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Rangel V, Sterrenberg JN, Garawi A, Mezcord V, Folkerts ML, Calderon SE, Garcia YE, Wang J, Soyfer EM, Eng OS, Valerin JB, Tanjasiri SP, Quintero-Rivera F, Seldin MM, Masri S, Frock RL, Fleischman AG, Pannunzio NR. Increased AID results in mutations at the CRLF2 locus implicated in Latin American ALL health disparities. Nat Commun 2024; 15:6331. [PMID: 39068148 PMCID: PMC11283463 DOI: 10.1038/s41467-024-50537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/10/2024] [Indexed: 07/30/2024] Open
Abstract
Activation-induced cytidine deaminase (AID) is a B cell-specific mutator required for antibody diversification. However, it is also implicated in the etiology of several B cell malignancies. Evaluating the AID-induced mutation load in patients at-risk for certain blood cancers is critical in assessing disease severity and treatment options. We have developed a digital PCR (dPCR) assay that allows us to quantify mutations resulting from AID modification or DNA double-strand break (DSB) formation and repair at sites known to be prone to DSBs. Implementation of this assay shows that increased AID levels in immature B cells increase genome instability at loci linked to chromosomal translocation formation. This includes the CRLF2 locus that is often involved in translocations associated with a subtype of acute lymphoblastic leukemia (ALL) that disproportionately affects Hispanics, particularly those with Latin American ancestry. Using dPCR, we characterize the CRLF2 locus in B cell-derived genomic DNA from both Hispanic ALL patients and healthy Hispanic donors and found increased mutations in both, suggesting that vulnerability to DNA damage at CRLF2 may be driving this health disparity. Our ability to detect and quantify these mutations will potentiate future risk identification, early detection of cancers, and reduction of associated cancer health disparities.
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Affiliation(s)
- Valeria Rangel
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Jason N Sterrenberg
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Aya Garawi
- School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Vyanka Mezcord
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA, USA
| | - Melissa L Folkerts
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Sabrina E Calderon
- School of Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Yadhira E Garcia
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Jinglong Wang
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eli M Soyfer
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Oliver S Eng
- Division of Surgical Oncology, Department of Surgery, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Jennifer B Valerin
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Sora Park Tanjasiri
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
- Department of Health, Society and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA
- Department of Pediatrics, University of California, Irvine, Irvine, CA, USA
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Selma Masri
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Richard L Frock
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela G Fleischman
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Nicholas R Pannunzio
- Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, Irvine, CA, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA.
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Liu D, Hsieh CL, Lieber MR. The RNA tether model for human chromosomal translocation fragile zones. Trends Biochem Sci 2024; 49:391-400. [PMID: 38490833 PMCID: PMC11069435 DOI: 10.1016/j.tibs.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
One of the two chromosomal breakage events in recurring translocations in B cell neoplasms is often due to the recombination-activating gene complex (RAG complex) releasing DNA ends before end joining. The other break occurs in a fragile zone of 20-600 bp in a non-antigen receptor gene locus, with a more complex and intriguing set of mechanistic factors underlying such narrow fragile zones. These factors include activation-induced deaminase (AID), which acts only at regions of single-stranded DNA (ssDNA). Recent work leads to a model involving the tethering of AID to the nascent RNA as it emerges from the RNA polymerase. This mechanism may have relevance in class switch recombination (CSR) and somatic hypermutation (SHM), as well as broader relevance for other DNA enzymes.
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Affiliation(s)
- Di Liu
- Institute of Molecular and Translational Medicine (IMTM), and Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, and Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Center, Department of Urology, University of Southern California, Los Angeles, CA 90089-9176, USA
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Center, Departments of Pathology and Laboratory Medicine, of Molecular Microbiology and Immunology, of Biochemistry and Molecular Medicine, and in the Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-9176, USA.
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3
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Lauring MC, Basu U. Somatic hypermutation mechanisms during lymphomagenesis and transformation. Curr Opin Genet Dev 2024; 85:102165. [PMID: 38428317 DOI: 10.1016/j.gde.2024.102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
B cells undergoing physiologically programmed or aberrant genomic alterations provide an opportune system to study the causes and consequences of genome mutagenesis. Activated B cells in germinal centers express activation-induced cytidine deaminase (AID) to accomplish physiological somatic hypermutation (SHM) of their antibody-encoding genes. In attempting to diversify their immunoglobulin (Ig) heavy- and light-chain genes, several B-cell clones successfully optimize their antigen-binding affinities. However, SHM can sometimes occur at non-Ig loci, causing genetic alternations that lay the foundation for lymphomagenesis, particularly diffuse large B-cell lymphoma. Thus, SHM acts as a double-edged sword, bestowing superb humoral immunity at the potential risk of initiating disease. We refer to off-target, non-Ig AID mutations - that are often but not always associated with disease - as aberrant SHM (aSHM). A key challenge in understanding SHM and aSHM is determining how AID targets and mutates specific DNA sequences in the Ig loci to generate antibody diversity and non-Ig genes to initiate lymphomagenesis. Herein, we discuss some current advances regarding the regulation of AID's DNA mutagenesis activity in B cells.
