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Hao Q, Li J, Yeap LS. Molecular mechanisms of DNA lesion and repair during antibody somatic hypermutation. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2615-1. [PMID: 39048716 DOI: 10.1007/s11427-024-2615-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/08/2024] [Indexed: 07/27/2024]
Abstract
Antibody diversification is essential for an effective immune response, with somatic hypermutation (SHM) serving as a key molecular process in this adaptation. Activation-induced cytidine deaminase (AID) initiates SHM by inducing DNA lesions, which are ultimately resolved into point mutations, as well as small insertions and deletions (indels). These mutational outcomes contribute to antibody affinity maturation. The mechanisms responsible for generating point mutations and indels involve the base excision repair (BER) and mismatch repair (MMR) pathways, which are well coordinated to maintain genomic integrity while allowing for beneficial mutations to occur. In this regard, translesion synthesis (TLS) polymerases contribute to the diversity of mutational outcomes in antibody genes by enabling the bypass of DNA lesions. This review summarizes our current understanding of the distinct molecular mechanisms that generate point mutations and indels during SHM. Understanding these mechanisms is critical for elucidating the development of broadly neutralizing antibodies (bnAbs) and autoantibodies, and has implications for vaccine design and therapeutics.
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Affiliation(s)
- Qian Hao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jinfeng Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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2
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Kadyrova LY, Mieczkowski PA, Kadyrov FA. MutLα suppresses error-prone DNA mismatch repair and preferentially protects noncoding DNA from mutations. J Biol Chem 2024; 300:107406. [PMID: 38782208 PMCID: PMC11231602 DOI: 10.1016/j.jbc.2024.107406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
The DNA mismatch repair (MMR) system promotes genome stability and protects humans from certain types of cancer. Its primary function is the correction of DNA polymerase errors. MutLα is an important eukaryotic MMR factor. We have examined the contributions of MutLα to maintaining genome stability. We show here that loss of MutLα in yeast increases the genome-wide mutation rate by ∼130-fold and generates a genome-wide mutation spectrum that consists of small indels and base substitutions. We also show that loss of yeast MutLα leads to error-prone MMR that produces T > C base substitutions in 5'-ATA-3' sequences. In agreement with this finding, our examination of human whole-genome DNA sequencing data has revealed that loss of MutLα in induced pluripotent stem cells triggers error-prone MMR that leads to the formation of T > C mutations in 5'-NTN-3' sequences. Our further analysis has shown that MutLα-independent MMR plays a role in suppressing base substitutions in N3 homopolymeric runs. In addition, we describe that MutLα preferentially protects noncoding DNA from mutations. Our study defines the contributions of MutLα-dependent and independent mechanisms to genome-wide MMR.
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Affiliation(s)
- Lyudmila Y Kadyrova
- Division of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Farid A Kadyrov
- Division of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Southern Illinois University School of Medicine, Carbondale, Illinois, USA.
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3
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van Heyningen V. Stochasticity in genetics and gene regulation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230476. [PMID: 38432316 PMCID: PMC10909507 DOI: 10.1098/rstb.2023.0476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/20/2023] [Indexed: 03/05/2024] Open
Abstract
Development from fertilized egg to functioning multi-cellular organism requires precision. There is no precision, and often no survival, without plasticity. Plasticity is conferred partly by stochastic variation, present inherently in all biological systems. Gene expression levels fluctuate ubiquitously through transcription, alternative splicing, translation and turnover. Small differences in gene expression are exploited to trigger early differentiation, conferring distinct function on selected individual cells and setting in motion regulatory interactions. Non-selected cells then acquire new functions along the spatio-temporal developmental trajectory. The differentiation process has many stochastic components. Meiotic segregation, mitochondrial partitioning, X-inactivation and the dynamic DNA binding of transcription factor assemblies-all exhibit randomness. Non-random X-inactivation generally signals deleterious X-linked mutations. Correct neural wiring, such as retina to brain, arises through repeated confirmatory activity of connections made randomly. In immune system development, both B-cell antibody generation and the emergence of balanced T-cell categories begin through stochastic trial and error followed by functional selection. Aberrant selection processes lead to immune dysfunction. DNA sequence variants also arise through stochastic events: some involving environmental fluctuation (radiation or presence of pollutants), or genetic repair system malfunction. The phenotypic outcome of mutations is also fluid. Mutations may be advantageous in some circumstances, deleterious in others. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Veronica van Heyningen
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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4
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Kadyrova LY, Mieczkowski PA, Kadyrov FA. MutLα suppresses error-prone DNA mismatch repair and preferentially protects noncoding DNA from mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587563. [PMID: 38617288 PMCID: PMC11014525 DOI: 10.1101/2024.04.01.587563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The DNA mismatch repair (MMR) system promotes genome stability and protects humans from certain types of cancer. Its primary function is the correction of DNA polymerase errors. MutLα is an important eukaryotic MMR factor. We have examined the contributions of MutLα to maintaining genome stability. We show here that loss of MutLα in yeast increases the genome-wide mutation rate by ~130-fold and generates a genome-wide mutation spectrum that consists of small indels and base substitutions. We also show that loss of yeast MutLα leads to error-prone MMR that produces T>C base substitutions in 5'-ATA-3' sequences. In agreement with this finding, our examination of human whole genome DNA sequencing data has revealed that loss of MutLα in induced pluripotent stem cells triggers error-prone MMR that leads to the formation of T>C mutations in 5'-NTN-3' sequences. Our further analysis has shown that MutLα-independent MMR plays a role in suppressing base substitutions in N3 homopolymeric runs. In addition, we describe that MutLα preferentially defends noncoding DNA from mutations. Our study defines the contributions of MutLα-dependent and independent mechanisms to genome-wide MMR.
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Affiliation(s)
- Lyudmila Y. Kadyrova
- Division of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Piotr A. Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Farid A. Kadyrov
- Division of Biochemistry and Molecular Biology, Department of Biomedical Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
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5
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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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6
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Benitez-Cantos MS, Cano C, Cuadros M, Medina PP. Activation-induced cytidine deaminase causes recurrent splicing mutations in diffuse large B-cell lymphoma. Mol Cancer 2024; 23:42. [PMID: 38402205 PMCID: PMC10893679 DOI: 10.1186/s12943-024-01960-w] [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] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma. A major mutagenic process in DLBCL is aberrant somatic hypermutation (aSHM) by activation-induced cytidine deaminase (AID), which occurs preferentially at RCH/TW sequence motifs proximal to transcription start sites. Splice sequences are highly conserved, rich in RCH/TW motifs, and recurrently mutated in DLBCL. Therefore, we hypothesized that aSHM may cause recurrent splicing mutations in DLBCL. In a meta-cohort of > 1,800 DLBCLs, we found that 77.5% of splicing mutations in 29 recurrently mutated genes followed aSHM patterns. In addition, in whole-genome sequencing (WGS) data from 153 DLBCLs, proximal mutations in splice sequences, especially in donors, were significantly enriched in RCH/TW motifs (p < 0.01). We validated this enrichment in two additional DLBCL cohorts (N > 2,000; p < 0.0001) and confirmed its absence in 12 cancer types without aSHM (N > 6,300). Comparing sequencing data from mouse models with and without AID activity showed that the splice donor sequences were the top genomic feature enriched in AID-induced mutations (p < 0.0001). Finally, we observed that most AID-related splice site mutations are clonal within a sample, indicating that aSHM may cause early loss-of-function events in lymphomagenesis. Overall, these findings support that AID causes an overrepresentation of clonal splicing mutations in DLBCL.
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Affiliation(s)
- Maria S Benitez-Cantos
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, Granada, 18016, Spain
| | - Carlos Cano
- Department of Computer Science and Artificial Intelligence, School of Computer and Telecommunication Engineering, University of Granada, Calle Periodista Daniel Saucedo Aranda s/n, Granada, 18014, Spain
| | - Marta Cuadros
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, Granada, 18016, Spain
| | - Pedro P Medina
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain.
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain.
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Avenida de Fuentenueva s/n, Granada, 18071, Spain.
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7
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Fu ZH, He SZ, Wu Y, Zhao GR. Design and deep learning of synthetic B-cell-specific promoters. Nucleic Acids Res 2023; 51:11967-11979. [PMID: 37889080 PMCID: PMC10681721 DOI: 10.1093/nar/gkad930] [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: 05/27/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Synthetic biology and deep learning synergistically revolutionize our ability for decoding and recoding DNA regulatory grammar. The B-cell-specific transcriptional regulation is intricate, and unlock the potential of B-cell-specific promoters as synthetic elements is important for B-cell engineering. Here, we designed and pooled synthesized 23 640 B-cell-specific promoters that exhibit larger sequence space, B-cell-specific expression, and enable diverse transcriptional patterns in B-cells. By MPRA (Massively parallel reporter assays), we deciphered the sequence features that regulate promoter transcriptional, including motifs and motif syntax (their combination and distance). Finally, we built and trained a deep learning model capable of predicting the transcriptional strength of the immunoglobulin V gene promoter directly from sequence. Prediction of thousands of promoter variants identified in the global human population shows that polymorphisms in promoters influence the transcription of immunoglobulin V genes, which may contribute to individual differences in adaptive humoral immune responses. Our work helps to decipher the transcription mechanism in immunoglobulin genes and offers thousands of non-similar promoters for B-cell engineering.
