10/19/2022]
Abstract
Chromosomal translocations arising from aberrant repair of multiple DNA double-strand breaks (DSBs) are a defining characteristic of many cancers. DSBs are an essential part of physiological processes in antibody-producing B cells. The B cell environment is poised to generate genome instability leading to translocations relevant to the pathology of blood cancers. These are a diverse set of cancers, but limited data from under-represented groups have pointed to health disparities associated with each. We focus on the DSBs that occur in developing B cells and propose the most likely mechanism behind the formation of translocations. We also highlight specific cancers in which these rearrangements occur and address the growing concern of health disparities associated with them.
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7
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Liu D, Lieber MR. The mechanisms of human lymphoid chromosomal translocations and their medical relevance. Crit Rev Biochem Mol Biol 2021; 57:227-243. [PMID: 34875186 DOI: 10.1080/10409238.2021.2004576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of expression of AID can introduce long-lived T:G mismatch lesions at 20-600 bp fragile zones. Second, the V(D)J recombination process can occasionally fail to rejoin coding ends, and this failure may permit an opportunity for Artemis:DNA-dependent kinase catalytic subunit (DNA-PKcs) to convert the T:G mismatch sites at the fragile zones into double-strand breaks. The 20-600 bp fragile zones must be, at least transiently, in a single-stranded DNA (ssDNA) state for the first step to occur, because AID only acts on ssDNA. Here we discuss the key DNA sequence features that lead to AID action at a fragile zone, which are (a) the proximity and density of strings of cytosine nucleotides (C-strings) that cause a B/A-intermediate DNA conformation; (b) overlapping AID hotspots that contain a methyl CpG (WRCG), which AID converts to a long-lived T:G mismatch; and (c) transcription, which, though not essential, favors increased ssDNA in the fragile zone. We also summarize chromosomal features of the focal fragile zones in lymphoid malignancies and discuss the clinical relevance of understanding the translocation mechanisms. Many of the key principles covered here are also relevant to chromosomal translocations in non-lymphoid somatic cells as well.
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Affiliation(s)
- Di Liu
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael R Lieber
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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8
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Dalland JC, Smadbeck JB, Sharma N, Meyer RG, Pearce KE, Greipp PT, Peterson JF, Kumar S, Ketterling RP, King RL, Baughn LB. Increased complexity of t(11;14) rearrangements in plasma cell neoplasms compared with mantle cell lymphoma. Genes Chromosomes Cancer 2021; 60:678-686. [PMID: 34124820 PMCID: PMC8453742 DOI: 10.1002/gcc.22977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
Plasma cell neoplasms (PCN) and mantle cell lymphoma (MCL) can both harbor t(11;14)(q13;q32) (CCND1/IGH), usually resulting in cyclin D1 overexpression. In some cases, particularly at low levels of disease, it can be morphologically challenging to distinguish between these entities in the bone marrow (BM) since PCN with t(11;14) are often CD20-positive with lymphoplasmacytic cytology, while MCL can rarely have plasmacytic differentiation. We compared the difference in CCND1/IGH by fluorescence in situ hybridization (FISH) in PCN and MCL to evaluate for possible differentiating characteristics. We identified 326 cases of MCL with t(11;14) and 279 cases of PCN with t(11;14) from either formalin-fixed, paraffin-embedded tissue or fresh BM specimens. The "typical," balanced CCND1/IGH FISH signal pattern was defined as three total CCND1 signals, three total IGH signals, and two total fusion signals. Any deviation from the "typical" pattern was defined as an "atypical" pattern, which was further stratified into "gain of fusion" vs "complex" patterns. There was a significantly higher proportion of cases that showed an atypical FISH pattern in PCN compared with MCL (53% vs 27%, P < .0001). There was also a significantly higher proportion of cases that showed a complex FISH pattern in PCN compared with MCL (47% vs 17%, P < .0001). We confirmed these findings using mate-pair sequencing of 25 PCN and MCL samples. PCN more often have a complex CCND1/IGH FISH pattern compared with MCL, suggesting possible differences in the genomic mechanisms underlying these rearrangements in plasma cells compared with B cells.
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Affiliation(s)
- Joanna C. Dalland
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - James B. Smadbeck
- Division of Computational Biology, Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
| | - Neeraj Sharma
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Reid G. Meyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Kathryn E. Pearce
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Patricia T. Greipp
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Jess F. Peterson
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Shaji Kumar
- Division of Hematology, Department of Internal MedicineMayo ClinicRochesterMinnesotaUSA
| | - Rhett P. Ketterling
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Rebecca L. King
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
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9
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King JJ, Borzooee F, Im J, Asgharpour M, Ghorbani A, Diamond CP, Fifield H, Berghuis L, Larijani M. Structure-Based Design of First-Generation Small Molecule Inhibitors Targeting the Catalytic Pockets of AID, APOBEC3A, and APOBEC3B. ACS Pharmacol Transl Sci 2021; 4:1390-1407. [PMID: 34423273 PMCID: PMC8369683 DOI: 10.1021/acsptsci.1c00091] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 12/12/2022]
Abstract
![]()
Activation-induced
cytidine deaminase (AID) initiates antibody
diversification by mutating immunoglobulin loci in B lymphocytes.
AID and related APOBEC3 (A3) enzymes also induce genome-wide mutations
and lesions implicated in tumorigenesis and tumor progression. The
most prevalent mutation signatures across diverse tumor genomes are
attributable to the mistargeted mutagenic activities of AID/A3s. Thus,
inhibiting AID/A3s has been suggested to be of therapeutic benefit.
We previously used a computational-biochemical approach to gain insight
into the structure of AID’s catalytic pocket, which resulted
in the discovery of a novel type of regulatory catalytic pocket closure
that regulates AID/A3s that we termed the “Schrodinger’s
CATalytic pocket”. Our findings were subsequently confirmed
by direct structural studies. Here, we describe our search for small
molecules that target the catalytic pocket of AID. We identified small
molecules that inhibit purified AID, AID in cell extracts, and endogenous
AID of lymphoma cells. Analogue expansion yielded derivatives with
improved potencies. These were found to also inhibit A3A and A3B,
the two most tumorigenic siblings of AID. Two compounds exhibit low
micromolar IC50 inhibition of AID and A3A, exhibiting the
strongest potency for A3A. Docking suggests key interactions between
their warheads and residues lining the catalytic pockets of AID, A3A,
and A3B and between the tails and DNA-interacting residues on the
surface proximal to the catalytic pocket opening. Accordingly, mutants
of these residues decreased inhibition potency. The chemistry and
abundance of key stabilizing interactions between the small molecules
and residues within and immediately outside the catalytic pockets
are promising for therapeutic development.
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Affiliation(s)
- Justin J King
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Faezeh Borzooee
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Junbum Im
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada.,BC Cancer Research/Terry Fox Labs, University of British Columbia, Vancouver, British Columbia BC V5Z 1L3, Canada
| | - Mahdi Asgharpour
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Atefeh Ghorbani
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Cody P Diamond
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Heather Fifield
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Lesley Berghuis
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
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10
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Liu D, Loh YHE, Hsieh CL, Lieber MR. Mechanistic basis for chromosomal translocations at the E2A gene and its broader relevance to human B cell malignancies. Cell Rep 2021; 36:109387. [PMID: 34260910 PMCID: PMC8327686 DOI: 10.1016/j.celrep.2021.109387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
Analysis of translocation breakpoints in human B cell malignancies reveals that DNA double-strand breaks at oncogenes most frequently occur at CpG sites located within 20-600 bp fragile zones and depend on activation-induced deaminase (AID). AID requires single-stranded DNA (ssDNA) to act, but it has been unclear why or how this region transiently acquires a ssDNA state. Here, we demonstrate the ssDNA state in the 23 bp E2A fragile zone using several methods, including native bisulfite DNA structural analysis in live human pre-B cells. AID deamination within the E2A fragile zone does not require but is increased upon transcription. High C-string density, nascent RNA tails, and direct DNA sequence repeats prolong the ssDNA state of the E2A fragile zone and increase AID deamination at overlapping AID hotspots that contain the CpG sites at which breaks occur in patients. These features provide key insights into lymphoid fragile zones generally.