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Affiliation(s)
- Max C Lauring
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
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Wang Y, Meng FL, Yeap LS. DNA flexibility can shape the preferential hypermutation of antibody genes. Trends Immunol 2024; 45:167-176. [PMID: 38402044 DOI: 10.1016/j.it.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/26/2024]
Abstract
Antibody-coding genes accumulate somatic mutations to achieve antibody affinity maturation. Genetic dissection using various mouse models has shown that intrinsic hypermutations occur preferentially and are predisposed in the DNA region encoding antigen-contacting residues. The molecular basis of nonrandom/preferential mutations is a long-sought question in the field. Here, we summarize recent findings on how single-strand (ss)DNA flexibility facilitates activation-induced cytidine deaminase (AID) activity and fine-tunes the mutation rates at a mesoscale within the antibody variable domain exon. We propose that antibody coding sequences are selected based on mutability during the evolution of adaptive immunity and that DNA mechanics play a noncoding role in the genome. The mechanics code may also determine other cellular DNA metabolism processes, which awaits future investigation.
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Affiliation(s)
- Yanyan Wang
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei-Long Meng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Boehm T, Morimoto R, Trancoso I, Aleksandrova N. Genetic conflicts and the origin of self/nonself-discrimination in the vertebrate immune system. Trends Immunol 2023; 44:372-383. [PMID: 36941153 DOI: 10.1016/j.it.2023.02.007] [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: 01/23/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/22/2023]
Abstract
Genetic conflicts shape the genomes of prokaryotic and eukaryotic organisms. Here, we argue that some of the key evolutionary novelties of adaptive immune systems of vertebrates are descendants of prokaryotic toxin-antitoxin (TA) systems. Cytidine deaminases and RAG recombinase have evolved from genotoxic enzymes to programmable editors of host genomes, supporting the astounding discriminatory capability of variable lymphocyte receptors of jawless vertebrates, as well as immunoglobulins and T cell receptors of jawed vertebrates. The evolutionarily recent lymphoid lineage is uniquely sensitive to mutations of the DNA maintenance methylase, which is an orphaned distant relative of prokaryotic restriction-modification systems. We discuss how the emergence of adaptive immunity gave rise to higher order genetic conflicts between genetic parasites and their vertebrate host.
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Affiliation(s)
- Thomas Boehm
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Ryo Morimoto
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Inês Trancoso
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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Zhao H, Hartono SR, de Vera KMF, Yu Z, Satchi K, Zhao T, Sciammas R, Sanz L, Chédin F, Barlow J. Senataxin and RNase H2 act redundantly to suppress genome instability during class switch recombination. eLife 2022; 11:e78917. [PMID: 36542058 PMCID: PMC9771370 DOI: 10.7554/elife.78917] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Class switch recombination generates distinct antibody isotypes critical to a robust adaptive immune system, and defects are associated with autoimmune disorders and lymphomagenesis. Transcription is required during class switch recombination to recruit the cytidine deaminase AID-an essential step for the formation of DNA double-strand breaks-and strongly induces the formation of R loops within the immunoglobulin heavy-chain locus. However, the impact of R loops on double-strand break formation and repair during class switch recombination remains unclear. Here, we report that cells lacking two enzymes involved in R loop removal-senataxin and RNase H2-exhibit increased R loop formation and genome instability at the immunoglobulin heavy-chain locus without impacting its transcriptional activity, AID recruitment, or class switch recombination efficiency. Senataxin and RNase H2-deficient cells also exhibit increased insertion mutations at switch junctions, a hallmark of alternative end joining. Importantly, these phenotypes were not observed in cells lacking senataxin or RNase H2B alone. We propose that senataxin acts redundantly with RNase H2 to mediate timely R loop removal, promoting efficient repair while suppressing AID-dependent genome instability and insertional mutagenesis.
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Affiliation(s)
- Hongchang Zhao
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | | | - Zheyuan Yu
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
- Graduate Group in Biostatistics, University of California, DavisDavisUnited States
| | - Krishni Satchi
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Tracy Zhao
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California, DavisDavisUnited States
| | - Lionel Sanz
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Jacqueline Barlow
- Department of Microbiology and Molecular Genetics, University of California, DavisDavisUnited States
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