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Affiliation(s)
- Zong-Heng Fu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Si-Zhe He
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Guang-Rong Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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8
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Huang ZR, Chen XR, Liu DF, Cui YZ, Li BZ, Yuan YJ. Enhanced single-base mutation diversity by the combination of cytidine deaminase with DNA-repairing enzymes in yeast. Biotechnol J 2023; 18:e2300137. [PMID: 37529889 DOI: 10.1002/biot.202300137] [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: 03/26/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/03/2023]
Abstract
The occurrence of random mutations can increase the diversity of the genome and promote the evolutionary process of organisms. High efficiency mutagenesis techniques significantly accelerate the evolutionary process. In this work, we describe a targeted mutagenesis system named MutaT7trans to significantly increase mutation rate and generate mutations across all four nucleotides in yeast. We constructed different DNA-repairing enzyme-PmCDA1-T7 RNA polymerase (T7 RNAP) fusion proteins, achieved targeted mutagenesis by flanking the target gene with T7 promoters, and tuned the mutation spectra by introducing different DNA-repairing enzymes. With this mutagenesis tool, the proportion of non-C → T mutations was 10-11-fold higher than the cytidine deaminase-based evolutionary tools, and the transversion mutation frequency was also elevated. The mutation rate of the target gene was significantly increased to 5.25 × 10-3 substitutions per base (s. p. b.). We also demonstrated that MutaT7trans could be used to evolve the CrtE, CrtI, and CrtYB gene in the β-carotene biosynthesis process and generate different types of mutations.
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Affiliation(s)
- Zi-Rui Huang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Xiang-Rong Chen
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Dan-Feng Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - You-Zhi Cui
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
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9
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Hao Q, Zhan C, Lian C, Luo S, Cao W, Wang B, Xie X, Ye X, Gui T, Voena C, Pighi C, Wang Y, Tian Y, Wang X, Dai P, Cai Y, Liu X, Ouyang S, Sun S, Hu Q, Liu J, Ye Y, Zhao J, Lu A, Wang JY, Huang C, Su B, Meng FL, Chiarle R, Pan-Hammarström Q, Yeap LS. DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification. Sci Immunol 2023; 8:eade1167. [PMID: 36961908 PMCID: PMC10351598 DOI: 10.1126/sciimmunol.ade1167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023]
Abstract
Insertions and deletions (indels) are low-frequency deleterious genomic DNA alterations. Despite their rarity, indels are common, and insertions leading to long complementarity-determining region 3 (CDR3) are vital for antigen-binding functions in broadly neutralizing and polyreactive antibodies targeting viruses. Because of challenges in detecting indels, the mechanism that generates indels during immunoglobulin diversification processes remains poorly understood. We carried out ultra-deep profiling of indels and systematically dissected the underlying mechanisms using passenger-immunoglobulin mouse models. We found that activation-induced cytidine deaminase-dependent ±1-base pair (bp) indels are the most prevalent indel events, biasing deleterious outcomes, whereas longer in-frame indels, especially insertions that can extend the CDR3 length, are rare outcomes. The ±1-bp indels are channeled by base excision repair, but longer indels require additional DNA-processing factors. Ectopic expression of a DNA exonuclease or perturbation of the balance of DNA polymerases can increase the frequency of longer indels, thus paving the way for models that can generate antibodies with long CDR3. Our study reveals the mechanisms that generate beneficial and deleterious indels during the process of antibody somatic hypermutation and has implications in understanding the detrimental genomic alterations in various conditions, including tumorigenesis.
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Affiliation(s)
- Qian Hao
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chuanzong Zhan
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chaoyang Lian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Simin Luo
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Wenyi Cao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Binbin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
- Present address: Kindstar Global Precision Medicine Institute, Wuhan, China and Kindstar Biotech, Wuhan, China
| | - Tuantuan Gui
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
| | - Chiara Pighi
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Yanyan Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Ying Tian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Shengqun Ouyang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Shiqi Sun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Qianwen Hu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jun Liu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jingkun Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Aiguo Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ji-Yang Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Departments of Endocrinology and Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
| | - Leng-Siew Yeap
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
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10
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Pancotti C, Rollo C, Birolo G, Benevenuta S, Fariselli P, Sanavia T. Unravelling the instability of mutational signatures extraction via archetypal analysis. Front Genet 2023; 13:1049501. [PMID: 36685831 PMCID: PMC9846778 DOI: 10.3389/fgene.2022.1049501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
The high cosine similarity between some single-base substitution mutational signatures and their characteristic flat profiles could suggest the presence of overfitting and mathematical artefacts. The newest version (v3.3) of the signature database available in the Catalogue Of Somatic Mutations In Cancer (COSMIC) provides a collection of 79 mutational signatures, which has more than doubled with respect to previous version (30 profiles available in COSMIC signatures v2), making more critical the associations between signatures and specific mutagenic processes. This study both provides a systematic assessment of the de novo extraction task through simulation scenarios based on the latest version of the COSMIC signatures and highlights, through a novel approach using archetypal analysis, which COSMIC signatures are redundant and more likely to be considered as mathematical artefacts. 29 archetypes were able to reconstruct the profile of all the COSMIC signatures with cosine similarity > 0.8. Interestingly, these archetypes tend to group similar original signatures sharing either the same aetiology or similar biological processes. We believe that these findings will be useful to encourage the development of new de novo extraction methods avoiding the redundancy of information among the signatures while preserving the biological interpretation.
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11
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Leung W, Teater M, Durmaz C, Meydan C, Chivu AG, Chadburn A, Rice EJ, Muley A, Camarillo JM, Arivalagan J, Li Z, Flowers CR, Kelleher NL, Danko CG, Imielinski M, Dave SS, Armstrong SA, Mason CE, Melnick AM. SETD2 Haploinsufficiency Enhances Germinal Center-Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis. Cancer Discov 2022; 12:1782-1803. [PMID: 35443279 PMCID: PMC9262862 DOI: 10.1158/2159-8290.cd-21-1514] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/08/2022] [Accepted: 04/18/2022] [Indexed: 01/26/2023]
Abstract
SETD2 is the sole histone methyltransferase responsible for H3K36me3, with roles in splicing, transcription initiation, and DNA damage response. Homozygous disruption of SETD2 yields a tumor suppressor effect in various cancers. However, SETD2 mutation is typically heterozygous in diffuse large B-cell lymphomas. Here we show that heterozygous Setd2 deficiency results in germinal center (GC) hyperplasia and increased competitive fitness, with reduced DNA damage checkpoint activity and apoptosis, resulting in accelerated lymphomagenesis. Impaired DNA damage sensing in Setd2-haploinsufficient germinal center B (GCB) and lymphoma cells associated with increased AICDA-induced somatic hypermutation, complex structural variants, and increased translocations including those activating MYC. DNA damage was selectively increased on the nontemplate strand, and H3K36me3 loss was associated with greater RNAPII processivity and mutational burden, suggesting that SETD2-mediated H3K36me3 is required for proper sensing of cytosine deamination. Hence, Setd2 haploinsufficiency delineates a novel GCB context-specific oncogenic pathway involving defective epigenetic surveillance of AICDA-mediated effects on transcribed genes. SIGNIFICANCE Our findings define a B cell-specific oncogenic effect of SETD2 heterozygous mutation, which unleashes AICDA mutagenesis of nontemplate strand DNA in the GC reaction, resulting in lymphomas with heavy mutational burden. GC-derived lymphomas did not tolerate SETD2 homozygous deletion, pointing to a novel context-specific therapeutic vulnerability. This article is highlighted in the In This Issue feature, p. 1599.
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Affiliation(s)
- Wilfred Leung
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
- Department of Biomedical Sciences, Cornell University, Ithaca, New York
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Ceyda Durmaz
- Graduate Program of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Ashlesha Muley
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Jaison Arivalagan
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- New York Genome Center, New York, New York
- Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Sandeep S Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, New York
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, New York
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12
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Zhang H, Chen Y, Jiang Y, Mao Z. DNA double-strand break repair and nucleic acid-related immunity. Acta Biochim Biophys Sin (Shanghai) 2022; 54:828-835. [PMID: 35975605 PMCID: PMC9828507 DOI: 10.3724/abbs.2022061] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA damage repair and innate immunity are two conserved mechanisms that both function in cellular stress responses. Recently, an increasing amount of evidence has uncovered the close relationship between these two ancient biological processes. Here, we review the classical function of factors involved in DNA repair, and especially double-strand break repair, in innate immunity; more importantly, we discuss the novel roles of DNA repair factors in regulating innate immunity and vice versa. In addition, we also review the roles of DNA repair, innate immunity and their crosstalk in human diseases, which suggest that these two pathways may be compelling targets for disease prevention and treatment.
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Affiliation(s)
| | | | | | - Zhiyong Mao
- Correspondence address. Tel: +86-21-65978166; E-mail:
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13
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Wu L, Shukla V, Yadavalli AD, Dinesh RK, Xu D, Rao A, Schatz DG. HMCES protects immunoglobulin genes specifically from deletions during somatic hypermutation. Genes Dev 2022; 36:433-450. [PMID: 35450882 PMCID: PMC9067407 DOI: 10.1101/gad.349438.122] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/29/2022] [Indexed: 01/07/2023]
Abstract
Somatic hypermutation (SHM) produces point mutations in immunoglobulin (Ig) genes in B cells when uracils created by the activation-induced deaminase are processed in a mutagenic manner by enzymes of the base excision repair (BER) and mismatch repair (MMR) pathways. Such uracil processing creates DNA strand breaks and is susceptible to the generation of deleterious deletions. Here, we demonstrate that the DNA repair factor HMCES strongly suppresses deletions without significantly affecting other parameters of SHM in mouse and human B cells, thereby facilitating the production of antigen-specific antibodies. The deletion-prone repair pathway suppressed by HMCES operates downstream from the uracil glycosylase UNG and is mediated by the combined action of BER factor APE2 and MMR factors MSH2, MSH6, and EXO1. HMCES's ability to shield against deletions during SHM requires its capacity to form covalent cross-links with abasic sites, in sharp contrast to its DNA end-joining role in class switch recombination but analogous to its genome-stabilizing role during DNA replication. Our findings lead to a novel model for the protection of Ig gene integrity during SHM in which abasic site cross-linking by HMCES intercedes at a critical juncture during processing of vulnerable gapped DNA intermediates by BER and MMR enzymes.
