1
|
de Smith A, Liu T, Xu K, Pardeshi A, Myint SS, Kang A, Morimoto L, Lieber M, Wiemels J, Kogan S, Metayer C. Early-life tobacco exposure is causally implicated in aberrant RAG-mediated recombination in childhood acute lymphoblastic leukemia. RESEARCH SQUARE 2024:rs.3.rs-4510345. [PMID: 38946984 PMCID: PMC11213169 DOI: 10.21203/rs.3.rs-4510345/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, yet few environmental risk factors have been identified. We previously found an association between early-life tobacco smoke exposure and frequency of somatic deletions of 8 leukemia driver genes among childhood ALL patients in the California Childhood Leukemia Study. To expand analysis genome-wide and examine potential mechanisms, we conducted tumor whole-genome sequencing in 35 ALL patients, including 18 with high prenatal tobacco exposure and 17 with low exposure as determined by established epigenetic biomarkers. High tobacco exposure patients had significantly more structural variants (P < .001) and deletions (P = .001) genome-wide than low exposure patients. Investigation of off-target RAG recombination revealed that 41% of deletions in the high tobacco exposure patients were putatively RAG-mediated (full RAG motif identified at one or both breakpoints) compared with only 21% in the low exposure group (P = .001). In a multilevel model, deletions in high tobacco exposure patients were 2.44-fold (95% CI:1.13-5.38) more likely to be putatively RAG-mediated than deletions in low exposure patients. No point mutational signatures were associated with prenatal tobacco exposure. Our findings suggest that early-life tobacco smoke exposure may promote leukemogenesis by driving development of somatic deletions in pre-leukemic lymphocytes via off-target RAG recombination.
Collapse
Affiliation(s)
| | | | - Keren Xu
- University of Southern California
| | | | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | | | | | - Michael Lieber
- Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine
| | | | | | | |
Collapse
|
2
|
Ogana HA, Hurwitz S, Hsieh CL, Geng H, Müschen M, Bhojwani D, Wolf MA, Larocque J, Lieber MR, Kim YM. Artemis inhibition as a therapeutic strategy for acute lymphoblastic leukemia. Front Cell Dev Biol 2023; 11:1134121. [PMID: 37082620 PMCID: PMC10111164 DOI: 10.3389/fcell.2023.1134121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
As effective therapies for relapse and refractory B-cell acute lymphoblastic leukemia (B-ALL) remain problematic, novel therapeutic strategies are needed. Artemis is a key endonuclease in V(D)J recombination and nonhomologous end joining (NHEJ) of DNA double-strand break (DSB) repair. Inhibition of Artemis would cause chromosome breaks during maturation of RAG-expressing T- and B-cells. Though this would block generation of new B- and T-cells temporarily, it could be oncologically beneficial for reducing the proliferation of B-ALL and T-ALL cells by causing chromosome breaks in these RAG-expressing tumor cells. Currently, pharmacological inhibition is not available for Artemis. According to gene expression analyses from 207 children with high-risk pre-B acute lymphoblastic leukemias high Artemis expression is correlated with poor outcome. Therefore, we evaluated four compounds (827171, 827032, 826941, and 825226), previously generated from a large Artemis targeted drug screen. A biochemical assay using a purified Artemis:DNA-PKcs complex shows that the Artemis inhibitors 827171, 827032, 826941, 825226 have nanomolar IC50 values for Artemis inhibition. We compared these 4 compounds to a DNA-PK inhibitor (AZD7648) in three patient-derived B-ALL cell lines (LAX56, BLQ5 and LAX7R) and in two mature B-cell lines (3301015 and 5680001) as controls. We found that pharmacological Artemis inhibition substantially decreases proliferation of B-ALL cell lines while normal mature B-cell lines are not markedly affected. Inhibition of DNA-PKcs (which regulates Artemis) using the DNA-PK inhibitor AZD7648 had minor effects on these same primary patient-derived ALL lines, indicating that inhibition of V(D)J hairpin opening requires direct inhibition of Artemis, rather than indirect suppression of the kinase that regulates Artemis. Our data provides a basis for further evaluation of pharmacological Artemis inhibition of proliferation of B- and T-ALL.