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Affiliation(s)
- Di Liu
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Yong-Hwee Eddie Loh
- USC Libraries Bioinformatics Services, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Chih-Lin Hsieh
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Michael R Lieber
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA.
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11
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Alves de Souza Rios L, Mapekula L, Mdletshe N, Chetty D, Mowla S. HIV-1 Transactivator of Transcription (Tat) Co-operates With AP-1 Factors to Enhance c-MYC Transcription. Front Cell Dev Biol 2021; 9:693706. [PMID: 34277639 PMCID: PMC8278106 DOI: 10.3389/fcell.2021.693706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
HIV-1 infection often leads to the development of co-morbidities including cancer. Burkitt lymphoma (BL) is one of the most over-represented non-Hodgkin lymphoma among HIV-infected individuals, and displays a highly aggressive phenotype in this population group, with comparatively poorer outcomes, despite these patients being on anti-retroviral therapy. Accumulating evidence indicates that the molecular pathogenesis of HIV-associated malignancies is unique, with components of the virus playing an active role in driving oncogenesis, and in order to improve patient prognosis and treatment, a better understanding of disease pathobiology and progression is needed. In this study, we found HIV-1 Tat to be localized within the tumor cells of BL patients, and enhanced expression of oncogenic c-MYC in these cells. Using luciferase reporter assays we show that HIV-1 Tat enhances the c-MYC gene promoter activity and that this is partially mediated via two AP-1 binding elements located at positions -1128 and -1375 bp, as revealed by mutagenesis experiments. We further demonstrate, using pull-down assays, that Tat can exist within a protein complex with the AP-1 factor JunB, and that this complex can bind these AP-1 sites within the c-MYC promoter, as shown by in vivo chromatin immunoprecipitation assays. Therefore, these findings show that in HIV-infected individuals, Tat infiltrates B-cells, where it can enhance the expression of oncogenic factors, which contributes toward the more aggressive disease phenotype observed in these patients.
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Affiliation(s)
| | - Lungile Mapekula
- Division of Haematology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nontlantla Mdletshe
- Division of Haematology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Dharshnee Chetty
- Division of Anatomical Pathology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Shaheen Mowla
- Division of Haematology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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12
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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13
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Cao P, Li G, Xiang J. Genome instability and lymphoma. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:552-557. [PMID: 34148893 PMCID: PMC10930211 DOI: 10.11817/j.issn.1672-7347.2021.190427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Indexed: 11/03/2022]
Abstract
Lymphoma is one of the most common malignant tumor of the hematologic system. The genome instability is not only an important molecular basis for the development of lymphoma, but also has important value in the diagnosis and prognosis of lymphoma. There are 2 types of genome instability: Microsatellite instability (MSI/MIN) at gene level and chromosomal instability at chromosome level. Through the study on genes associated with lymphoma, the unstable genes associated with lymphoma could be found, meanwhile the mechanism of its occurrence and development of lymphoma could be explored, and the important basis of molecular biology could also be provided in the field of current hot lymphoma precision medical research.
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Affiliation(s)
- Pengfei Cao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008.
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha 410078, China.
| | - Guiyuan Li
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha 410078, China.
| | - Juanjuan Xiang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha 410078, China
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14
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Fukutsuka K, Iioka F, Maekawa F, Nakagawa M, Kishimori C, Hayashida M, Tagawa S, Akasaka T, Honjo G, Ohno H. Burkitt leukemia with precursor B-cell features that developed after ruxolitinib treatment in a patient with hydroxyurea-refractory JAK2 V617F-myeloproliferative neoplasm. J Clin Exp Hematop 2021; 61:114-119. [PMID: 33994432 PMCID: PMC8265492 DOI: 10.3960/jslrt.21001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A 62-year-old woman, who had a 16-year history of
JAK2V617F-mutated myeloproliferative neoplasm
(MPN), developed Burkitt leukemia (BL) 16 months after treatment with
ruxolitinib to control hydroxyurea-refractory conditions. BL cells were
CD10+, CD19+, CD20−,
CD34−, cytoplasmic CD79a+, and TdT+,
and lacked surface immunoglobulins but expressed the cytoplasmic μ heavy
chain. In the bone marrow, nuclear MYC+ BL cells displaced the MPN
tissues. t(8;14)(q24;q32) occurred at a CG dinucleotide within
MYC exon 1 and at the IGHJ3 segment, and an N-like segment
was inserted at the junction. The V-D-J sequence of the non-translocated IGH
allele had the unmutated configuration. DNA from peripheral blood at a time of
the course of MPN exhibited homozygous JAK2V617F
mutation, while that at BL development included both
JAK2V617F and wild-type DNAs. Although the
association between JAK1/2 inhibitor therapy for MPN and secondary development
of aggressive B-cell neoplasm remains controversial, this report suggests that,
in selected patients, close monitoring of clonal B-cells in the BM is required
before and during treatment with JAK1/2 inhibitors.
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Affiliation(s)
| | - Futoshi Iioka
- Department of Hematology, Tenri Hospital, Nara, Japan
| | | | | | | | | | | | | | - Gen Honjo
- Department of Diagnostic Surgical Pathology, Tenri Hospital, Nara, Japan
| | - Hitoshi Ohno
- Tenri Institute of Medical Research, Nara, Japan.,Department of Hematology, Tenri Hospital, Nara, Japan
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15
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Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 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.
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Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
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16
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Zhao X, Sun D, Zhang G. Clinicopathological characteristics of extranodal follicular dendritic cell sarcoma: A report of two cases. Oncol Lett 2021; 21:182. [PMID: 33574921 PMCID: PMC7816366 DOI: 10.3892/ol.2021.12443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
Follicular dendritic cell sarcoma (FDCS) is an extremely rare tumor, which mainly originates from FDCs in the lymph nodes. Sometimes FDCS can arise from outside the lymph nodes due to the existence of acquired lymphoid tissue, which becomes the histological basis of the tumor. The diagnosis of FDCS, particularly extranodal FDCS, presents a challenge for pathologists and hematopathologists. The present study presents two cases of extranodal FDCS based on clinical features and histomorphology. Soft tissue of the chest wall was involved in case 1 and right tonsil tissue in case 2. Case 1 underwent surgery, and was in good health post-operatively. During the 5-month post-operative follow-up period, the patient was healthy in all respects. Case 2 received surgery combined with radiotherapy, and the follow-up data reported that the patient remained alive, without signs of recurrence or metastasis during the 4-month post-operative follow-up period. Additionally, a total of 102 cases of extranodal FDCS were retrieved from the literature, which were extracted and reviewed carefully. The rates of recurrence, metastasis and mortality were 14.63 (12/82), 17.07 (14/82) and 8.29% (15/82), respectively. The overall survival rates of the 102 cases, showing 2-year total survival rates, were 70%, the same with that of 5-year total survival rates. The 2-year tumor-free total survival rates were 68%, and the 5-year equivalents were 32%. Female patients had a poorer prognosis than male patients (P<0.05). Kaplan-Meier estimation presented no statistically significant differences between disease-free survival rates or overall survival rates and age, tumor size or treatment (P>0.05).