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Affiliation(s)
- Lizhen Wu
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Vipul Shukla
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California 92037, USA
| | | | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Dijin Xu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California 92037, USA
- Department of Pharmacology, Moores Cancer Center, University of California at San Diego, La Jolla, California 92093, USA
- Consortium for Regenerative Medicine, La Jolla, California 92037, USA
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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14
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Tarsalainen A, Maman Y, Meng FL, Kyläniemi MK, Soikkeli A, Budzynska P, McDonald JJ, Šenigl F, Alt FW, Schatz DG, Alinikula J. Ig Enhancers Increase RNA Polymerase II Stalling at Somatic Hypermutation Target Sequences. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:143-154. [PMID: 34862258 PMCID: PMC8702490 DOI: 10.4049/jimmunol.2100923] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 01/03/2023]
Abstract
Somatic hypermutation (SHM) drives the genetic diversity of Ig genes in activated B cells and supports the generation of Abs with increased affinity for Ag. SHM is targeted to Ig genes by their enhancers (diversification activators [DIVACs]), but how the enhancers mediate this activity is unknown. We show using chicken DT40 B cells that highly active DIVACs increase the phosphorylation of RNA polymerase II (Pol II) and Pol II occupancy in the mutating gene with little or no accompanying increase in elongation-competent Pol II or production of full-length transcripts, indicating accumulation of stalled Pol II. DIVAC has similar effect also in human Ramos Burkitt lymphoma cells. The DIVAC-induced stalling is weakly associated with an increase in the detection of ssDNA bubbles in the mutating target gene. We did not find evidence for antisense transcription, or that DIVAC functions by altering levels of H3K27ac or the histone variant H3.3 in the mutating gene. These findings argue for a connection between Pol II stalling and cis-acting targeting elements in the context of SHM and thus define a mechanistic basis for locus-specific targeting of SHM in the genome. Our results suggest that DIVAC elements render the target gene a suitable platform for AID-mediated mutation without a requirement for increasing transcriptional output.
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Affiliation(s)
- Alina Tarsalainen
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Yaakov Maman
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, 1311502, Israel
| | - Fei-Long Meng
- Department of Genetics, Harvard Medical School and Program in Cellular and Molecular Medicine, HHMI, Boston Children’s Hospital, Boston, MA 02115, USA.,Current address: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Minna K. Kyläniemi
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland,Current address: Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Anni Soikkeli
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Paulina Budzynska
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland
| | - Jessica J. McDonald
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA,Current address: The Annenberg Public Policy Center, Philadelphia, PA 19104-3806, USA
| | - Filip Šenigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Praha 4, Czech Republic
| | - Frederic W. Alt
- Department of Genetics, Harvard Medical School and Program in Cellular and Molecular Medicine, HHMI, Boston Children’s Hospital, Boston, MA 02115, USA
| | - David G. Schatz
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA,Correspondence should be addressed to and
| | - Jukka Alinikula
- Unit of Infections and Immunity, Institute of Biomedicine, University of Turku, 20520 Turku, Finland,Correspondence should be addressed to and
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15
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Genomic Uracil and Aberrant Profile of Demethylation Intermediates in Epigenetics and Hematologic Malignancies. Int J Mol Sci 2021; 22:ijms22084212. [PMID: 33921666 PMCID: PMC8073381 DOI: 10.3390/ijms22084212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/30/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
DNA of all living cells undergoes continuous structural and chemical alterations resulting from fundamental cellular metabolic processes and reactivity of normal cellular metabolites and constituents. Examples include enzymatically oxidized bases, aberrantly methylated bases, and deaminated bases, the latter largely uracil from deaminated cytosine. In addition, the non-canonical DNA base uracil may result from misincorporated dUMP. Furthermore, uracil generated by deamination of cytosine in DNA is not always damage as it is also an intermediate in normal somatic hypermutation (SHM) and class shift recombination (CSR) at the Ig locus of B-cells in adaptive immunity. Many of the modifications alter base-pairing properties and may thus cause replicative and transcriptional mutagenesis. The best known and most studied epigenetic mark in DNA is 5-methylcytosine (5mC), generated by a methyltransferase that uses SAM as methyl donor, usually in CpG contexts. Oxidation products of 5mC are now thought to be intermediates in active demethylation as well as epigenetic marks in their own rights. The aim of this review is to describe the endogenous processes that surround the generation and removal of the most common types of DNA nucleobase modifications, namely, uracil and certain epigenetic modifications, together with their role in the development of hematological malignances. We also discuss what dictates whether the presence of an altered nucleobase is defined as damage or a natural modification.
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16
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Zheng S, Matthews AJ, Rahman N, Herrick-Reynolds K, Sible E, Choi JE, Wishnie A, Ng YK, Rhodes D, Elledge SJ, Vuong BQ. The uncharacterized SANT and BTB domain-containing protein SANBR inhibits class switch recombination. J Biol Chem 2021; 296:100625. [PMID: 33831416 PMCID: PMC8141524 DOI: 10.1016/j.jbc.2021.100625] [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] [Received: 08/17/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 01/21/2023] Open
Abstract
Class switch recombination (CSR) is the process by which B cells switch production from IgM/IgD to other immunoglobulin isotypes, enabling them to mount an effective immune response against pathogens. Timely resolution of CSR prevents damage due to an uncontrolled and prolonged immune response. While many positive regulators of CSR have been described, negative regulators of CSR are relatively unknown. Using an shRNA library screen targeting more than 28,000 genes in a mouse B cell line, we have identified a novel, uncharacterized protein of 82kD (KIAA1841, NM_027860), which we have named SANBR (SANT and BTB domain regulator of CSR), as a negative regulator of CSR. The purified, recombinant BTB domain of SANBR exhibited characteristic properties such as homodimerization and interaction with corepressor proteins, including HDAC and SMRT. Overexpression of SANBR inhibited CSR in primary mouse splenic B cells, and inhibition of CSR is dependent on the BTB domain while the SANT domain is largely dispensable. Thus, we have identified a new member of the BTB family that serves as a negative regulator of CSR. Future investigations to identify transcriptional targets of SANBR in B cells will reveal further insights into the specific mechanisms by which SANBR regulates CSR as well as fundamental gene regulatory activities of this protein.
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Affiliation(s)
- Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Allysia J Matthews
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA; Department of Biology, The Graduate Center and The City College of New York, New York, New York, USA
| | - Numa Rahman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Emily Sible
- Department of Biology, The Graduate Center and The City College of New York, New York, New York, USA
| | - Jee Eun Choi
- Department of Biology, The Graduate Center and The City College of New York, New York, New York, USA
| | - Alec Wishnie
- Department of Biology, The Graduate Center and The City College of New York, New York, New York, USA
| | - Yan Kee Ng
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Stephen J Elledge
- Department of Genetics, Program in Virology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Bao Q Vuong
- Department of Biology, The Graduate Center and The City College of New York, New York, New York, USA.
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17
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Cravens A, Jamil OK, Kong D, Sockolosky JT, Smolke CD. Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering. Nat Commun 2021; 12:1579. [PMID: 33707425 PMCID: PMC7952560 DOI: 10.1038/s41467-021-21876-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/11/2021] [Indexed: 12/17/2022] Open
Abstract
Random mutagenesis is a technique used to generate diversity and engineer biological systems. In vivo random mutagenesis generates diversity directly in a host organism, enabling applications such as lineage tracing, continuous evolution, and protein engineering. Here we describe TRIDENT (TaRgeted In vivo Diversification ENabled by T7 RNAP), a platform for targeted, continual, and inducible diversification at genes of interest at mutation rates one-million fold higher than natural genomic error rates. TRIDENT targets mutagenic enzymes to precise genetic loci by fusion to T7 RNA polymerase, resulting in mutation windows following a mutation targeting T7 promoter. Mutational diversity is tuned by DNA repair factors localized to sites of deaminase-driven mutation, enabling sustained mutation of all four DNA nucleotides at rates greater than 10-4 mutations per bp. We show TRIDENT can be applied to routine in vivo mutagenesis applications by evolving a red-shifted fluorescent protein and drug-resistant mutants of an essential enzyme.
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Affiliation(s)
- Aaron Cravens
- Department of Bioengineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA, USA
| | - Osman K Jamil
- Department of Chemical Engineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA, USA
| | - Deze Kong
- Department of Bioengineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA, USA
| | - Jonathan T Sockolosky
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina D Smolke
- Department of Bioengineering, 443 Via Ortega, MC 4245, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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18
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Pálinkás HL, Békési A, Róna G, Pongor L, Papp G, Tihanyi G, Holub E, Póti Á, Gemma C, Ali S, Morten MJ, Rothenberg E, Pagano M, Szűts D, Győrffy B, Vértessy BG. Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments. eLife 2020; 9:e60498. [PMID: 32956035 PMCID: PMC7505663 DOI: 10.7554/elife.60498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/23/2020] [Indexed: 12/17/2022] Open
Abstract
Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell line models derived from HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards segments that are normally more active/functional. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can be applied to study the dynamic spatio-temporal nature of genomic uracil.
