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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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2
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Zhu Z, Dong S, Qin S, Gu K, Zhou Y. ANOS1 accelerates the progression of esophageal cancer identified by multi-omic approaches. Am J Cancer Res 2024; 14:2343-2370. [PMID: 38859828 PMCID: PMC11162658 DOI: 10.62347/spcp3536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/27/2024] [Indexed: 06/12/2024] Open
Abstract
To assess the role of ANOS1 in esophageal cancer (ESCA) progression, multi-omic analysis and experimental validation were employed. It was revealed that ANOS1 expression is significantly enhanced in ESCA patients and cell lines. The expression level of ANOS1 in ESCA patients can distinguish the malignancy from normal tissue with an area under curve (AUC) >0.75. Moreover, increased expression of ANOS1 is associated with advanced T stage and worse disease-free survival of ESCA patients. Therefore, a clinically applicable nomogram with ANOS1 was established with strong predictive power. Furthermore, high expression of ANOS1 in ESCA is correlated with (i) the enrichment of epithelial-mesenchymal transition by gene set enrichment analysis, (ii) the involvement in hypoxia, angiogenesis, WNT signaling pathway, and TGFβ signaling pathway by gene set variation analysis, (iii) the presence of the small insertion and deletion mutational signature ID9, associated with chromothripsis, in the single-nucleotide polymorphism analysis, (iv) the amplification of 11q13.3 in the copy number variants analysis, (v) the enrichment of cancer-associated fibroblasts and mesenchymal stromal cells in the tumor microenvironment. All the results from multi-omic analysis indicate that ANOS1 plays a pivotal role in accelerating the progression of ESCA. Results from in vivo and in vitro experiments show that the knockdown of ANOS1 hampers the proliferation of ESCA cells, further validating the oncogenic role of ANOS1 in ESCA. Additionally, potential chemotherapeutics with sensitivity were identified in the high-ANOS1 group. In conclusion, ANOS1 accelerates the progression of ESCA.
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Affiliation(s)
- Zuoquan Zhu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Shikun Dong
- Department of Otorhinolaryngology, Zhongda Hospital, Southeast UniversityNanjing 210009, Jiangsu, China
| | - Shaolei Qin
- Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Ke Gu
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
| | - Yanjun Zhou
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Jiangnan UniversityWuxi 214000, Jiangsu, China
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3
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Granadillo Rodríguez M, Wong L, Chelico L. Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells. Front Genome Ed 2023; 5:1196697. [PMID: 37324648 PMCID: PMC10267419 DOI: 10.3389/fgeed.2023.1196697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation and in vitro deamination. Cell migration and soft agar colony formation assays assessed cellular transformation potential. We found that all three A3 enzymes had similar γH2AX foci formation, despite different deamination activities in vitro. Notably, in nuclear lysates, the in vitro deaminase activity of A3A, A3B, and A3H did not require digestion of cellular RNA, in contrast to that of A3B and A3H in whole-cell lysates. Their similar activities in cells, nonetheless, resulted in distinct phenotypes where A3A decreased colony formation in soft agar, A3B decreased colony formation in soft agar after hydroxyurea treatment, and A3H Hap I promoted cell migration. Overall, we show that in vitro deamination data do not always reflect cell DNA damage, all three A3s induce DNA damage, and the impact of each is different.
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4
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Boehm T, Morimoto R, Trancoso I, Aleksandrova N. Genetic conflicts and the origin of self/nonself-discrimination in the vertebrate immune system. Trends Immunol 2023; 44:372-383. [PMID: 36941153 DOI: 10.1016/j.it.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/22/2023]
Abstract
Genetic conflicts shape the genomes of prokaryotic and eukaryotic organisms. Here, we argue that some of the key evolutionary novelties of adaptive immune systems of vertebrates are descendants of prokaryotic toxin-antitoxin (TA) systems. Cytidine deaminases and RAG recombinase have evolved from genotoxic enzymes to programmable editors of host genomes, supporting the astounding discriminatory capability of variable lymphocyte receptors of jawless vertebrates, as well as immunoglobulins and T cell receptors of jawed vertebrates. The evolutionarily recent lymphoid lineage is uniquely sensitive to mutations of the DNA maintenance methylase, which is an orphaned distant relative of prokaryotic restriction-modification systems. We discuss how the emergence of adaptive immunity gave rise to higher order genetic conflicts between genetic parasites and their vertebrate host.