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Affiliation(s)
- Xing Zhao
- Department of Pathology, Affiliated Hospital of Chengde Medical College, Chengde, Hebei 067000, P.R. China
| | - Dayong Sun
- Department of Tumor Radiation and Chemotherapy Center, Chengde Central Hospital, Chengde, Hebei 067000, P.R. China
| | - Gang Zhang
- Department of General Surgery IV, Baoding First Hospital, Baoding, Hebei 071000, P.R. China
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17
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Nadeu F, Martin-Garcia D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, Valdés-Mas R, López C, Chapaprieta V, Puiggros M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera-Cortada I, Siebert R, Colomer D, Torrents D, Gine E, López-Guillermo A, Küppers R, Martin-Subero JI, Puente XS, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes. Blood 2020; 136:1419-1432. [PMID: 32584970 PMCID: PMC7498364 DOI: 10.1182/blood.2020005289] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/14/2020] [Indexed: 01/03/2023] Open
Abstract
Mantle cell lymphoma (MCL) is a mature B-cell neoplasm initially driven by CCND1 rearrangement with 2 molecular subtypes, conventional MCL (cMCL) and leukemic non-nodal MCL (nnMCL), that differ in their clinicobiological behavior. To identify the genetic and epigenetic alterations determining this diversity, we used whole-genome (n = 61) and exome (n = 21) sequencing (74% cMCL, 26% nnMCL) combined with transcriptome and DNA methylation profiles in the context of 5 MCL reference epigenomes. We identified that open and active chromatin at the major translocation cluster locus might facilitate the t(11;14)(q13;32), which modifies the 3-dimensional structure of the involved regions. This translocation is mainly acquired in precursor B cells mediated by recombination-activating genes in both MCL subtypes, whereas in 8% of cases the translocation occurs in mature B cells mediated by activation-induced cytidine deaminase. We identified novel recurrent MCL drivers, including CDKN1B, SAMHD1, BCOR, SYNE1, HNRNPH1, SMARCB1, and DAZAP1. Complex structural alterations emerge as a relevant early oncogenic mechanism in MCL, targeting key driver genes. Breakage-fusion-bridge cycles and translocations activated oncogenes (BMI1, MIR17HG, TERT, MYC, and MYCN), generating gene amplifications and remodeling regulatory regions. cMCL carried significant higher numbers of structural variants, copy number alterations, and driver changes than nnMCL, with exclusive alterations of ATM in cMCL, whereas TP53 and TERT alterations were slightly enriched in nnMCL. Several drivers had prognostic impact, but only TP53 and MYC aberrations added value independently of genomic complexity. An increasing genomic complexity, together with the presence of breakage-fusion-bridge cycles and high DNA methylation changes related to the proliferative cell history, defines patients with different clinical evolution.
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - David Martin-Garcia
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Ander Díaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Roser Vilarrasa-Blasi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Romina Royo
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Jesús Gutiérrez-Abril
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Rafael Valdés-Mas
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Cristina López
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Vicente Chapaprieta
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | | | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
| | - Pedro Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clinics, Universitat de Barcelona, Barcelona, Spain
| | - Blanca Espinet
- Laboratori de Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | - Ana Muntañola
- Servei d'Hematologia, Hospital Mútua de Terrassa, Terrassa, Spain
| | - Inmaculada Ribera-Cortada
- Hospital Clínic of Barcelona, Barcelona, Spain
- Hospital Nostra Senyora de Meritxell, Escaldes-Engordany, Andorra la Vella, Andorra
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clinics, Universitat de Barcelona, Barcelona, Spain
| | | | - Eva Gine
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
| | - Armando López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clinics, Universitat de Barcelona, Barcelona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany
- German Consortium for Cancer Research, Heidelberg, Germany; and
| | - Jose I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Departament de Fonaments Clinics, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clinics, Universitat de Barcelona, Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Departament de Fonaments Clinics, Universitat de Barcelona, Barcelona, Spain
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18
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Activation-induced cytidine deaminase: in sickness and in health. J Cancer Res Clin Oncol 2020; 146:2721-2730. [PMID: 32772231 DOI: 10.1007/s00432-020-03348-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022]
Abstract
Activation Induced cytidine Deaminase (AID) is an essential enzyme of the adaptive immune system. Its canonical activity is restricted to B lymphocytes, playing an essential role in the diversification of antibodies by enhancing specificity and changing affinity. This is possible through its DNA deaminase function, leading to mutations in DNA. In the last decade, AID has been assigned an additional function: that of a powerful DNA demethylator. Adverse cellular conditions such as chronic inflammation can lead to its deregulation and overexpression. It is an important driver of B-cell lymphoma due to its natural ability to modify DNA through deamination, leading to mutations and epigenetic changes. However, the deregulation of AID is not restricted to lymphoid cells. Recent findings have provided new insights into the role that this protein plays in the development of non-lymphoid cancers, with some research shedding light on novel AID-driven mechanisms of cellular transformation. In this review, we provide an updated narrative of the normal physiological functions of AID. Additionally, we review and discuss the recent research studies that have implicated AID in carcinogenesis in varying tissue types including lymphoid and non-lymphoid cancers. We review the mechanisms, whereby AID promotes carcinogenesis and highlight important areas of future research.
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19
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Romero-Masters JC, Ohashi M, Djavadian R, Eichelberg MR, Hayes M, Bristol JA, Ma S, Ranheim EA, Gumperz J, Johannsen EC, Kenney SC. An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model. PLoS Pathog 2018; 14:e1007221. [PMID: 30125329 PMCID: PMC6117096 DOI: 10.1371/journal.ppat.1007221] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/30/2018] [Accepted: 07/16/2018] [Indexed: 12/15/2022] Open
Abstract
EBV causes human B-cell lymphomas and transforms B cells in vitro. EBNA3C, an EBV protein expressed in latently-infected cells, is required for EBV transformation of B cells in vitro. While EBNA3C undoubtedly plays a key role in allowing EBV to successfully infect B cells, many EBV+ lymphomas do not express this protein, suggesting that cellular mutations and/or signaling pathways may obviate the need for EBNA3C in vivo under certain conditions. EBNA3C collaborates with EBNA3A to repress expression of the CDKN2A-encoded tumor suppressors, p16 and p14, and EBNA3C-deleted EBV transforms B cells containing a p16 germline mutation in vitro. Here we have examined the phenotype of an EBNAC-deleted virus (Δ3C EBV) in a cord blood-humanized mouse model (CBH). We found that the Δ3C virus induced fewer lymphomas (occurring with a delayed onset) in comparison to the wild-type (WT) control virus, although a subset (10/26) of Δ3C-infected CBH mice eventually developed invasive diffuse large B cell lymphomas with type III latency. Both WT and Δ3C viruses induced B-cell lymphomas with restricted B-cell populations and heterogeneous T-cell infiltration. In comparison to WT-infected tumors, Δ3C-infected tumors had greatly increased p16 levels, and RNA-seq analysis revealed a decrease in E2F target gene expression. However, we found that Δ3C-infected tumors expressed c-Myc and cyclin E at similar levels compared to WT-infected tumors, allowing cells to at least partially bypass p16-mediated cell cycle inhibition. The anti-apoptotic proteins, BCL2 and IRF4, were expressed in Δ3C-infected tumors, likely helping cells avoid c-Myc-induced apoptosis. Unexpectedly, Δ3C-infected tumors had increased T-cell infiltration, increased expression of T-cell chemokines (CCL5, CCL20 and CCL22) and enhanced type I interferon response in comparison to WT tumors. Together, these results reveal that EBNA3C contributes to, but is not essential for, EBV-induced lymphomagenesis in CBH mice, and suggest potentially important immunologic roles of EBNA3C in vivo.
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MESH Headings
- Animals
- Cell Transformation, Viral/genetics
- Cells, Cultured
- Disease Models, Animal
- Epstein-Barr Virus Infections/complications
- Epstein-Barr Virus Infections/genetics
- Epstein-Barr Virus Nuclear Antigens/genetics
- Fetal Blood/immunology
- HEK293 Cells
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/physiology
- Humans
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/pathology
- Lymphoma, B-Cell/virology
- Mice
- Mice, Inbred NOD
- Mice, Transgenic
- Virus Latency/genetics
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Affiliation(s)
- James C. Romero-Masters
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Makoto Ohashi
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Reza Djavadian
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mark R. Eichelberg
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mitch Hayes
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jillian A. Bristol
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shidong Ma
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Erik A. Ranheim
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jenny Gumperz
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eric C. Johannsen
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shannon C. Kenney
- Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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20
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Pannunzio NR, Lieber MR. Concept of DNA Lesion Longevity and Chromosomal Translocations. Trends Biochem Sci 2018; 43:490-498. [PMID: 29735400 DOI: 10.1016/j.tibs.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/07/2018] [Accepted: 04/08/2018] [Indexed: 01/11/2023]
Abstract
A subset of chromosomal translocations related to B cell malignancy in human patients arises due to DNA breaks occurring within defined 20-600 base pair (bp) zones. Several factors influence the breakage rate at these sites including transcription, DNA sequence, and topological tension. These factors favor non-B DNA structures that permit formation of transient single-stranded DNA (ssDNA), making the DNA more vulnerable to agents such as the enzyme activation-induced cytidine deaminase (AID) and reactive oxygen species (ROS). Certain DNA lesions created during the ssDNA state persist after the DNA resumes its normal duplex structure. We propose that factors favoring both formation of transient ssDNA and persistent DNA lesions are key in determining the DNA breakage mechanism.