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Affiliation(s)
- Hajnalka L Pálinkás
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Doctoral School of Multidisciplinary Medical Science, University of SzegedSzegedHungary
| | - Angéla Békési
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Róna
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Lőrinc Pongor
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Gábor Papp
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Gergely Tihanyi
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Eszter Holub
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
| | - Ádám Póti
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Carolina Gemma
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital CampusLondonUnited Kingdom
| | - Michael J Morten
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Howard Hughes Medical Institute, New York University School of MedicineNew YorkUnited States
| | - Dávid Szűts
- Genome Stability Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
| | - Balázs Győrffy
- Cancer Biomarker Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Bioinformatics and 2nd Department of Pediatrics, Semmelweis UniversityBudapestHungary
| | - Beáta G Vértessy
- Genome Metabolism Research Group, Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and EconomicsBudapestHungary
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19
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Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SSP, Weisz D, Buerstedde JM, Aiden EL, Casellas R, Hejnar J, Schatz DG. Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. Cell Rep 2020; 29:3902-3915.e8. [PMID: 31851922 PMCID: PMC6980758 DOI: 10.1016/j.celrep.2019.11.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM.
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Affiliation(s)
- Filip Senigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Rashu B Seth
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Lubomira Pecnova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Arina D Omer
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jiri Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
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20
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Zhang J, Shi Y, Zhao M, Hu H, Huang H. Activation-induced cytidine deaminase overexpression in double-hit lymphoma: potential target for novel anticancer therapy. Sci Rep 2020; 10:14164. [PMID: 32843697 PMCID: PMC7447639 DOI: 10.1038/s41598-020-71058-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/29/2020] [Indexed: 12/12/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is one kind of the mutant enzymes, which target regulating the immunoglobulin (Ig) gene in Burkitt's lymphoma to initiate class switch recombination (CSR), resulting in c-Myc chromosomal translocation. However, it is not clear that whether AID induces c-Myc/IgH translocation in double-hit lymphoma (DHL) with c-Myc gene translocation. In this study, the AID in DHL tissues and classical diffuse large b-cell lymphoma (DLBCL) tissues were compared. The results suggested that AID is of important value in predicting DHL, stronger CSR of AID was observed in DHL patients, which exhibited AID overexpression and c-Myc gene translocation of DHL after CSR induction. It is concluded that AID directly induces CSR in DHL and may result in c-Myc gene translocation. Targeting AID may be a good treatment regimen for DHL.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Cytidine Deaminase/biosynthesis
- Cytidine Deaminase/genetics
- Cytidine Deaminase/physiology
- Enzyme Induction/drug effects
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Genes, bcl-2
- Genes, myc
- Humans
- Immunoglobulin Class Switching/genetics
- Immunoglobulin Isotypes/biosynthesis
- Immunoglobulin Isotypes/blood
- Immunoglobulin Isotypes/genetics
- Kaplan-Meier Estimate
- Ki-67 Antigen/genetics
- Lipopolysaccharides/pharmacology
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/enzymology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Male
- Middle Aged
- Molecular Targeted Therapy
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Prognosis
- Proto-Oncogene Proteins c-bcl-6/genetics
- Translocation, Genetic
- Up-Regulation/drug effects
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Affiliation(s)
- Jingcheng Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejian, People's Republic of China
- Department of Hematology, Jinhua Hospital of Zhejiang University (Jinhua Municipal Central Hospital), Jinhua, 321100, Zhejiang, People's Republic of China
| | - Yifen Shi
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, People's Republic of China
| | - Mingzhe Zhao
- Department of Hematology, Jinhua Hospital of Zhejiang University (Jinhua Municipal Central Hospital), Jinhua, 321100, Zhejiang, People's Republic of China
| | - Huixian Hu
- Department of Hematology, Jinhua Hospital of Zhejiang University (Jinhua Municipal Central Hospital), Jinhua, 321100, Zhejiang, People's Republic of China.
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejian, People's Republic of China.
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21
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Kara H, Chazal N, Bouaziz S. Is Uracil-DNA Glycosylase UNG2 a New Cellular Weapon Against HIV-1? Curr HIV Res 2020; 17:148-160. [PMID: 31433761 DOI: 10.2174/1570162x17666190821154331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/01/2019] [Accepted: 08/09/2019] [Indexed: 01/12/2023]
Abstract
Uracil-DNA glycosylase-2 (UNG2) is a DNA repair protein that removes uracil from single and double-stranded DNA through a basic excision repair process. UNG2 is packaged into new virions by interaction with integrase (IN) and is needed during the early stages of the replication cycle. UNG2 appears to play both a positive and negative role during HIV-1 replication; UNG2 improves the fidelity of reverse transcription but the nuclear isoform of UNG2 participates in the degradation of cDNA and the persistence of the cellular genome by repairing its uracil mismatches. In addition, UNG2 is neutralized by Vpr, which redirects it to the proteasome for degradation, suggesting that UNG2 may be a new cellular restriction factor. So far, we have not understood why HIV-1 imports UNG2 via its IN and why it causes degradation of endogenous UNG2 by redirecting it to the proteasome via Vpr. In this review, we propose to discuss the ambiguous role of UNG2 during the HIV-1 replication cycle.
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Affiliation(s)
- Hesna Kara
- Cibles Therapeutiques et Conception de Medicaments (CiTCoM), CNRS UMR8038, Faculte des Sciences Pharmaceutiques et Biologiques, Universite Paris Descartes, Paris, France
| | - Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR9004, Universite de Montpellier, Montpellier, France
| | - Serge Bouaziz
- Cibles Therapeutiques et Conception de Medicaments (CiTCoM), CNRS UMR8038, Faculte des Sciences Pharmaceutiques et Biologiques, Universite Paris Descartes, Paris, France
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22
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The prognostic importance of double-expressor subgroup and AID , UNG and mismatch repair protein expressions in diffuse large B-cell lymphomas. MARMARA MEDICAL JOURNAL 2020. [DOI: 10.5472/marumj.741651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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Stratigopoulou M, van Dam TP, Guikema JEJ. Base Excision Repair in the Immune System: Small DNA Lesions With Big Consequences. Front Immunol 2020; 11:1084. [PMID: 32547565 PMCID: PMC7272602 DOI: 10.3389/fimmu.2020.01084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
The integrity of the genome is under constant threat of environmental and endogenous agents that cause DNA damage. Endogenous damage is particularly pervasive, occurring at an estimated rate of 10,000–30,000 per cell/per day, and mostly involves chemical DNA base lesions caused by oxidation, depurination, alkylation, and deamination. The base excision repair (BER) pathway is primary responsible for removing and repairing these small base lesions that would otherwise lead to mutations or DNA breaks during replication. Next to preventing DNA mutations and damage, the BER pathway is also involved in mutagenic processes in B cells during immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM), which are instigated by uracil (U) lesions derived from activation-induced cytidine deaminase (AID) activity. BER is required for the processing of AID-induced lesions into DNA double strand breaks (DSB) that are required for CSR, and is of pivotal importance for determining the mutagenic outcome of uracil lesions during SHM. Although uracils are generally efficiently repaired by error-free BER, this process is surprisingly error-prone at the Ig loci in proliferating B cells. Breakdown of this high-fidelity process outside of the Ig loci has been linked to mutations observed in B-cell tumors and DNA breaks and chromosomal translocations in activated B cells. Next to its role in preventing cancer, BER has also been implicated in immune tolerance. Several defects in BER components have been associated with autoimmune diseases, and animal models have shown that BER defects can cause autoimmunity in a B-cell intrinsic and extrinsic fashion. In this review we discuss the contribution of BER to genomic integrity in the context of immune receptor diversification, cancer and autoimmune diseases.
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Affiliation(s)
- Maria Stratigopoulou
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tijmen P van Dam
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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24
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Kazadi D, Lim J, Rothschild G, Grinstein V, Laffleur B, Becherel O, Lavin MJ, Basu U. Effects of senataxin and RNA exosome on B-cell chromosomal integrity. Heliyon 2020; 6:e03442. [PMID: 32195383 PMCID: PMC7075999 DOI: 10.1016/j.heliyon.2020.e03442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Loss of function of senataxin (SETX), a bona-fide RNA/DNA helicase, is associated with neuronal degeneration leading to Ataxia and Ocular Apraxia (AOA) in human patients. SETX is proposed to promote transcription termination, DNA replication, DNA repair, and to unwind deleterious RNA:DNA hybrids in the genome. In all the above-mentioned mechanisms, SETX unwinds transcription complex-associated nascent RNA which is then degraded by the RNA exosome complex. Here we have used B cells isolated from a SETX mutant mouse model and compared genomic instability and immunoglobulin heavy chain locus (IgH) class switch recombination (CSR) to evaluate aberrant and programmed genomic rearrangements, respectively. Similar to RNA exosome mutant primary B cells, SETX mutant primary B cells display genomic instability but a modest decrease in efficiency of CSR. Furthermore, knockdown of Setx mRNAs from CH12–F3 B-cell lines leads to a defect in IgA CSR and accumulation of aberrant patterns of mutations in IgH switch sequences. Given that SETX mutant mice do not recapitulate the AOA neurodegenerative phenotype, it is possible that some aspects of SETX biology are rescued by redundant helicases in mice. Overall, our study provides new insights into the role of the SETX/RNA exosome axis in suppressing genomic instability so that programmed DNA breaks are properly orchestrated.