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Affiliation(s)
- Thomas Boehm
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Ryo Morimoto
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Inês Trancoso
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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5
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Zhou Y, Zhu J, Gu M, Gu K. Prognosis and Characterization of Microenvironment in Cervical Cancer Influenced by Fatty Acid Metabolism-Related Genes. JOURNAL OF ONCOLOGY 2023; 2023:6851036. [PMID: 36936374 PMCID: PMC10017219 DOI: 10.1155/2023/6851036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/13/2022] [Accepted: 02/08/2023] [Indexed: 03/21/2023]
Abstract
Increasing evidence suggests that diverse activation patterns of metabolic signalling pathways may lead to molecular diversity of cervical cancer (CC). But rare research focuses on the alternation of fatty acid metabolism (FAM) in CC. Therefore, we constructed and compared models based on the expression of FAM-related genes from the Cancer Genome Atlas by different machine learning algorithms. The most reliable model was built with 14 significant genes by LASSO-Cox regression, and the CC cohort was divided into low-/high-risk groups by the median of risk score. Then, a feasible nomogram was established and validated by C-index, calibration curve, net benefit, and decision curve analysis. Furthermore, the hub genes among differential expression genes were identified and the post-transcriptional and translational regulation networks were characterized. Moreover, the somatic mutation and copy number variation landscapes were depicted. Importantly, the specific mutation drivers and signatures of the FAM phenotypes were excavated. As a result, the high-risk samples were featured by activated de novo fatty acid synthesis, epithelial to mesenchymal transition, angiogenesis, and chronic inflammation response, which might be caused by mutations of oncogenic driver genes in RTK/RAS, PI3K, and NOTCH signalling pathways. Besides the hyperactivity of cytidine deaminase and deficiency of mismatch repair, the mutations of POLE might be partially responsible for the mutations in the high-risk group. Next, the antigenome including the neoantigen and cancer germline antigens was estimated. The decreasing expression of a series of cancer germline antigens was identified to be related to reduction of CD8 T cell infiltration in the high-risk group. Then, the comprehensive evaluation of connotations between the tumour microenvironment and FAM phenotypes demonstrated that the increasing risk score was related to the suppressive immune microenvironment. Finally, the prediction of therapy targets revealed that the patients with high risk might be sensitive to the RAF inhibitor AZ628. Our findings provide a novel insight for personalized treatment in CC.
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Affiliation(s)
- Yanjun Zhou
- 1Department of Radiotherapy and Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214000, China
| | - Jiahao Zhu
- 2Department of Outpatient Chemotherapy, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150000, China
| | - Mengxuan Gu
- 3Jiangnan University, Wuxi, Jiangsu 214000, China
| | - Ke Gu
- 1Department of Radiotherapy and Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214000, China
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6
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Serrano JC, von Trentini D, Berríos KN, Barka A, Dmochowski IJ, Kohli RM. Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A. ACS Chem Biol 2022; 17:3379-3388. [PMID: 36475588 PMCID: PMC9990883 DOI: 10.1021/acschembio.2c00796] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleic acid structure plays a critical role in governing the selectivity of DNA- and RNA-modifying enzymes. In the case of the APOBEC3 family of cytidine deaminases, these enzymes catalyze the conversion of cytosine (C) to uracil (U) in single-stranded DNA, primarily in the context of innate immunity. DNA deamination can also have pathological consequences, accelerating the evolution of viral genomes or, when the host genome is targeted by either APOBEC3A (A3A) or APOBEC3B (A3B), promoting tumor evolution leading to worse patient prognosis and chemotherapeutic resistance. For A3A, nucleic acid secondary structure has emerged as a critical determinant of substrate targeting, with a predilection for DNA that can form stem loop hairpins. Here, we report the development of a specific nanomolar-level, nucleic acid-based inhibitor of A3A. Our strategy relies on embedding the nucleobase 5-methylzebularine, a mechanism-based inhibitor, into a DNA dumbbell structure, which mimics the ideal substrate secondary structure for A3A. Structure-activity relationship studies using a panel of diverse inhibitors reveal a critical role for the stem and position of the inhibitor moiety in achieving potent inhibition. Moreover, we demonstrate that DNA dumbbell inhibitors, but not nonstructured inhibitors, show specificity against A3A relative to the closely related catalytic domain of A3B. Overall, our work demonstrates the feasibility of leveraging secondary structural preferences in inhibitor design, offering a blueprint for further development of modulators of DNA-modifying enzymes and potential therapeutics to circumvent APOBEC-driven viral and tumor evolution.