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Affiliation(s)
- Nicholas R Pannunzio
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Michael R Lieber
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Department of Molecular Microbiology and Immunology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Department of Biochemistry and Molecular Biology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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21
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Uchida A, Isobe Y, Uemura Y, Nishio Y, Sakai H, Kato M, Otsubo K, Hoshikawa M, Takagi M, Miura I. De novo acute lymphoblastic leukemia-like disease of high grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements: a case report and literature review. BMC Clin Pathol 2017; 17:21. [PMID: 29151814 PMCID: PMC5679186 DOI: 10.1186/s12907-017-0060-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/30/2017] [Indexed: 12/15/2022] Open
Abstract
Background B-cell lymphomas harboring the 8q24/MYC plus 18q21/BCL2 translocations are now referred to as high grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-MBR). Although HGBL-MBR is frequently found in cases with diffuse large B-cell lymphoma or Burkitt lymphoma-like B-cell lymphoma, acute lymphoblastic leukemia (ALL)-like disease of HGBL-MBR (AL-HGBL-MBR) has been reported incidentally. Case presentation A 69-year-old Japanese woman developed remittent fever and increasing systemic bone pain. The bone marrow examination revealed that more than 90% of nuclear cells were blastoid cells, which were positive for CD10, CD19, CD20, and surface IgMκ and negative for terminal deoxynucleotidyl transferase (TdT). Cytogenetic studies confirmed that the patient had de novo AL-HGBL-MBR with the extra copies of MYC and loss of chromosome 17p. She showed resistance to chemoimmunotherapy and died seven months after the diagnosis. The literature review identified further 47 de novo AL-HGBL-MBR cases within the last 32 years. The median age was 61 years (range, 27 − 86); the male/female ratio was 2.0. Thirty-eight cases (79%) presented a clinical picture of ALL at diagnosis; 14 (36%) of 39 available cases showed central nervous system involvement. Loss of 17p and translocations at 2p12–13, 3q27, 9p13 were frequently observed as additional cytogenetic abnormalities. Although the median survival of 46 available cases was only five months (range, 0.1–18), rituximab use significantly improved the survival of AL-HGBL-MBR (log-rank test, P = 0.0294). Conclusion Our patient and most reported de novo AL-HGBL-MBR cases showed resistance to conventional chemoimmunotherapy and disastrous consequences. AL-HGBL-MBL is a rare, but should be considered a distinct clinical condition in HGBL-MBR. Other therapeutic strategies, such as using inhibitors of MYC and BCL2, are needed to overcome the chemoresistance of AL-HGBL-MBR.
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Affiliation(s)
- Akiko Uchida
- Division of Hematology & Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511 Japan
| | - Yasushi Isobe
- Division of Hematology & Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511 Japan
| | - Yu Uemura
- Division of Hematology & Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511 Japan
| | - Yuji Nishio
- Division of Hematology & Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511 Japan
| | - Hirotaka Sakai
- Division of Hematology & Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511 Japan
| | - Masayuki Kato
- Division of Hematology & Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511 Japan
| | - Kaori Otsubo
- Department of cytogenetics, SRL Diagnostics, Hachioji Laboratory, Tokyo, Japan
| | - Masahiro Hoshikawa
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Masayuki Takagi
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ikuo Miura
- Division of Hematology & Oncology, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa 216-8511 Japan
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22
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New Insights in the Cytogenetic Practice: Karyotypic Chaos, Non-Clonal Chromosomal Alterations and Chromosomal Instability in Human Cancer and Therapy Response. Genes (Basel) 2017; 8:genes8060155. [PMID: 28587191 PMCID: PMC5485519 DOI: 10.3390/genes8060155] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022] Open
Abstract
Recently, non-clonal chromosomal alterations previously unappreciated are being proposed to be included in cytogenetic practice. The aim of this inclusion is to obtain a greater understanding of chromosomal instability (CIN) and tumor heterogeneity and their role in cancer evolution and therapy response. Although several genetic assays have allowed the evaluation of the variation in a population of cancer cells, these assays do not provide information at the level of individual cells, therefore limiting the information of the genomic diversity within tumors (heterogeneity). The karyotype is one of the few available cytogenetic techniques that allow us not only to identify the chromosomal alterations present within a single cell, but also allows us to profile both clonal (CCA) and non-clonal chromosomal alterations (NCCAs). A greater understanding of CIN and tumor heterogeneity in cancer could not only improve existing therapeutic regimens but could also be used as targets for the design of new therapeutic approaches. In this review we indicate the importance and significance of karyotypic chaos, NCCAs and CIN in the prognosis of human cancers.
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23
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High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis. Blood Adv 2017; 1:535-544. [PMID: 29296973 DOI: 10.1182/bloodadvances.2016000794] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/30/2017] [Indexed: 11/20/2022] Open
Abstract
Burkitt lymphoma (BL), the most common pediatric cancer in sub-Saharan Africa, is a malignancy of antigen-experienced B lymphocytes. High-throughput sequencing (HTS) of the immunoglobulin heavy (IGH) and light chain (IGK/IGL) loci was performed on genomic DNA from 51 primary BL tumors: 19 from Uganda and 32 from Ghana. Reverse transcription polymerase chain reaction analysis and tumor RNA sequencing (RNAseq) was performed on the Ugandan tumors to confirm and extend the findings from the HTS of tumor DNA. Clonal IGH and IGK/IGL rearrangements were identified in 41 and 46 tumors, respectively. Evidence for rearrangement of the second IGH allele was observed in only 6 of 41 tumor samples with a clonal IGH rearrangement, suggesting that the normal process of biallelic IGHD to IGHJ diversity-joining (DJ) rearrangement is often disrupted in BL progenitor cells. Most tumors, including those with a sole dominant, nonexpressed DJ rearrangement, contained many IGH and IGK/IGL sequences that differed from the dominant rearrangement by < 10 nucleotides, suggesting that the target of ongoing mutagenesis of these loci in BL tumor cells is not limited to expressed alleles. IGHV usage in both BL tumor cohorts revealed enrichment for IGHV genes that are infrequently used in memory B cells from healthy subjects. Analysis of publicly available DNA sequencing and RNAseq data revealed that these same IGHV genes were overrepresented in dominant tumor-associated IGH rearrangements in several independent BL tumor cohorts. These data suggest that BL derives from an abnormal B-cell progenitor and that aberrant mutational processes are active on the immunoglobulin loci in BL cells.
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24
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Green AM, Landry S, Budagyan K, Avgousti DC, Shalhout S, Bhagwat AS, Weitzman MD. APOBEC3A damages the cellular genome during DNA replication. Cell Cycle 2017; 15:998-1008. [PMID: 26918916 DOI: 10.1080/15384101.2016.1152426] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The human APOBEC3 family of DNA-cytosine deaminases comprises 7 members (A3A-A3H) that act on single-stranded DNA (ssDNA). The APOBEC3 proteins function within the innate immune system by mutating DNA of viral genomes and retroelements to restrict infection and retrotransposition. Recent evidence suggests that APOBEC3 enzymes can also cause damage to the cellular genome. Mutational patterns consistent with APOBEC3 activity have been identified by bioinformatic analysis of tumor genome sequences. These mutational signatures include clusters of base substitutions that are proposed to occur due to APOBEC3 deamination. It has been suggested that transiently exposed ssDNA segments provide substrate for APOBEC3 deamination leading to mutation signatures within the genome. However, the mechanisms that produce single-stranded substrates for APOBEC3 deamination in mammalian cells have not been demonstrated. We investigated ssDNA at replication forks as a substrate for APOBEC3 deamination. We found that APOBEC3A (A3A) expression leads to DNA damage in replicating cells but this is reduced in quiescent cells. Upon A3A expression, cycling cells activate the DNA replication checkpoint and undergo cell cycle arrest. Additionally, we find that replication stress leaves cells vulnerable to A3A-induced DNA damage. We propose a model to explain A3A-induced damage to the cellular genome in which cytosine deamination at replication forks and other ssDNA substrates results in mutations and DNA breaks. This model highlights the risk of mutagenesis by A3A expression in replicating progenitor cells, and supports the emerging hypothesis that APOBEC3 enzymes contribute to genome instability in human tumors.