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Affiliation(s)
- David Kazadi
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Veronika Grinstein
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Olivier Becherel
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Martin J Lavin
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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25
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Choi JE, Matthews AJ, Michel G, Vuong BQ. AID Phosphorylation Regulates Mismatch Repair-Dependent Class Switch Recombination and Affinity Maturation. THE JOURNAL OF IMMUNOLOGY 2020; 204:13-22. [PMID: 31757865 DOI: 10.4049/jimmunol.1900809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023]
Abstract
Activation-induced cytidine deaminase (AID) generates U:G mismatches in Ig genes that can be converted into untemplated mutations during somatic hypermutation or DNA double-strand breaks during class switch recombination (CSR). Null mutations in UNG and MSH2 demonstrate the complementary roles of the base excision repair (BER) and mismatch repair pathways, respectively, in CSR. Phosphorylation of AID at serine 38 was previously hypothesized to regulate BER during CSR, as the AID phosphorylation mutant, AID(S38A), cannot interact with APE1, a BER protein. Consistent with these findings, we observe a complete block in CSR in AIDS38A/S38AMSH2-/- mouse B cells that correlates with an impaired mutation frequency at 5'Sμ. Similarly, somatic hypermutation is almost negligible at the JH4 intron in AIDS38A/S38AMSH2-/- mouse B cells, and, consistent with this, NP-specific affinity maturation in AIDS38A/S38AMSH2-/- mice is not significantly elevated in response to NP-CGG immunization. Surprisingly, AIDS38A/S38AUNG-/- mouse B cells also cannot complete CSR or affinity maturation despite accumulating significant mutations in 5'Sμ as well as the JH4 intron. These data identify a novel role for phosphorylation of AID at serine 38 in mismatch repair-dependent CSR and affinity maturation.
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Affiliation(s)
- Jee Eun Choi
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Allysia J Matthews
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Genesis Michel
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Bao Q Vuong
- The Graduate Center, The City University of New York, New York, NY 10016
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26
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Liu LD, Huang M, Dai P, Liu T, Fan S, Cheng X, Zhao Y, Yeap LS, Meng FL. Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation. Cell Rep 2019; 25:884-892.e3. [PMID: 30355495 DOI: 10.1016/j.celrep.2018.09.090] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/13/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Base editors (BEs) are emerging tools used for precision correction or diversifying mutation. It provides a potential way to recreate somatic hypermutations (SHM) for generating high-affinity antibody, which is usually screened from antigen-challenged animal models or synthetic combinatorial libraries. By comparing somatic mutations in the same genomic context, we screened engineered deaminases and CRISPR-deaminase coupling approaches and updated diversifying base editors (DBEs) to generate SHM. The deaminase used in DBEs retains its intrinsic nucleotide preference and mutates cytidines at its preferred motifs. DBE with AID targets the same hotspots as physiological AID does in vivo, while DBE with other deaminases generates distinct mutation profiles from the same DNA substrate. Downstream DNA repair pathways further diversified the sequence, while Cas9-nickase restricted mutation spreading. Finally, application of DBE in an antibody display system achieved antibody affinity maturation ex vivo. Our findings provide insight of DBE working mechanism and an alternative antibody engineering approach.
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Affiliation(s)
- Liu Daisy Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Min Huang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Tingting Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shuangshuang Fan
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
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27
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Ciccarese S, Burger PA, Ciani E, Castelli V, Linguiti G, Plasil M, Massari S, Horin P, Antonacci R. The Camel Adaptive Immune Receptors Repertoire as a Singular Example of Structural and Functional Genomics. Front Genet 2019; 10:997. [PMID: 31681428 PMCID: PMC6812646 DOI: 10.3389/fgene.2019.00997] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 09/18/2019] [Indexed: 01/08/2023] Open
Abstract
The adaptive immune receptors repertoire is highly plastic, with its ability to produce antigen-binding molecules and select those with high affinity for their antigen. Species have developed diverse genetic and structural strategies to create their respective repertoires required for their survival in the different environments. Camelids, until now, considered as a case of evolutionary innovation because of their only heavy-chain antibodies, represent a new mammalian model particularly useful for understanding the role of diversity in the immune system function. Here, we review the structural and functional characteristics and the current status of the genomic organization of camel immunoglobulins (IG) or antibodies, α/ß and γ/δ T cell receptors (TR), and major histocompatibility complex (MHC). In camelid humoral response, in addition to the conventional antibodies, there are IG with “only-heavy-chain” (no light chain, and two identical heavy gamma chains lacking CH1 and with a VH domain designated as VHH). The unique features of these VHH offer advantages in biotechnology and for clinical applications. The TRG and TRD rearranged variable domains of Camelus dromedarius (Arabian camel) display somatic hypermutation (SHM), increasing the intrinsic structural stability in the γ/δ heterodimer and influencing the affinity maturation to a given antigen similar to immunoglobulin genes. The SHM increases the dromedary γ/δ repertoire diversity. In Camelus genus, the general structural organization of the TRB locus is similar to that of the other artiodactyl species, with a pool of TRBV genes positioned at the 5’ end of three in tandem D-J-C clusters, followed by a single TRBV gene with an inverted transcriptional orientation located at the 3’ end. At the difference of TRG and TRD, the diversity of the TRB variable domains is not shaped by SHM and depends from the classical combinatorial and junctional diversity. The MHC locus is located on chromosome 20 in Camelus dromedarius. Cytogenetic and comparative whole genome analyses revealed the order of the three major regions “Centromere-ClassII-ClassIII-ClassI”. Unexpectedly low extent of polymorphisms and haplotypes was observed in all Old World camels despite different geographic origins.
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Affiliation(s)
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro," Bari, Italy
| | - Vito Castelli
- Department of Biology, University of Bari "Aldo Moro," Bari, Italy
| | | | - Martin Plasil
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, RG Animal Immunogenomics, Brno, Czechia
| | - Serafina Massari
- Department of Biological and Environmental Science and Technologies, University of Salento, Lecce, Italy
| | - Petr Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czechia.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, RG Animal Immunogenomics, Brno, Czechia
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28
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Datta M, Aroli S, Karmakar K, Dutta S, Chakravortty D, Varshney U. Development of mCherry tagged UdgX as a highly sensitive molecular probe for specific detection of uracils in DNA. Biochem Biophys Res Commun 2019; 518:38-43. [PMID: 31402116 DOI: 10.1016/j.bbrc.2019.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Uracil is not always a mistakenly occurring base in DNA. Uracils in DNA genomes are known to be important in the life cycles of Bacillus subtilis phages (PBS1/2) and the malarial parasite, Plasmodium falciparum; and have been implicated in the development of fruit fly and antibody maturation in B-lymphocytes. Availability of a sensitive, specific and robust technique for the detection uracils in genes/genomes is essential to understand its varied biological roles. Mycobacterium smegmatis UdgX (MsmUdgX), identified and characterised in our laboratory, forms covalent complexes with the uracil sites in DNA in a specific manner. MsmUdgX cleaves the glycosidic bond between uracil and the deoxyribose sugar in DNA to produce uracilate and oxocarbenium ions. The oxocarbenium ion is then captured into a covalent complex by the nucleophilic attack of a histidine side chain of MsmUdgX. Here, we describe the use of a fusion protein, mCherry tagged MsmUdgX (mChUdgX), which combines the property of MsmUdgX to covalently and specifically bind the uracil sites in the genome, with the sensitivity of fluorescent detection of mCherry as a reporter. We show that both the purified mChUdgX and the Escherichia coli cell-extracts overexpressing mChUdgX provide high sensitivity and specificity of detecting uracils in DNA.
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Affiliation(s)
- Madhurima Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Shashanka Aroli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Kapudeep Karmakar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
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29
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Roco JA, Mesin L, Binder SC, Nefzger C, Gonzalez-Figueroa P, Canete PF, Ellyard J, Shen Q, Robert PA, Cappello J, Vohra H, Zhang Y, Nowosad CR, Schiepers A, Corcoran LM, Toellner KM, Polo JM, Meyer-Hermann M, Victora GD, Vinuesa CG. Class-Switch Recombination Occurs Infrequently in Germinal Centers. Immunity 2019; 51:337-350.e7. [PMID: 31375460 DOI: 10.1016/j.immuni.2019.07.001] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/26/2019] [Accepted: 07/09/2019] [Indexed: 01/06/2023]
Abstract
Class-switch recombination (CSR) is a DNA recombination process that replaces the immunoglobulin (Ig) constant region for the isotype that can best protect against the pathogen. Dysregulation of CSR can cause self-reactive BCRs and B cell lymphomas; understanding the timing and location of CSR is therefore important. Although CSR commences upon T cell priming, it is generally considered a hallmark of germinal centers (GCs). Here, we have used multiple approaches to show that CSR is triggered prior to differentiation into GC B cells or plasmablasts and is greatly diminished in GCs. Despite finding a small percentage of GC B cells expressing germline transcripts, phylogenetic trees of GC BCRs from secondary lymphoid organs revealed that the vast majority of CSR events occurred prior to the onset of somatic hypermutation. As such, we have demonstrated the existence of IgM-dominated GCs, which are unlikely to occur under the assumption of ongoing switching.
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Affiliation(s)
- Jonathan A Roco
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, Rockefeller University, New York, NY, 10065, USA
| | - Sebastian C Binder
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106 Braunschweig, Germany
| | - Christian Nefzger
- Department of Anatomy and Developmental Biology and Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton VIC 3800, Australia
| | - Paula Gonzalez-Figueroa
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Pablo F Canete
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Julia Ellyard
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Qian Shen
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Philippe A Robert
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106 Braunschweig, Germany
| | - Jean Cappello
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Harpreet Vohra
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia
| | - Yang Zhang
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Carla R Nowosad
- Laboratory of Lymphocyte Dynamics, Rockefeller University, New York, NY, 10065, USA
| | - Arien Schiepers
- Laboratory of Lymphocyte Dynamics, Rockefeller University, New York, NY, 10065, USA
| | - Lynn M Corcoran
- Molecular Immunology Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville VIC 3052, Australia
| | - Kai-Michael Toellner
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Jose M Polo
- Department of Anatomy and Developmental Biology and Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton VIC 3800, Australia
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106 Braunschweig, Germany; Institute for Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, Rockefeller University, New York, NY, 10065, USA
| | - Carola G Vinuesa
- Department of Immunology and Infectious Disease and Centre for Personalised Immunology, The John Curtin School of Medical Research, The Australian National University, Canberra ACT 0200, Australia; China-Australia Centre for Personalised Immunology, Department of Rheumatology, Shanghai Renji Hospital, Shanghai JiaoTong University, Shanghai, China.