Collapse
Affiliation(s)
- Heather A. Ogana
- Department of Pediatrics, Children’s Hospital Los Angeles, Division of Hematology and Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Samantha Hurwitz
- Department of Pediatrics, Children’s Hospital Los Angeles, Division of Hematology and Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Chih-Lin Hsieh
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Huimin Geng
- Department of Laboratory Medicine, UCSF, San Francisco, CA, United States
| | - Markus Müschen
- Department of Immunobiology, Center of Molecular and Cellular Oncology, Yale University, New Haven, CT, United States
| | - Deepa Bhojwani
- Department of Pediatrics, Children’s Hospital Los Angeles, Division of Hematology and Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | | | | | - Michael R. Lieber
- Departments of Pathology, The Molecular and Computational Biology Section of the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Yong Mi Kim
- Department of Pediatrics, Children’s Hospital Los Angeles, Division of Hematology and Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
3
|
Bolland DJ, Koohy H, Wood AL, Matheson LS, Krueger F, Stubbington MJT, Baizan-Edge A, Chovanec P, Stubbs BA, Tabbada K, Andrews SR, Spivakov M, Corcoran AE. Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination. Cell Rep 2016; 15:2475-87. [PMID: 27264181 PMCID: PMC4914699 DOI: 10.1016/j.celrep.2016.05.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/01/2016] [Accepted: 05/02/2016] [Indexed: 12/02/2022] Open
Abstract
Variable (V), diversity (D), and joining (J) (V(D)J) recombination is the first determinant of antigen receptor diversity. Understanding how recombination is regulated requires a comprehensive, unbiased readout of V gene usage. We have developed VDJ sequencing (VDJ-seq), a DNA-based next-generation-sequencing technique that quantitatively profiles recombination products. We reveal a 200-fold range of recombination efficiency among recombining V genes in the primary mouse Igh repertoire. We used machine learning to integrate these data with local chromatin profiles to identify combinatorial patterns of epigenetic features that associate with active VH gene recombination. These features localize downstream of VH genes and are excised by recombination, revealing a class of cis-regulatory element that governs recombination, distinct from expression. We detect two mutually exclusive chromatin signatures at these elements, characterized by CTCF/RAD21 and PAX5/IRF4, which segregate with the evolutionary history of associated VH genes. Thus, local chromatin signatures downstream of VH genes provide an essential layer of regulation that determines recombination efficiency. VDJ-seq enables precise quantification of antibody V(D)J recombination products Two distinct cis-regulatory designs characterize actively recombining V genes Putative recombination regulatory elements map downstream of mouse Igh V genes Recombination regulatory architecture reflects the V genes’ evolutionary history
Collapse
Affiliation(s)
- Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Hashem Koohy
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Andrew L Wood
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michael J T Stubbington
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Amanda Baizan-Edge
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Peter Chovanec
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Bryony A Stubbs
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Kristina Tabbada
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Simon R Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
| |
Collapse
|
4
|
Byrum JN, Zhao S, Rahman NS, Gwyn LM, Rodgers W, Rodgers KK. An interdomain boundary in RAG1 facilitates cooperative binding to RAG2 in formation of the V(D)J recombinase complex. Protein Sci 2015; 24:861-73. [PMID: 25676158 DOI: 10.1002/pro.2660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 11/09/2022]
Abstract
V(D)J recombination assembles functional antigen receptor genes during lymphocyte development. Formation of the recombination complex containing the recombination activating proteins, RAG1 and RAG2, is essential for the site-specific DNA cleavage steps in V(D)J recombination. However, little is known concerning how complex formation leads to a catalytically-active complex. Here, we combined limited proteolysis and mass spectrometry methods to identify regions of RAG1 that are sequestered upon association with RAG2. These results show that RAG2 bridges an interdomain boundary in the catalytic region of RAG1. In a second approach, mutation of RAG1 residues within the interdomain boundary were tested for disruption of RAG1:RAG2 complex formation using fluorescence-based pull down assays. The core RAG1 mutants demonstrated varying effects on complex formation with RAG2. Interestingly, two mutants showed opposing results for the ability to interact with core versus full length RAG2, indicating that the non-core region of RAG2 participates in binding to core RAG1. Significantly, all of the RAG1 interdomain mutants demonstrated altered stoichiometries of the RAG complexes, with an increased number of RAG2 per RAG1 subunit compared to the wild type complex. Based on our results, we propose that interaction of RAG2 with RAG1 induces cooperative interactions of multiple binding sites, induced through conformational changes at the RAG1 interdomain boundary, and resulting in formation of the DNA cleavage active site.
Collapse
Affiliation(s)
- Jennifer N Byrum
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73190
| | | | | | | | | | | |
Collapse
|
5
|
An autoregulatory mechanism imposes allosteric control on the V(D)J recombinase by histone H3 methylation. Cell Rep 2014; 10:29-38. [PMID: 25543141 DOI: 10.1016/j.celrep.2014.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 09/29/2014] [Accepted: 11/25/2014] [Indexed: 01/15/2023] Open
Abstract
V(D)J recombination is initiated by a specialized transposase consisting of the subunits RAG-1 and RAG-2. The susceptibility of gene segments to DNA cleavage by the V(D)J recombinase is correlated with epigenetic modifications characteristic of active chromatin, including trimethylation of histone H3 on lysine 4 (H3K4me3). Engagement of H3K4me3 by a plant homeodomain (PHD) in RAG-2 promotes recombination in vivo and stimulates DNA cleavage by RAG in vitro. We now show that H3K4me3 acts allosterically at the PHD finger to relieve autoinhibition imposed by a separate domain within RAG-2. Disruption of this autoinhibitory domain was associated with constitutive increases in recombination frequency, DNA cleavage activity, substrate binding affinity, and catalytic rate, thus mimicking the stimulatory effects of H3K4me3. Our observations support a model in which allosteric control of RAG is enforced by an autoinhibitory domain whose action is relieved by engagement of active chromatin.