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Affiliation(s)
- Abby M Green
- a Division of Oncology , Department of Pediatrics , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.,b Center for Childhood Cancer Research, Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - Sébastien Landry
- c Faculty of Pharmacy, Université de Montréal , Montréal , QC , Canada
| | - Konstantin Budagyan
- d Division of Cancer Pathobiology , Department of Pathology and Laboratory Medicine , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Daphne C Avgousti
- d Division of Cancer Pathobiology , Department of Pathology and Laboratory Medicine , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Sophia Shalhout
- e Department of Chemistry , Wayne State University , Detroit , MI , USA
| | - Ashok S Bhagwat
- e Department of Chemistry , Wayne State University , Detroit , MI , USA.,f Department of Immunology and Microbiology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Matthew D Weitzman
- b Center for Childhood Cancer Research, Children's Hospital of Philadelphia , Philadelphia , PA , USA.,d Division of Cancer Pathobiology , Department of Pathology and Laboratory Medicine , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
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25
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Abstract
Analysis of chromosomal translocation sequence locations in human lymphomas has provided valuable clues about the mechanism of the translocations and when they occur. Biochemical analyses on the mechanisms of DNA breakage and rejoining permit formulation of detailed models of the human chromosomal translocation process in lymphoid neoplasms. Most human lymphomas are derived from B cells in which a DNA break at an oncogene is initiated by activation-induced deaminase (AID). The partner locus in many cases is located at one of the antigen receptor loci, and this break is generated by the recombination activating gene (RAG) complex or by AID. After breakage, the joining process typically occurs by non-homologous DNA end-joining (NHEJ). Some of the insights into this mechanism also apply to translocations that occur in non-lymphoid neoplasms.
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Affiliation(s)
- Michael R Lieber
- USC Norris Comprehensive Cancer Center, Room 5428, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, MC9176, Los Angeles, California 90089-9176, USA
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26
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Shi Y, Zhao X, Durkin L, Rogers HJ, Hsi ED. Aberrant activation-induced cytidine deaminase expression in Philadelphia chromosome-positive B-cell acute lymphoblastic leukemia. Hum Pathol 2016; 52:173-8. [PMID: 26980048 DOI: 10.1016/j.humpath.2016.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 11/30/2022]
Abstract
Activation-induced cytidine deaminase (AID) is expressed in germinal center B cells and plays a critical role in somatic hypermutation and class-switch recombination of immunoglobulin genes. Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL) carries a poor prognosis and is specifically treated with tyrosine kinase inhibitors. Interestingly, AID has been shown to be aberrantly expressed and functional in Ph+ ALL and is thought to contribute to genetic instability. We hypothesized that AID might be detectable in routinely processed bone marrow biopsies by immunohistochemistry (IHC) and assist in identifying Ph+ ALL. We found that AID was expressed in 26 (70%) of 37 cases of Ph+ ALL but only 1 (2.9%) of 38 cases of Ph- ALL cases. There was a significant difference in AID expression between these 2 ALL groups (P < .001, Fisher exact test). The expression of AID was confirmed by RT-PCR (reverse-transcriptase polymerase chain reaction) and correlated with IHC scoring. AID protein is expressed in a large proportion of Ph+ ALL cases at levels detectable by IHC in clinical samples and might be useful to rapidly identify cases likely to have a BCR/ABL1 fusion.
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Affiliation(s)
- Yang Shi
- Department of Laboratory Medicine, Cleveland Clinic, L-11, Cleveland, OH, USA 44195.
| | - Xiaoxian Zhao
- Department of Laboratory Medicine, Cleveland Clinic, L-11, Cleveland, OH, USA 44195.
| | - Lisa Durkin
- Department of Laboratory Medicine, Cleveland Clinic, L-11, Cleveland, OH, USA 44195.
| | - Heesun Joyce Rogers
- Department of Laboratory Medicine, Cleveland Clinic, L-11, Cleveland, OH, USA 44195.
| | - Eric D Hsi
- Department of Laboratory Medicine, Cleveland Clinic, L-11, Cleveland, OH, USA 44195.
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27
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Bregenhorn S, Kallenberger L, Artola-Borán M, Peña-Diaz J, Jiricny J. Non-canonical uracil processing in DNA gives rise to double-strand breaks and deletions: relevance to class switch recombination. Nucleic Acids Res 2016; 44:2691-705. [PMID: 26743004 PMCID: PMC4824095 DOI: 10.1093/nar/gkv1535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/23/2015] [Indexed: 12/24/2022] Open
Abstract
During class switch recombination (CSR), antigen-stimulated B-cells rearrange their immunoglobulin constant heavy chain (CH) loci to generate antibodies with different effector functions. CSR is initiated by activation-induced deaminase (AID), which converts cytosines in switch (S) regions, repetitive sequences flanking the CH loci, to uracils. Although U/G mispairs arising in this way are generally efficiently repaired to C/Gs by uracil DNA glycosylase (UNG)-initiated base excision repair (BER), uracil processing in S-regions of activated B-cells occasionally gives rise to double strand breaks (DSBs), which trigger CSR. Surprisingly, genetic experiments revealed that CSR is dependent not only on AID and UNG, but also on mismatch repair (MMR). To elucidate the role of MMR in CSR, we studied the processing of uracil-containing DNA substrates in extracts of MMR-proficient and –deficient human cells, as well as in a system reconstituted from recombinant BER and MMR proteins. Here, we show that the interplay of these repair systems gives rise to DSBs in vitro and to genomic deletions and mutations in vivo, particularly in an S-region sequence. Our findings further suggest that MMR affects pathway choice in DSB repair. Given its amenability to manipulation, our system represents a powerful tool for the molecular dissection of CSR.
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Affiliation(s)
- Stephanie Bregenhorn
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Department of Biology, Swiss Federal Institute of Technology (ETH) Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lia Kallenberger
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Mariela Artola-Borán
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Javier Peña-Diaz
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland University of Copenhagen, Faculty of Health Sciences Center for Healthy Aging, Department of Neuroscience and Pharmacology, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Department of Biology, Swiss Federal Institute of Technology (ETH) Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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28
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Mantle cell lymphoma—a spectrum from indolent to aggressive disease. Virchows Arch 2015; 468:245-57. [DOI: 10.1007/s00428-015-1840-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 01/18/2023]
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29
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Blombery PA, Wall M, Seymour JF. The molecular pathogenesis of B-cell non-Hodgkin lymphoma. Eur J Haematol 2015; 95:280-93. [DOI: 10.1111/ejh.12589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 12/17/2022]
Affiliation(s)
| | - Meaghan Wall
- Victorian Cancer Cytogenetics Service; St Vincent's Hospital Melbourne; University of Melbourne; Fitzroy Vic. Australia
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30
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Krem MM, Press OW, Horwitz MS, Tidwell T. Mechanisms and clinical applications of chromosomal instability in lymphoid malignancy. Br J Haematol 2015; 171:13-28. [PMID: 26018193 DOI: 10.1111/bjh.13507] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lymphocytes are unique among cells in that they undergo programmed DNA breaks and translocations, but that special property predisposes them to chromosomal instability (CIN), a cardinal feature of neoplastic lymphoid cells that manifests as whole chromosome- or translocation-based aneuploidy. In several lymphoid malignancies translocations may be the defining or diagnostic markers of the diseases. CIN is a cornerstone of the mutational architecture supporting lymphoid neoplasia, though it is perhaps one of the least understood components of malignant transformation in terms of its molecular mechanisms. CIN is associated with prognosis and response to treatment, making it a key area for impacting treatment outcomes and predicting prognoses. Here we will review the types and mechanisms of CIN found in Hodgkin lymphoma, non-Hodgkin lymphoma, multiple myeloma and the lymphoid leukaemias, with emphasis placed on pathogenic mutations affecting DNA recombination, replication and repair; telomere function; and mitotic regulation of spindle attachment, centrosome function, and chromosomal segregation. We will discuss the means by which chromosome-level genetic aberrations may give rise to multiple pathogenic mutations required for carcinogenesis and conclude with a discussion of the clinical applications of CIN and aneuploidy to diagnosis, prognosis and therapy.