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Leeman-Neill RJ, Lim J, Basu U. The Common Key to Class-Switch Recombination and Somatic Hypermutation: Discovery of AID and Its Role in Antibody Gene Diversification. THE JOURNAL OF IMMUNOLOGY 2019; 201:2527-2529. [PMID: 30348657 DOI: 10.4049/jimmunol.1801246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032; and.,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032; and
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032; and
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31
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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Abstract
Class switch recombination (CSR) generates isotype-switched antibodies with distinct effector functions essential for mediating effective humoral immunity. CSR is catalyzed by activation-induced deaminase (AID) that initiates DNA lesions in the evolutionarily conserved switch (S) regions at the immunoglobulin heavy chain (Igh) locus. AID-initiated DNA lesions are subsequently converted into DNA double stranded breaks (DSBs) in the S regions of Igh locus, repaired by non-homologous end-joining to effect CSR in mammalian B lymphocytes. While molecular mechanisms of CSR are well characterized, it remains less well understood how upstream signaling pathways regulate AID expression and CSR. B lymphocytes express multiple receptors including the B cell antigen receptor (BCR) and co-receptors (e.g., CD40). These receptors may share common signaling pathways or may use distinct signaling elements to regulate CSR. Here, we discuss how signals emanating from different receptors positively or negatively regulate AID expression and CSR.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
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33
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Ogawa S, Matsuoka Y, Takada M, Matsui K, Yamane F, Kubota E, Yasuhara S, Hieda K, Kanayama N, Hatano N, Tokumitsu H, Magari M. Interleukin 34 (IL-34) cell-surface localization regulated by the molecular chaperone 78-kDa glucose-regulated protein facilitates the differentiation of monocytic cells. J Biol Chem 2018; 294:2386-2396. [PMID: 30573681 DOI: 10.1074/jbc.ra118.006226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/07/2018] [Indexed: 01/06/2023] Open
Abstract
Interleukin 34 (IL-34) constitutes a cytokine that shares a common receptor, colony-stimulating factor-1 receptor (CSF-1R), with CSF-1. We recently identified a novel type of monocytic cell termed follicular dendritic cell-induced monocytic cells (FDMCs), whose differentiation depended on CSF-1R signaling through the IL-34 produced from a follicular dendritic cell line, FL-Y. Here, we report the functional mechanisms of the IL-34-mediated CSF-1R signaling underlying FDMC differentiation. CRIPSR/Cas9-mediated knockout of the Il34 gene confirmed that the ability of FL-Y cells to induce FDMCs completely depends on the IL-34 expressed by FL-Y cells. Transwell culture experiments revealed that FDMC differentiation requires a signal from a membrane-anchored form of IL-34 on the FL-Y cell surface, but not from a secreted form, in a direct interaction between FDMC precursor cells and FL-Y cells. Furthermore, flow cytometric analysis using an anti-IL-34 antibody indicated that IL-34 was also expressed on the FL-Y cell surface. Thus, we explored proteins interacting with IL-34 in FL-Y cells. Mass spectrometry analysis and pulldown assay identified that IL-34 was associated with the molecular chaperone 78-kDa glucose-regulated protein (GRP78) in the plasma membrane fraction of FL-Y cells. Consistent with this finding, GRP78-heterozygous FL-Y cells expressed a lower level of IL-34 protein on their cell surface and exhibited a reduced competency to induce FDMC differentiation compared with the original FL-Y cells. These results indicated a novel GRP78-dependent localization and specific function of IL-34 in FL-Y cells related to monocytic cell differentiation.
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Affiliation(s)
- Sayaka Ogawa
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology
| | - Yukiko Matsuoka
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology
| | - Miho Takada
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology
| | - Kazue Matsui
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology
| | - Fumihiro Yamane
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology
| | - Eri Kubota
- the Department of Applied Chemistry and Biotechnology, Faculty of Engineering, and
| | - Shiori Yasuhara
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology
| | - Kentaro Hieda
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology
| | - Naoki Kanayama
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology.,the Laboratory of Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka 3-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Naoya Hatano
- the Laboratory of Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka 3-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Hiroshi Tokumitsu
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology.,the Laboratory of Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka 3-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Masaki Magari
- From the Division of Medical Bioengineering, Graduate School of Natural Science and Technology, .,the Laboratory of Applied Cell Biology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka 3-1-1, Kita-ku, Okayama 700-8530, Japan
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Patel B, Banerjee R, Samanta M, Das S. Diversity of Immunoglobulin (Ig) Isotypes and the Role of Activation-Induced Cytidine Deaminase (AID) in Fish. Mol Biotechnol 2018; 60:435-453. [PMID: 29704159 DOI: 10.1007/s12033-018-0081-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The disparate diversity in immunoglobulin (Ig) repertoire has been a subject of fascination since the emergence of prototypic adaptive immune system in vertebrates. The carboxy terminus region of activation-induced cytidine deaminase (AID) has been well established in tetrapod lineage and is crucial for its function in class switch recombination (CSR) event of Ig diversification. The absence of CSR in the paraphyletic group of fish is probably due to changes in catalytic domain of AID and lack of cis-elements in IgH locus. Therefore, understanding the arrangement of Ig genes in IgH locus and functional facets of fish AID opens up new realms of unravelling the alternative mechanisms of isotype switching and antibody diversity. Further, the teleost AID has been recently reported to have potential of catalyzing CSR in mammalian B cells by complementing AID deficiency in them. In that context, the present review focuses on the recent advances regarding the generation of diversity in Ig repertoire in the absence of AID-regulated class switching in teleosts and the possible role of T cell-independent pathway involving B cell activating factor and a proliferation-inducing ligand in activation of CSR machinery.
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Affiliation(s)
- Bhakti Patel
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India
| | - Rajanya Banerjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India
| | - Mrinal Samanta
- Immunology Laboratory, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751 002, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India.
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35
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Chakraborty A, Viswanathan P. Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury. Anal Cell Pathol (Amst) 2018. [DOI: https://doi.org/10.1155/2018/8764384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Over the years, the epigenetic landscape has grown increasingly complex. Until recently, methylation of DNA and histones was considered one of the most important epigenetic modifications. However, with the discovery of enzymes involved in the demethylation process, several exciting prospects have emerged that focus on the dynamic regulation of methylation and its crucial role in development and disease. An interplay of the methylation-demethylation machinery controls the process of gene expression. Since acute kidney injury (AKI), a major risk factor for chronic kidney disease and death, is characterised by aberrant expression of genes, understanding the dynamics of methylation and demethylation will provide new insights into the intricacies of the disease. Research on epigenetics in AKI has only made its mark in the recent years but has provided compelling evidence that implicates the involvement of methylation and demethylation changes in its pathophysiology. In this review, we explore the role of methylation and demethylation machinery in cellular epigenetic control and further discuss the contribution of methylomic changes and histone modifications to the pathophysiology of AKI.
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Affiliation(s)
- Anubhav Chakraborty
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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36
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Martin OA, Garot A, Le Noir S, Aldigier JC, Cogné M, Pinaud E, Boyer F. Detecting Rare AID-Induced Mutations in B-Lineage Oncogenes from High-Throughput Sequencing Data Using the Detection of Minor Variants by Error Correction Method. THE JOURNAL OF IMMUNOLOGY 2018; 201:950-956. [DOI: 10.4049/jimmunol.1800203] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022]
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37
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Tan Q, Ku W, Zhang C, Heyilimu P, Tian Y, Ke Y, Lu Z. Mutation analysis of the EBV-lymphoblastoid cell line cautions their use as antigen-presenting cells. Immunol Cell Biol 2018; 96:204-211. [PMID: 29363169 DOI: 10.1111/imcb.1030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 12/13/2022]
Abstract
Lymphoblastoid cell lines (LCLs) have been widely used as professional antigen-presenting cells (APCs). However, neoantigen-loaded LCLs could induce nonspecific T-cell response, which could be due to expression of both Epstein-Barr virus (EBV) antigens and nonsynonymous mutations arising in LCLs. Since the number of passages could influence mutational characteristics of LCLs, and moreover extensive proliferation of LCLs in vitro is necessary to activate T cells for immunotherapy, we comprehensively profiled mutational characteristics by comparing eight sets of B cells and matched high-passage LCLs using whole-exome sequencing in order to assess the effect of nonsynonymous mutations arising in LCLs on nonspecific T-cell response. We found 315 nongermline mutations (approximately 40mut/subject) randomly distributed across all chromosomes including 18 mutations in immunoglobulin V and J genes in eight LCLs, of which 137 candidate neoantigens (approximately 17mut/subject) were identified. The underlying mutational processes linked to EBV-transformed LCLs could be attributed to activation induced cytidine deaminase gene expression which contributes to cytosine mutation clusters in LCLs through cytosine deamination. Pathways significantly enriched by nonsilent mutations of each LCL were totally different among all LCLs. In conclusion, high-passage LCLs may not be suitable to serve as APCs due to random nonsilent mutations, particularly for presentation of neoantigens of low immunogenicity, although further experimental proofs are needed.