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Affiliation(s)
- Juan C. Serrano
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Dora von Trentini
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Kiara N. Berríos
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Aleksia Barka
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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7
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Schrank TP, Landess L, Stepp WH, Rehmani H, Weir WH, Lenze N, Lal A, Wu D, Kothari A, Hackman TG, Sheth S, Patel S, Jefferys SR, Issaeva N, Yarbrough WG. Comprehensive Viral Genotyping Reveals Prognostic Viral Phylogenetic Groups in HPV16-Associated Squamous Cell Carcinoma of the Oropharynx. Mol Cancer Res 2022; 20:1489-1501. [PMID: 35731223 PMCID: PMC11249119 DOI: 10.1158/1541-7786.mcr-21-0443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/05/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
Human papillomavirus-positive (HPV+) squamous cell carcinoma of the oropharynx (OPSCC) is the most prevalent HPV-associated malignancy in the United States and is primarily caused by HPV subtype 16 (HPV16). Favorable treatment outcomes have led to increasing interest in treatment deescalation to reduce treatment-related morbidity. Prognostic biomarkers are needed to identify appropriately low-risk patients for reduced treatment intensity. Targeted DNA sequencing including all HPV16 open reading frames was performed on tumors from 104 patients with HPV16+ OPSCC treated at a single center. Genotypes closely related to the HPV16-A1 reference were associated with increased numbers of somatic copy-number variants in the human genome and poor recurrence-free survival (RFS). Genotypes divergent from HPV16-A1 were associated with favorable RFS. These findings were independent of tobacco smoke exposure. Total RNA sequencing was performed on a second independent cohort of 89 HPV16+ OPSCC cases. HPV16 genotypes divergent from HPV16-A1 were again validated in this independent cohort, to be prognostic of improved RFS in patients with moderate (less than 30 pack-years) or low (no more than 10 pack-years) of tobacco smoke exposure. In summary, we show in two independent cohorts that viral sequence divergence from the HPV16-A1 reference is correlated with improved RFS in patients with moderate or low tobacco smoke exposure. IMPLICATIONS HPV16 genotype is a potential biomarker that could be easily adopted to guide therapeutic decision-making related to deescalation therapy.
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Affiliation(s)
- Travis P Schrank
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
- Linberger Comprehensive Cancer Center, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Lee Landess
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Wesley H Stepp
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Hina Rehmani
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - William H Weir
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Nicholas Lenze
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Asim Lal
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Di Wu
- Linberger Comprehensive Cancer Center, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Aditi Kothari
- Linberger Comprehensive Cancer Center, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Trevor G Hackman
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Siddharth Sheth
- Department of Medicne, Division of Oncology, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Shetal Patel
- Department of Medicne, Division of Oncology, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Stuart R Jefferys
- Linberger Comprehensive Cancer Center, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Natalia Issaeva
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
- Linberger Comprehensive Cancer Center, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
- Department of Pathology and Lab Medicine, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
| | - Wendell G Yarbrough
- Department of Otolaryngology-Head and Neck Surgery, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
- Linberger Comprehensive Cancer Center, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
- Department of Pathology and Lab Medicine, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, North Carolina
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8
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Cisneros LH, Vaske C, Bussey KJ. Identification of a signature of evolutionarily conserved stress-induced mutagenesis in cancer. Front Genet 2022; 13:932763. [PMID: 36147501 PMCID: PMC9488704 DOI: 10.3389/fgene.2022.932763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The clustering of mutations observed in cancer cells is reminiscent of the stress-induced mutagenesis (SIM) response in bacteria. Bacteria deploy SIM when faced with DNA double-strand breaks in the presence of conditions that elicit an SOS response. SIM employs DinB, the evolutionary precursor to human trans-lesion synthesis (TLS) error-prone polymerases, and results in mutations concentrated around DNA double-strand breaks with an abundance that decays with distance. We performed a quantitative study on single nucleotide variant calls for whole-genome sequencing data from 1950 tumors, non-inherited mutations from 129 normal samples, and acquired mutations in 3 cell line models of stress-induced adaptive mutation. We introduce statistical methods to identify mutational clusters, quantify their shapes and tease out the potential mechanism that produced them. Our results show that mutations in both normal and cancer samples are indeed clustered and have shapes indicative of SIM. Clusters in normal samples occur more often in the same genomic location across samples than in cancer suggesting loss of regulation over the mutational process during carcinogenesis. Additionally, the signatures of TLS contribute the most to mutational cluster formation in both patient samples as well as experimental models of SIM. Furthermore, a measure of cluster shape heterogeneity was associated with cancer patient survival with a hazard ratio of 5.744 (Cox Proportional Hazard Regression, 95% CI: 1.824-18.09). Our results support the conclusion that the ancient and evolutionary-conserved adaptive mutation response found in bacteria is a source of genomic instability in cancer. Biological adaptation through SIM might explain the ability of tumors to evolve in the face of strong selective pressures such as treatment and suggests that the conventional 'hit it hard' approaches to therapy could prove themselves counterproductive.