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Affiliation(s)
- Maxwell M Krem
- Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Oliver W Press
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marshall S Horwitz
- Department of Pathology and Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Timothy Tidwell
- Department of Pathology and Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, USA
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31
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Ganapathi KA, Pittaluga S, Odejide OO, Freedman AS, Jaffe ES. Early lymphoid lesions: conceptual, diagnostic and clinical challenges. Haematologica 2015; 99:1421-32. [PMID: 25176983 DOI: 10.3324/haematol.2014.107938] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
There are no "benign lymphomas", a fact due to the nature of lymphoid cells to circulate and home as part of their normal function. Thus, benign clonal expansions of lymphocytes are only rarely recognized when localized. Recent studies have identified a number of lymphoid proliferations that lie at the interface between benign and malignant. Some of these are clonal proliferations that carry many of the molecular hallmarks of their malignant counterparts, such as BCL2/IGH and CCND1/IGH translocations associated with the in situ forms of follicular lymphoma and mantle cell lymphoma, respectively. There are other clonal B-cell proliferations with low risk of progression; these include the pediatric variants of follicular lymphoma and marginal zone lymphoma. Historically, early or incipient forms of T/NK-cell neoplasia also have been identified, such as lymphomatoid papulosis and refractory celiac disease. More recently an indolent form of T-cell lymphoproliferative disease affecting the gastrointestinal tract has been described. Usually, CD8(+), the clonal cells are confined to the mucosa. The clinical course is chronic, but non-progressive. NK-cell enteropathy is a clinically similar condition, composed of cytologically atypical NK-cells that may involve the stomach, small bowel or colon. Breast implant-associated anaplastic large cell lymphoma is a cytologically alarming lesion that is self-limited if confined to the seroma cavity. Atypical lymphoid proliferations that lie at the border of benign and malignant can serve as instructive models of lymphomagenesis. It is also critical that they be correctly diagnosed to avoid unnecessary and potentially harmful therapy.
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Affiliation(s)
- Karthik A Ganapathi
- Hematopathology Section, Center for Cancer Research, Laboratory of Pathology, National Cancer Institute, Harvard Medical School, Boston, USA
| | - Stefania Pittaluga
- Hematopathology Section, Center for Cancer Research, Laboratory of Pathology, National Cancer Institute, Harvard Medical School, Boston, USA
| | - Oreofe O Odejide
- Center for Hematologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Arnold S Freedman
- Center for Hematologic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Elaine S Jaffe
- Hematopathology Section, Center for Cancer Research, Laboratory of Pathology, National Cancer Institute, Harvard Medical School, Boston, USA
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33
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Lu Z, Lieber MR, Tsai AG, Pardo CE, Müschen M, Kladde MP, Hsieh CL. Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin. Mol Cell Biol 2015; 35:1209-22. [PMID: 25624348 PMCID: PMC4355534 DOI: 10.1128/mcb.01085-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/26/2014] [Accepted: 01/16/2015] [Indexed: 12/19/2022] Open
Abstract
Chromosomal translocations are a hallmark of hematopoietic malignancies. CG motifs within translocation fragile zones (typically 20 to 600 bp in size) are prone to chromosomal translocation in lymphomas. Here we demonstrate that the CG motifs in human translocation fragile zones are hypomethylated relative to the adjacent DNA. Using a methyltransferase footprinting assay on isolated nuclei (in vitro), we find that the chromatin at these fragile zones is accessible. We also examined in vivo accessibility using cellular expression of a prokaryotic methylase. Based on this assay, which measures accessibility over a much longer time interval than is possible with in vitro methods, these fragile zones were found to be more accessible than the adjacent DNA. Because DNA within the fragile zones can be methylated by both cellular and exogenous methyltransferases, the fragile zones are predominantly in a duplex DNA conformation. These observations permit more-refined models for why these zones are 100- to 1,000-fold more prone to undergo chromosomal translocation than the adjacent regions.
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Affiliation(s)
- Zhengfei Lu
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Albert G Tsai
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Carolina E Pardo
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Markus Müschen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Michael P Kladde
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
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34
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Twa DDW, Steidl C. Structural genomic alterations in primary mediastinal large B-cell lymphoma. Leuk Lymphoma 2015; 56:2239-50. [DOI: 10.3109/10428194.2014.985673] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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35
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Wright RL, Slemmons KK, Vaughan ATM. Estradiol induces gene proximity and MLL-MLLT3 fusion in an activation-induced cytidine deaminase-mediated pathway. Leuk Lymphoma 2014; 56:1460-5. [PMID: 25130479 DOI: 10.3109/10428194.2014.954112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Epidemiological data have linked birth control formulations to an increased risk of infant acute leukemia involving MLL rearrangements. Reverse transcription polymerase chain reaction (RT-PCR) studies showed that 10 nM estradiol enhanced MLL transcription in addition to its common translocation partners, MLLT2 (AF4) and MLLT3 (AF9). The same concentration of estradiol triggered MLL and MLLT3 co-localization without affecting the interaction of genes located on the same chromosomes. Estradiol also stimulated the generation of MLL-MLLT3 fusion transcripts as seen by RT-PCR. RNAi knockdown of activation-induced cytidine deaminase (AICDA) suppressed the induction of MLL-MLLT3 fusion transcript formation observed with estradiol. Additionally, chromatin immunoprecipitation (ChIP) analysis showed estradiol dependent localization of AICDA in MLL intron 11, upstream of a hotspot for both DNA cleavage and rearrangement, but not downstream within intron 12. Combined, these studies show that levels of estradiol consistent with that observed during pregnancy have the potential to initiate MLL fusions through an AICDA-mediated mechanism.
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Affiliation(s)
- Rebecca L Wright
- Department of Radiation Oncology, University of California at Davis , Sacramento, CA , USA
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36
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Nygren L, Wasik AM, Baumgartner-Wennerholm S, Jeppsson-Ahlberg Å, Klimkowska M, Andersson P, Buhrkuhl D, Christensson B, Kimby E, Wahlin BE, Sander B. T-Cell Levels Are Prognostic in Mantle Cell Lymphoma. Clin Cancer Res 2014; 20:6096-104. [DOI: 10.1158/1078-0432.ccr-14-0889] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Tepsuporn S, Hu J, Gostissa M, Alt FW. Mechanisms that can promote peripheral B-cell lymphoma in ATM-deficient mice. Cancer Immunol Res 2014; 2:857-66. [PMID: 24913718 PMCID: PMC4156541 DOI: 10.1158/2326-6066.cir-14-0090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Ataxia Telangiectasia-mutated (ATM) kinase senses DNA double-strand breaks (DSB) and facilitates their repair. In humans, ATM deficiency predisposes to B- and T-cell lymphomas, but in mice it leads only to thymic lymphomas. We tested the hypothesis that increased DSB frequency at a cellular oncogene could promote B-cell lymphoma by generating ATM-deficient mice with a V(D)J recombination target (DJβ cassette) within c-myc intron 1 ("DA" mice). We also generated ATM-deficient mice carrying an Eμ-Bcl-2 transgene (AB mice) to test whether enhanced cellular survival could promote B-cell lymphomas. About 30% of DA or AB mice and nearly 100% of mice harboring the combined genotypes (DAB mice) developed mature B-cell lymphomas. In all genotypes, B-cell tumors harbored oncogenic c-myc amplification generated by breakage-fusion-bridge (BFB) from dicentric chromosomes formed through fusion of IgH V(D)J recombination-associated DSBs on chromosome 12 to sequences downstream of c-myc on chromosome 15. AB tumors demonstrate that B lineage cells harboring spontaneous DSBs leading to IgH/c-myc dicentrics are blocked from progressing to B-cell lymphomas by cellular apoptotic responses. DA and DAB tumor translocations were strictly linked to the cassette, but occurred downstream, frequently in a 6-kb region adjacent to c-myc that harbors multiple cryptic V(D)J recombination targets, suggesting that bona fide V(D)J target sequences may activate linked cryptic targets. Our findings indicate that ATM deficiency allows IgH V(D)J recombination DSBs in developing B cells to generate dicentric translocations that, via BFB cycles, lead to c-myc-activating oncogenic translocations and amplifications in mature B cells.