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Affiliation(s)
- Qin Tan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenjing Ku
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Chaoting Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Palashati Heyilimu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuan Tian
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zheming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
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38
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Chakraborty A, Viswanathan P. Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury. Anal Cell Pathol (Amst) 2018; 2018:8764384. [PMID: 30073137 PMCID: PMC6057397 DOI: 10.1155/2018/8764384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 02/05/2023] Open
Abstract
Over the years, the epigenetic landscape has grown increasingly complex. Until recently, methylation of DNA and histones was considered one of the most important epigenetic modifications. However, with the discovery of enzymes involved in the demethylation process, several exciting prospects have emerged that focus on the dynamic regulation of methylation and its crucial role in development and disease. An interplay of the methylation-demethylation machinery controls the process of gene expression. Since acute kidney injury (AKI), a major risk factor for chronic kidney disease and death, is characterised by aberrant expression of genes, understanding the dynamics of methylation and demethylation will provide new insights into the intricacies of the disease. Research on epigenetics in AKI has only made its mark in the recent years but has provided compelling evidence that implicates the involvement of methylation and demethylation changes in its pathophysiology. In this review, we explore the role of methylation and demethylation machinery in cellular epigenetic control and further discuss the contribution of methylomic changes and histone modifications to the pathophysiology of AKI.
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Affiliation(s)
- Anubhav Chakraborty
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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39
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Tepper S, Jeschke J, Böttcher K, Schmidt A, Davari K, Müller P, Kremmer E, Hemmerich P, Pfeil I, Jungnickel B. PARP activation promotes nuclear AID accumulation in lymphoma cells. Oncotarget 2017; 7:13197-208. [PMID: 26921193 PMCID: PMC4914351 DOI: 10.18632/oncotarget.7603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/12/2016] [Indexed: 12/20/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates immunoglobulin diversification in germinal center B cells by targeted introduction of DNA damage. As aberrant nuclear AID action contributes to the generation of B cell lymphoma, the protein's activity is tightly regulated, e.g. by nuclear/cytoplasmic shuttling and nuclear degradation. In the present study, we asked whether DNA damage may affect regulation of the AID protein. We show that exogenous DNA damage that mainly activates base excision repair leads to prevention of proteasomal degradation of AID and hence its nuclear accumulation. Inhibitor as well as knockout studies indicate that activation of poly (ADP-ribose) polymerase (PARP) by DNA damaging agents promotes both phenomena. These findings suggest that PARP inhibitors influence DNA damage dependent AID regulation, with interesting implications for the regulation of AID function and chemotherapy of lymphoma.
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Affiliation(s)
- Sandra Tepper
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Julia Jeschke
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany.,Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Katrin Böttcher
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Angelika Schmidt
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Kathrin Davari
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Peter Müller
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Peter Hemmerich
- Imaging Facility, Leibniz- Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Ines Pfeil
- Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Berit Jungnickel
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany.,Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
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40
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Amin AD, Peters TL, Li L, Rajan SS, Choudhari R, Puvvada SD, Schatz JH. Diffuse large B-cell lymphoma: can genomics improve treatment options for a curable cancer? Cold Spring Harb Mol Case Stud 2017; 3:a001719. [PMID: 28487884 PMCID: PMC5411687 DOI: 10.1101/mcs.a001719] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gene-expression profiling and next-generation sequencing have defined diffuse large B-cell lymphoma (DLBCL), the most common lymphoma diagnosis, as a heterogeneous group of subentities. Despite ongoing explosions of data illuminating disparate pathogenic mechanisms, however, the five-drug chemoimmunotherapy combination R-CHOP remains the frontline standard treatment. This has not changed in 15 years, since the anti-CD20 monoclonal antibody rituximab was added to the CHOP backbone, which first entered use in the 1970s. At least a third of patients are not cured by R-CHOP, and relapsed or refractory DLBCL is fatal in ∼90%. Targeted small-molecule inhibitors against distinct molecular pathways activated in different subgroups of DLBCL have so far translated poorly into the clinic, justifying the ongoing reliance on R-CHOP and other long-established chemotherapy-driven combinations. New drugs and improved identification of biomarkers in real time, however, show potential to change the situation eventually, despite some recent setbacks. Here, we review established and putative molecular drivers of DLBCL identified through large-scale genomics, highlighting among other things the care that must be taken when differentiating drivers from passengers, which is influenced by the promiscuity of activation-induced cytidine deaminase. Furthermore, we discuss why, despite having so much genomic data available, it has been difficult to move toward personalized medicine for this umbrella disorder and some steps that may be taken to hasten the process.
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Affiliation(s)
- Amit Dipak Amin
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Tara L Peters
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Lingxiao Li
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soumya Sundara Rajan
- Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Ramesh Choudhari
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
| | - Soham D Puvvada
- Department of Medicine, Division of Hematology-Oncology, University of Arizona Comprehensive Cancer Center, Tucson, Arizona 85719, USA
| | - Jonathan H Schatz
- Department of Medicine, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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41
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Zaprazna K, Basu A, Tom N, Jha V, Hodawadekar S, Radova L, Malcikova J, Tichy B, Pospisilova S, Atchison ML. Transcription factor YY1 can control AID-mediated mutagenesis in mice. Eur J Immunol 2017; 48:273-282. [PMID: 29080214 DOI: 10.1002/eji.201747065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 09/24/2017] [Accepted: 10/20/2017] [Indexed: 12/18/2022]
Abstract
Activation-induced cytidine deminase (AID) is crucial for controlling the immunoglobulin (Ig) diversification processes of somatic hypermutation (SHM) and class switch recombination (CSR). AID initiates these processes by deamination of cytosine, ultimately resulting in mutations or double strand DNA breaks needed for SHM and CSR. Levels of AID control mutation rates, and off-target non-Ig gene mutations can contribute to lymphomagenesis. Therefore, factors that control AID levels in the nucleus can regulate SHM and CSR, and may contribute to disease. We previously showed that transcription factor YY1 can regulate the level of AID in the nucleus and Ig CSR. Therefore, we hypothesized that conditional knock-out of YY1 would lead to reduction in AID localization at the Ig locus, and reduced AID-mediated mutations. Using mice that overexpress AID (IgκAID yy1f/f ) or that express normal AID levels (yy1f/f ), we found that conditional knock-out of YY1 results in reduced AID nuclear levels, reduced localization of AID to the Sμ switch region, and reduced AID-mediated mutations. We find that the mechanism of YY1 control of AID nuclear accumulation is likely due to YY1-AID physical interaction which blocks AID ubiquitination.
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Affiliation(s)
- Kristina Zaprazna
- Central European Institute of Technology, Masaryk University, Centre of Molecular Medicine, Brno, Czech Republic
| | - Arindam Basu
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
| | - Nikola Tom
- Central European Institute of Technology, Masaryk University, Centre of Molecular Medicine, Brno, Czech Republic
| | - Vibha Jha
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
| | - Suchita Hodawadekar
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Centre of Molecular Medicine, Brno, Czech Republic
| | - Jitka Malcikova
- Central European Institute of Technology, Masaryk University, Centre of Molecular Medicine, Brno, Czech Republic
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, Centre of Molecular Medicine, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Centre of Molecular Medicine, Brno, Czech Republic
| | - Michael L Atchison
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
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42
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Olinski R, Gackowski D, Cooke MS. Endogenously generated DNA nucleobase modifications source, and significance as possible biomarkers of malignant transformation risk, and role in anticancer therapy. Biochim Biophys Acta Rev Cancer 2017; 1869:29-41. [PMID: 29128527 DOI: 10.1016/j.bbcan.2017.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 01/26/2023]
Abstract
The DNA of all living cells undergoes continuous structural and chemical alteration, which may be derived from exogenous sources, or endogenous, metabolic pathways, such as cellular respiration, replication and DNA demethylation. It has been estimated that approximately 70,000 DNA lesions may be generated per day in a single cell, and this has been linked to a wide variety of diseases, including cancer. However, it is puzzling why potentially mutagenic DNA modifications, occurring at a similar level in different organs/tissue, may lead to organ/tissue specific cancers, or indeed non-malignant disease - what is the basis for this differential response? We suggest that it is perhaps the precise location of damage, within the genome, that is a key factor. Finally, we draw attention to the requirement for reliable methods for identification and quantification of DNA adducts/modifications, and stress the need for these assays to be fully validated. Once these prerequisites are satisfied, measurement of DNA modifications may be helpful as a clinical parameter for treatment monitoring, risk group identification and development of prevention strategies.
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Affiliation(s)
- Ryszard Olinski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85-095 Bydgoszcz, Poland.