Collapse
|
6
|
Shimazaki N, Lieber MR. Histone methylation and V(D)J recombination. Int J Hematol 2014; 100:230-7. [PMID: 25060705 DOI: 10.1007/s12185-014-1637-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/08/2014] [Accepted: 07/08/2014] [Indexed: 01/27/2023]
Abstract
V(D)J recombination is the process by which the diversity of antigen receptor genes is generated and is also indispensable for lymphocyte development. This recombination event occurs in a cell lineage- and stage-specific manner, and is carefully controlled by chromatin structure and ordered histone modifications. The recombinationally active V(D)J loci are associated with hypermethylation at lysine4 of histone H3 and hyperacetylation of histones H3/H4. The recombination activating gene 1 (RAG1) and RAG2 complex initiates recombination by introducing double-strand DNA breaks at recombination signal sequences (RSS) adjacent to each coding sequence. To be recognized by the RAG complex, RSS sites must be within an open chromatin context. In addition, the RAG complex specifically recognizes hypermethylated H3K4 through its plant homeodomain (PHD) finger in the RAG2 C terminus, which stimulates RAG catalytic activity via that interaction. In this review, we describe how histone methylation controls V(D)J recombination and discuss its potential role in lymphoid malignancy by mistargeting the RAG complex.
Collapse
Affiliation(s)
- Noriko Shimazaki
- Section of Molecular and Computational Biology, Departments of Pathology, Biochemistry and Molecular Biology, Molecular Microbiology and Immunology, USC Norris Comprehensive Cancer Ctr., Rm. 5428, 1441 Eastlake Ave., MC 9176, Los Angeles, CA, 90089-9176, USA,
| | | |
Collapse
|
7
|
Modeling of the RAG reaction mechanism. Cell Rep 2014; 7:307-315. [PMID: 24703851 DOI: 10.1016/j.celrep.2014.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/18/2013] [Accepted: 03/03/2014] [Indexed: 11/24/2022] Open
Abstract
In vertebrate V(D)J recombination, it remains unclear how the RAG complex coordinates its catalytic steps with binding to two distant recombination sites. Here, we test the ability of the plausible reaction schemes to fit observed time courses for RAG nicking and DNA hairpin formation. The reaction schemes with the best fitting capability (1) strongly favor a RAG tetrameric complex over a RAG octameric complex; (2) indicate that once a RAG complex brings two recombination signal sequence (RSS) sites into synapsis, the synaptic complex rarely disassembles; (3) predict that the binding of both RSS sites (synapsis) occurs before catalysis (nicking); and (4) show that the RAG binding properties permit strong distinction between RSS sites within active chromatin versus nonspecific DNA or RSS sites within inactive chromatin. The results provide general insights for synapsis by nuclear proteins as well as more specific testable predictions for the RAG proteins.
Collapse
|
8
|
Wang G, Dhar K, Swanson PC, Levitus M, Chang Y. Real-time monitoring of RAG-catalyzed DNA cleavage unveils dynamic changes in coding end association with the coding end complex. Nucleic Acids Res 2012; 40:6082-96. [PMID: 22434887 PMCID: PMC3401440 DOI: 10.1093/nar/gks255] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
During V(D)J recombination, the RAG1/2 recombinase is thought to play an active role in transferring newly excised recombination ends from the RAG post-cleavage complex (PCC) to the non-homologous end joining (NHEJ) machinery to promote appropriate antigen receptor gene assembly. However, this transfer mechanism is poorly understood, partly because of the technical difficulty in revealing weak association of coding ends (CEs) with one of the PCCs, coding end complex (CEC). Using fluorescence resonance energy transfer (FRET) and anisotropy measurement, we present here real-time monitoring of the RAG1/2-catalyzed cleavage reaction, and provide unequivocal evidence that CEs are retained within the CEC in the presence of Mg(2+). By examining the dynamic fluorescence changes during the cleavage reaction, we compared the stability of CEC assembled with core RAG1 paired with full-length RAG2, core RAG2 or a frameshift RAG2 mutant that was speculated to destabilize the PCC, leading to increased aberrant joining. While the latter two CECs exhibit similar stability, the full-length RAG2 renders a less stable CEC unless H3K4me3 peptides are added. Interestingly, the RAG2 mutant appears to modulate the structure of the RAG-12RSS pre-cleavage complex. Thus, the fluorescence-based detection offers a sensitive, quantitative and continuous assessment of pre-cleavage complex assembly and CEC stability.
Collapse
Affiliation(s)
- Guannan Wang
- Center of Infectious Disease and Vaccinology, The Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | | | | | | | | |
Collapse
|