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Affiliation(s)
- Suprawee Tepsuporn
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jiazhi Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Monica Gostissa
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
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38
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Wright RL, Vaughan ATM. A systematic description of MLL fusion gene formation. Crit Rev Oncol Hematol 2014; 91:283-91. [PMID: 24787275 DOI: 10.1016/j.critrevonc.2014.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/21/2014] [Accepted: 03/28/2014] [Indexed: 11/25/2022] Open
Abstract
Rearrangements of the MLL gene involve multiple partners and are implicated in both therapy related acute leukemia [tAL] and infant acute leukemia. For these diseases, recently compiled clinical data confirms an elevated frequency of such breakpoints within a 4 kb tract between exon 11 and a region of structural instability adjacent to exon 12. Linked primarily to cases of tAL, interference with topoisomerase II activity may either contribute to the initial DNA lesion directly or indirectly by, for example, providing a physical block to transcription progression. Alternatively, sites of fragmentation may be mis-repaired, guided by intergenic spliced transcripts of the participating genes. Co-transcription of MLL and potential fusion partners may provide the localization that enhances the probability of gene interaction. An indirect role for the leukemogenic activity of topoisomerase II inhibitors would imply that the negative consequences of their use may be separated from their therapeutic effects.
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Affiliation(s)
- Rebecca L Wright
- Department of Radiation Oncology, University of California at Davis, 4501 X Street, Sacramento, CA 95817, United States
| | - Andrew T M Vaughan
- Department of Radiation Oncology, University of California at Davis, 4501 X Street, Sacramento, CA 95817, United States.
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39
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Allinne J, Pichugin A, Iarovaia O, Klibi M, Barat A, Zlotek-Zlotkiewicz E, Markozashvili D, Petrova N, Camara-Clayette V, Ioudinkova E, Wiels J, Razin SV, Ribrag V, Lipinski M, Vassetzky YS. Perinucleolar relocalization and nucleolin as crucial events in the transcriptional activation of key genes in mantle cell lymphoma. Blood 2014; 123:2044-53. [PMID: 24452204 DOI: 10.1182/blood-2013-06-510511] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In mantle cell lymphoma (MCL), one allele of the cyclin D1 (Ccnd1) gene is translocated from its normal localization on chromosome 11 to chromosome 14. This is considered as the crucial event in the transformation process of a normal naive B-cell; however, the actual molecular mechanism leading to Ccnd1 activation remains to be deciphered. Using a combination of three-dimensional and immuno-fluorescence in situ hybridization experiments, the radial position of the 2 Ccnd1 alleles was investigated in MCL-derived cell lines and malignant cells from affected patients. The translocated Ccnd1 allele was observed significantly more distant from the nuclear membrane than its nontranslocated counterpart, with a very high proportion of IgH-Ccnd1 chromosomal segments localized next to a nucleolus. These perinucleolar areas were found to contain active RNA polymerase II (PolII) clusters. Nucleoli are rich in nucleolin, a potent transcription factor that we found to bind sites within the Ccnd1 gene specifically in MCL cells and to activate Ccnd1 transcription. We propose that the Ccnd1 transcriptional activation in MCL cells relates to the repositioning of the rearranged IgH-Ccnd1-carrying chromosomal segment in a nuclear territory with abundant nucleolin and active PolII molecules. Similar transforming events could occur in Burkitt and other B-cell lymphomas.
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Affiliation(s)
- Jeanne Allinne
- Unité Mixte de Recherche 8126, Université Paris-Sud, National Centre for Scientific Research, Institut de Cancérologie Gustave Roussy, Villejuif, France
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40
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Sklyar IV, Iarovaia OV, Lipinski M, Vassetzky YS. Translocations affecting human immunoglobulin heavy chain locus. ACTA ACUST UNITED AC 2014. [DOI: 10.7124/bc.000886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- I. V. Sklyar
- CNRS UMR8126, Paris-Sud University, Gustave Roussy Institute
- Institute of Gene Biology, Russian Academy of Sciences
- LIA 1066 French-Russian Joint Cancer Research Laboratory
| | - O. V. Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences
- LIA 1066 French-Russian Joint Cancer Research Laboratory
| | - M. Lipinski
- CNRS UMR8126, Paris-Sud University, Gustave Roussy Institute
- LIA 1066 French-Russian Joint Cancer Research Laboratory
| | - Y. S. Vassetzky
- Institute of Gene Biology, Russian Academy of Sciences
- LIA 1066 French-Russian Joint Cancer Research Laboratory
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41
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Non-homologous end joining often uses microhomology: implications for alternative end joining. DNA Repair (Amst) 2014; 17:74-80. [PMID: 24613510 DOI: 10.1016/j.dnarep.2014.02.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/27/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022]
Abstract
Artemis and PALF (also called APLF) appear to be among the primary nucleases involved in non-homologous end joining (NHEJ) and responsible for most nucleolytic end processing in NHEJ. About 60% of NHEJ events show an alignment of the DNA ends that use 1 or 2bp of microhomology (MH) between the two DNA termini. Thus, MH is a common feature of NHEJ. For most naturally occurring human chromosomal deletions (e.g., after oxidative damage or radiation) and translocations, such as those seen in human neoplasms and as well as inherited chromosomal structural variations, MH usage occurs at a frequency that is typical of NHEJ, and does not suggest major involvement of alternative pathways that require more extensive MH. Though we mainly focus on human NHEJ at double-strand breaks, comparison on these points to other eukaryotes, primarily S. cerevisiae, is informative.
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42
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Nagel S, Ehrentraut S, Meyer C, Kaufmann M, Drexler HG, MacLeod RAF. Oncogenic deregulation of NKL homeobox gene MSX1 in mantle cell lymphoma. Leuk Lymphoma 2014; 55:1893-903. [PMID: 24237447 DOI: 10.3109/10428194.2013.864762] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
NKL homeobox gene MSX1 is physiologically expressed during embryonic hematopoiesis. Here, we detected MSX1 overexpression in three examples of mantle cell lymphoma (MCL) and one of acute myeloid leukemia (AML) by screening 96 leukemia/lymphoma cell lines via microarray profiling. Moreover, in silico analysis identified significant overexpression of MSX1 in 3% each of patients with MCL and AML, confirming aberrant activity in subsets of both types of malignancies. Comparative expression profiling analysis and subsequent functional studies demonstrated overexpression of histone acetyltransferase PHF16 together with transcription factors FOXC1 and HLXB9 as activators of MSX1 transcription. Additionally, we identified regulation of cyclin D1/CCND1 by MSX1 and its repressive cofactor histone H1C. Fluorescence in situ hybridization in MCL cells showed that t(11;14)(q13;q32) results in detachment of CCND1 from its corresponding repressive MSX1 binding site. Taken together, we uncovered regulators and targets of homeobox gene MSX1 in leukemia/lymphoma cells, supporting the view of a recurrent genetic network that is reactivated in malignant transformation.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures , Braunschweig , Germany
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43
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Antigen selection in B-cell lymphomas—Tracing the evidence. Semin Cancer Biol 2013; 23:399-409. [DOI: 10.1016/j.semcancer.2013.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 12/22/2022]
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44
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Interplay among viral antigens, cellular pathways and tumor microenvironment in the pathogenesis of EBV-driven lymphomas. Semin Cancer Biol 2013; 23:441-56. [DOI: 10.1016/j.semcancer.2013.07.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 11/22/2022]
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45
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Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. Proc Natl Acad Sci U S A 2013; 110:18250-5. [PMID: 24145436 DOI: 10.1073/pnas.1314608110] [Citation(s) in RCA: 397] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive tumor, but a subset of patients may follow an indolent clinical course. To understand the mechanisms underlying this biological heterogeneity, we performed whole-genome and/or whole-exome sequencing on 29 MCL cases and their respective matched normal DNA, as well as 6 MCL cell lines. Recurrently mutated genes were investigated by targeted sequencing in an independent cohort of 172 MCL patients. We identified 25 significantly mutated genes, including known drivers such as ataxia-telangectasia mutated (ATM), cyclin D1 (CCND1), and the tumor suppressor TP53; mutated genes encoding the anti-apoptotic protein BIRC3 and Toll-like receptor 2 (TLR2); and the chromatin modifiers WHSC1, MLL2, and MEF2B. We also found NOTCH2 mutations as an alternative phenomenon to NOTCH1 mutations in aggressive tumors with a dismal prognosis. Analysis of two simultaneous or subsequent MCL samples by whole-genome/whole-exome (n = 8) or targeted (n = 19) sequencing revealed subclonal heterogeneity at diagnosis in samples from different topographic sites and modulation of the initial mutational profile at the progression of the disease. Some mutations were predominantly clonal or subclonal, indicating an early or late event in tumor evolution, respectively. Our study identifies molecular mechanisms contributing to MCL pathogenesis and offers potential targets for therapeutic intervention.