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85-095 Bydgoszcz, Poland
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Modesto A. Maidique Campus, AHC5 355 11200 SW 8th Street, Miami, FL 33199, United States; Biomolecular Sciences Institute, Florida International University, United States
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43
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Liu J, Xiong E, Zhu H, Mori H, Yasuda S, Kinoshita K, Tsubata T, Wang JY. Efficient Induction of Ig Gene Hypermutation in Ex Vivo–Activated Primary B Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:3023-3030. [DOI: 10.4049/jimmunol.1700868] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/29/2017] [Indexed: 11/19/2022]
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44
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Bahjat M, Guikema JEJ. The Complex Interplay between DNA Injury and Repair in Enzymatically Induced Mutagenesis and DNA Damage in B Lymphocytes. Int J Mol Sci 2017; 18:ijms18091876. [PMID: 28867784 PMCID: PMC5618525 DOI: 10.3390/ijms18091876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/25/2022] Open
Abstract
Lymphocytes are endowed with unique and specialized enzymatic mutagenic properties that allow them to diversify their antigen receptors, which are crucial sensors for pathogens and mediators of adaptive immunity. During lymphocyte development, the antigen receptors expressed by B and T lymphocytes are assembled in an antigen-independent fashion by ordered variable gene segment recombinations (V(D)J recombination), which is a highly ordered and regulated process that requires the recombination activating gene products 1 & 2 (RAG1, RAG2). Upon activation by antigen, B lymphocytes undergo additional diversifications of their immunoglobulin B-cell receptors. Enzymatically induced somatic hypermutation (SHM) and immunoglobulin class switch recombination (CSR) improves the affinity for antigen and shape the effector function of the humoral immune response, respectively. The activation-induced cytidine deaminase (AID) enzyme is crucial for both SHM and CSR. These processes have evolved to both utilize as well as evade different DNA repair and DNA damage response pathways. The delicate balance between enzymatic mutagenesis and DNA repair is crucial for effective immune responses and the maintenance of genomic integrity. Not surprisingly, disturbances in this balance are at the basis of lymphoid malignancies by provoking the formation of oncogenic mutations and chromosomal aberrations. In this review, we discuss recent mechanistic insight into the regulation of RAG1/2 and AID expression and activity in lymphocytes and the complex interplay between these mutagenic enzymes and DNA repair and DNA damage response pathways, focusing on the base excision repair and mismatch repair pathways. We discuss how disturbances of this interplay induce genomic instability and contribute to oncogenesis.
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Affiliation(s)
- Mahnoush Bahjat
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
| | - Jeroen E J Guikema
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
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Abstract
Helicobacter pylori infection is the most important cause of human gastric cancer worldwide. Gastric cancer develops over a long time after H. pylori infection via stepwise accumulation of genetic alterations and positive selection of cells with growth advantages. H. pylori itself and the resultant chronic inflammation lead to the emergence of genetic alterations in gastric epithelial cells via increased susceptibility of these cells to DNA damage. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) in inflammatory and gastric epithelial cells, as well as the expression of cytidine deaminase in gastric epithelial cells, may link H. pylori-related inflammation and DNA damage. Recent comprehensive analyses of gastric cancer genomes provide clues for the possible molecular mechanisms of gastric carcinogenesis. In this chapter, we describe how genetic alterations emerge during gastric carcinogenesis related to H. pylori infection.
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46
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Rees HA, Komor AC, Yeh WH, Caetano-Lopes J, Warman M, Edge ASB, Liu DR. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery. Nat Commun 2017; 8:15790. [PMID: 28585549 PMCID: PMC5467206 DOI: 10.1038/ncomms15790] [Citation(s) in RCA: 303] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/27/2017] [Indexed: 12/26/2022] Open
Abstract
We recently developed base editing, a genome-editing approach that enables the programmable conversion of one base pair into another without double-stranded DNA cleavage, excess stochastic insertions and deletions, or dependence on homology-directed repair. The application of base editing is limited by off-target activity and reliance on intracellular DNA delivery. Here we describe two advances that address these limitations. First, we greatly reduce off-target base editing by installing mutations into our third-generation base editor (BE3) to generate a high-fidelity base editor (HF-BE3). Next, we purify and deliver BE3 and HF-BE3 as ribonucleoprotein (RNP) complexes into mammalian cells, establishing DNA-free base editing. RNP delivery of BE3 confers higher specificity even than plasmid transfection of HF-BE3, while maintaining comparable on-target editing levels. Finally, we apply these advances to deliver BE3 RNPs into both zebrafish embryos and the inner ear of live mice to achieve specific, DNA-free base editing in vivo. Third-generation base editors consist of a catalytically disabled Cas9 fused to a cytidine deaminase and a base excision repair inhibitor, enabling efficient, precise editing of individual base pairs in DNA. Here the authors describe engineering and protein delivery of base editors to improve their DNA specificity and enable specific base editing in live animals.
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Affiliation(s)
- Holly A Rees
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Wei-Hsi Yeh
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joana Caetano-Lopes
- Orthopaedic Research Laboratories, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Matthew Warman
- Orthopaedic Research Laboratories, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Albert S B Edge
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
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47
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Tubbs A, Nussenzweig A. Endogenous DNA Damage as a Source of Genomic Instability in Cancer. Cell 2017; 168:644-656. [PMID: 28187286 DOI: 10.1016/j.cell.2017.01.002] [Citation(s) in RCA: 850] [Impact Index Per Article: 121.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/22/2016] [Accepted: 01/04/2017] [Indexed: 12/19/2022]
Abstract
Genome instability, defined as higher than normal rates of mutation, is a double-edged sword. As a source of genetic diversity and natural selection, mutations are beneficial for evolution. On the other hand, genomic instability can have catastrophic consequences for age-related diseases such as cancer. Mutations arise either from inactivation of DNA repair pathways or in a repair-competent background due to genotoxic stress from celluar processes such as transcription and replication that overwhelm high-fidelity DNA repair. Here, we review recent studies that shed light on endogenous sources of mutation and epigenomic features that promote genomic instability during cancer evolution.
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Affiliation(s)
- Anthony Tubbs
- Laboratory of Genome Integrity, NIH, Bethesda, MD 20892, USA
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48
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Eid MMA, Shimoda M, Singh SK, Almofty SA, Pham P, Goodman MF, Maeda K, Sakaguchi N. Integrity of immunoglobulin variable regions is supported by GANP during AID-induced somatic hypermutation in germinal center B cells. Int Immunol 2017; 29:211-220. [PMID: 28541550 PMCID: PMC5890899 DOI: 10.1093/intimm/dxx032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/22/2017] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin affinity maturation depends on somatic hypermutation (SHM) in immunoglobulin variable (IgV) regions initiated by activation-induced cytidine deaminase (AID). AID induces transition mutations by C→U deamination on both strands, causing C:G→T:A. Error-prone repairs of U by base excision and mismatch repairs (MMRs) create transversion mutations at C/G and mutations at A/T sites. In Neuberger’s model, it remained to be clarified how transition/transversion repair is regulated. We investigate the role of AID-interacting GANP (germinal center-associated nuclear protein) in the IgV SHM profile. GANP enhances transition mutation of the non-transcribed strand G and reduces mutation at A, restricted to GYW of the AID hotspot motif. It reduces DNA polymerase η hotspot mutations associated with MMRs followed by uracil-DNA glycosylase. Mutation comparison between IgV complementary and framework regions (FWRs) by Bayesian statistical estimation demonstrates that GANP supports the preservation of IgV FWR genomic sequences. GANP works to maintain antibody structure by reducing drastic changes in the IgV FWR in affinity maturation.
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Affiliation(s)
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan.,Laboratory of Host Defense, World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC).,Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shailendra Kumar Singh
- Laboratory of Host Defense, World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC)
| | - Sarah Ameen Almofty
- Laboratory of Immunology, Institute for Research and Medical Consultations (IRMC), University Of Dammam (UOD), PO Box 1982, Dammam 31441, Saudi Arabia
| | - Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, 1050 Childs Way, University Park, Los Angeles, CA 90089-2910, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, 1050 Childs Way, University Park, Los Angeles, CA 90089-2910, USA
| | - Kazuhiko Maeda
- Laboratory of Host Defense, World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC).,Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Nobuo Sakaguchi
- World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.,Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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49
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Girelli Zubani G, Zivojnovic M, De Smet A, Albagli-Curiel O, Huetz F, Weill JC, Reynaud CA, Storck S. Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs. J Exp Med 2017; 214:1169-1180. [PMID: 28283534 PMCID: PMC5379981 DOI: 10.1084/jem.20161576] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 11/06/2022] Open
Abstract
Girelli Zubani et al. show that the Pms2 component of the mismatch repair complex and multiple uracil glycosylases contribute, each with a distinct strand bias, to enlarge the Ig gene mutation spectrum from G-C to A-T bases. During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung−/−Pms2−/− mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases.
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Affiliation(s)
- Giulia Girelli Zubani
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Marija Zivojnovic
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Annie De Smet
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Olivier Albagli-Curiel
- Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Faculté de Médecine-Site Cochin, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - François Huetz
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France.,Département d'Immunologie, Institut Pasteur, 75015 Paris, France
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Sébastien Storck
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
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50
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Zan H, Tat C, Qiu Z, Taylor JR, Guerrero JA, Shen T, Casali P. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends to modulate antibody class-switch DNA recombination. Nat Commun 2017; 8:14244. [PMID: 28176781 PMCID: PMC5309807 DOI: 10.1038/ncomms14244] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
Antibody class-switch DNA recombination (CSR) is initiated by AID-introduced DSBs in the switch (S) regions targeted for recombination, as effected by Ku70/Ku86-mediated NHEJ. Ku-deficient B cells, however, undergo (reduced) CSR through an alternative(A)-NHEJ pathway, which introduces microhomologies in S-S junctions. As microhomology-mediated end-joining requires annealing of single-strand DNA ends, we addressed the contribution of single-strand annealing factors HR Rad52 and translesion DNA polymerase θ to CSR. Compared with their Rad52+/+ counterparts, which display normal CSR, Rad52-/- B cells show increased CSR, fewer intra-Sμ region recombinations, no/minimal microhomologies in S-S junctions, decreased c-Myc/IgH translocations and increased Ku70/Ku86 recruitment to S-region DSB ends. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends. It also facilitates a Ku-independent DSB repair, which favours intra-S region recombination and mediates, particularly in Ku absence, inter-S-S recombination, as emphasized by the significantly greater CSR reduction in Rad52-/- versus Rad52+/+ B cells on Ku86 knockdown.
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Affiliation(s)
- Hong Zan
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Connie Tat
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Zhifang Qiu
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Julia R. Taylor
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Justin A. Guerrero
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Tian Shen
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Paolo Casali
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
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