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46
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Karube K, Scarfò L, Campo E, Ghia P. Monoclonal B cell lymphocytosis and "in situ" lymphoma. Semin Cancer Biol 2013; 24:3-14. [PMID: 23999128 DOI: 10.1016/j.semcancer.2013.08.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/15/2013] [Accepted: 08/21/2013] [Indexed: 01/09/2023]
Abstract
The finding of monoclonal B-cell populations not fulfilling criteria for a lymphoid malignancy has given great impulse to study mechanisms involved in lymphomagenesis and factors responsible for the transition from B-cell precursor states to overt lymphoproliferative disorders. Monoclonal B cell expansions were initially recognized in peripheral blood of otherwise healthy subjects (thus defined monoclonal B-cell lymphocytosis, MBL) and in most cases share the immunophenotypic profile of chronic lymphocytic leukemia (CLL). The clinical relevance of this phenomenon is different according to B-cell count: high-count MBL is considered a preneoplastic condition and progresses to CLL requiring treatment at a rate of 1-2% per year, while low-count MBL, though persisting over time, has not shown a clinical correlation with frank leukemia so far. MBL other than CLL-like represent a minority of cases and are ill-defined entities for which clinical and biological information is still scanty. In situ follicular lymphoma (FL) and mantle cell lymphoma (MCL) are characterized by the localization of atypical lymphoid cells, carrying t(14;18)(q32;q21) or t(11;14)(q13;q32), only in the germinal centers and mantle zones respectively, where their normal counterparts are localized. The localization of these cells indicates that germinal centers or mantle zones provide appropriate microenvironments for cells carrying these oncogenic alterations to survive or proliferate. The progression of these lesions to overt lymphomas occurs rarely and may require the accumulation of additional genetic events. Individuals with these lymphoid proliferations should be managed with caution.
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MESH Headings
- B-Lymphocytes/pathology
- Cell Lineage
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphocytosis/blood
- Lymphocytosis/genetics
- Lymphocytosis/pathology
- Lymphoma, Follicular/blood
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Lymphoma, Mantle-Cell/blood
- Lymphoma, Mantle-Cell/pathology
- Translocation, Genetic
- Tumor Microenvironment/genetics
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Affiliation(s)
- Kennosuke Karube
- Department of Anatomic Pathology, Hospital Clínic, Villarroel 170, 08036 Barcelona, Spain
| | - Lydia Scarfò
- Laboratory of B-cell Neoplasia, Division of Molecular Oncology, San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milano, Italy; Clinical Unit of Lymphoid Malignancies, Department of Onco-Hematology, San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Via Olgettina 60, 20132 Milano, Italy
| | - Elias Campo
- Department of Anatomic Pathology, Hospital Clínic, Villarroel 170, 08036 Barcelona, Spain.
| | - Paolo Ghia
- Laboratory of B-cell Neoplasia, Division of Molecular Oncology, San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milano, Italy; Clinical Unit of Lymphoid Malignancies, Department of Onco-Hematology, San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Via Olgettina 60, 20132 Milano, Italy
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47
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Characterization of IGH locus breakpoints in multiple myeloma indicates a subset of translocations appear to occur in pregerminal center B cells. Blood 2013; 121:3413-9. [DOI: 10.1182/blood-2012-12-471888] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Key Points
IGH translocations in myeloma can occur through at least 5 mechanisms. t(11;14) and t(14;20) DH-JH rearrangement-mediated translocations occur indicating these appear to occur in a pregerminal center cell.
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48
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Burmeister T, Molkentin M, Schwartz S, Gökbuget N, Hoelzer D, Thiel E, Reinhardt R. Erroneous class switching and false VDJ recombination: molecular dissection of t(8;14)/MYC-IGH translocations in Burkitt-type lymphoblastic leukemia/B-cell lymphoma. Mol Oncol 2013; 7:850-8. [PMID: 23673335 DOI: 10.1016/j.molonc.2013.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/04/2013] [Accepted: 04/16/2013] [Indexed: 12/30/2022] Open
Abstract
The chromosomal translocation t(8;14)(q24;q32) with juxtaposition of MYC to enhancer elements in the immunoglobulin heavy chain (IGH) gene locus is the genetic hallmark of the majority of Burkitt lymphoma and a subset of Diffuse large B-cell lymphoma patients. Around 3% of adult B-lineage acute lymphoblastic leukemia (ALL) patients show this aberration. Flow cytometry mostly reveals a "mature B-ALL" or "Burkitt-type" ALL immunophenotype. Using long-distance PCR for t(8;14)/MYC-IGH fusion, we investigated bone marrow, peripheral blood and a few other samples with suspected Burkitt-ALL or mature B-ALL and identified 133 MYC-IGH-positive cases. The location of the chromosomal breaks in the IGH joining and the 8 different switch regions was determined using a set of long-distance PCRs. The chromosomal breakpoints with the adjacent MYC regions on 8q24 were characterized by direct sequencing in 49 cases. The distribution of chromosomal breaks among the IGH joining and switch regions was the following: JH 23.3%, M 21.8%, G1 15.0%, G2 7.5%, G3 3.8%, G4 4.5%, A1 12.8%, A2 3.8%, E 7.5%. Two breakpoint clusters near MYC were delineated. There was no clear correlation between the degree of somatic hypermutation and the chromosomal break locations. Epstein Barr virus was detected in 5 cases (4%). This detailed and extensive molecular analysis illustrates the molecular complexity of the MYC-IGH translocations and the detected distribution of breakpoints provides additional evidence that this translocation results from failed switch and VDJ recombinations. This study may serve as a model for the analysis of other IGH translocations in B-cell lymphoma.
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Affiliation(s)
- Thomas Burmeister
- Charité, Med. Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany.
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49
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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.
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50
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Both CpG methylation and activation-induced deaminase are required for the fragility of the human bcl-2 major breakpoint region: implications for the timing of the breaks in the t(14;18) translocation. Mol Cell Biol 2012; 33:947-57. [PMID: 23263985 DOI: 10.1128/mcb.01436-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The t(14;18) chromosomal translocation typically involves breakage at the bcl-2 major breakpoint region (MBR) to cause human follicular lymphoma. A theory to explain the striking propensity of the MBR breaks at three CpG clusters within the 175-bp MBR region invoked activation-induced deaminase (AID). In a test of that theory, we used here minichromosomal substrates in human pre-B cell lines. Consistent with the essential elements of the theory, we found that the MBR breakage process is indeed highly dependent on DNA methylation at the CpG sites and highly dependent on the AID enzyme to create lesions at peak locations within the MBR. Interestingly, breakage of the phosphodiester bonds at the AID-initiated MBR lesions is RAG dependent, but, unexpectedly, most are also dependent on Artemis. We found that Artemis is capable of nicking small heteroduplex structures and is even able to nick single-base mismatches. This raises the possibility that activated Artemis, derived from the unjoined D to J(H) DNA ends at the IgH locus on chromosome 14, nicks AID-generated TG mismatches at methyl CpG sites, and this would explain why the breaks at the chromosome 18 MBR occur within the same time window as those on chromosome 14.
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