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Affiliation(s)
- Luis H. Cisneros
- NantOmics, LLC, Santa Cruz, CA, United States
- The Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, United States
| | | | - Kimberly J. Bussey
- NantOmics, LLC, Santa Cruz, CA, United States
- The Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, United States
- Precision Medicine, Midwestern University, Glendale, AZ, United States
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9
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Osia B, Twarowski J, Jackson T, Lobachev K, Liu L, Malkova A. Migrating bubble synthesis promotes mutagenesis through lesions in its template. Nucleic Acids Res 2022; 50:6870-6889. [PMID: 35748867 PMCID: PMC9262586 DOI: 10.1093/nar/gkac520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/23/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
Break-induced replication (BIR) proceeds via a migrating D-loop for hundreds of kilobases and is highly mutagenic. Previous studies identified long single-stranded (ss) nascent DNA that accumulates during leading strand synthesis to be a target for DNA damage and a primary source of BIR-induced mutagenesis. Here, we describe a new important source of mutagenic ssDNA formed during BIR: the ssDNA template for leading strand BIR synthesis formed during D-loop migration. Specifically, we demonstrate that this D-loop bottom template strand (D-BTS) is susceptible to APOBEC3A (A3A)-induced DNA lesions leading to mutations associated with BIR. Also, we demonstrate that BIR-associated ssDNA promotes an additional type of genetic instability: replication slippage between microhomologies stimulated by inverted DNA repeats. Based on our results we propose that these events are stimulated by both known sources of ssDNA formed during BIR, nascent DNA formed by leading strand synthesis, and the D-BTS that we describe here. Together we report a new source of mutagenesis during BIR that may also be shared by other homologous recombination pathways driven by D-loop repair synthesis.
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Affiliation(s)
| | | | - Tyler Jackson
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kirill Lobachev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Liping Liu
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Anna Malkova
- To whom correspondence should be addressed. Tel: +1 319 384 1285;
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10
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Barka A, Berríos KN, Bailer P, Schutsky EK, Wang T, Kohli RM. The Base-Editing Enzyme APOBEC3A Catalyzes Cytosine Deamination in RNA with Low Proficiency and High Selectivity. ACS Chem Biol 2022; 17:629-636. [PMID: 35262324 PMCID: PMC9949940 DOI: 10.1021/acschembio.1c00919] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human APOBEC3A (A3A) is a nucleic acid-modifying enzyme that belongs to the cytidine deaminase family. Canonically, A3A catalyzes the deamination of cytosine into uracil in single-stranded DNA, an activity that makes A3A both a critical antiviral defense factor and a useful tool for targeted genome editing. However, mutagenesis by A3A has also been readily detected in both cellular DNA and RNA, activities that have been implicated in cancer. Given the importance of substrate discrimination for the physiological, pathological, and biotechnological activities of A3A, here we explore the mechanistic basis for its preferential targeting of DNA over RNA. Using a chimeric substrate containing a target ribocytidine within an otherwise DNA backbone, we demonstrate that a single hydroxyl at the sugar of the target base acts as a major selectivity determinant for deamination. To assess the contribution of bases neighboring the target cytosine, we show that overall RNA deamination is greatly reduced relative to that of DNA but can be observed when ideal features are present, such as preferred sequence context and secondary structure. A strong dependence on idealized substrate features can also be observed with a mutant of A3A (eA3A, N57G), which has been employed for genome editing due to altered selectivity for DNA over RNA. Altogether, our work reveals a relationship between the overall decreased reactivity of A3A and increased substrate selectivity, and our results hold implications both for characterizing off-target mutagenesis and for engineering optimized DNA deaminases for base-editing technologies.
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Affiliation(s)
- Aleksia Barka
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Kiara N. Berríos
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Peter Bailer
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Emily K. Schutsky
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tong Wang
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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11
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Natesan D, Zhang L, Martell HJ, Jindal T, Devine P, Stohr B, Espinosa-Mendez C, Grenert J, Van Ziffle J, Joseph N, Umetsu S, Onodera C, Turski M, Chan E, Desai A, Aggarwal R, Wong A, Porten S, Chou J, Friedlander T, Fong L, Small EJ, Sweet-Cordero A, Koshkin VS. APOBEC Mutational Signature and Tumor Mutational Burden as Predictors of Clinical Outcomes and Treatment Response in Patients With Advanced Urothelial Cancer. Front Oncol 2022; 12:816706. [PMID: 35321431 PMCID: PMC8935010 DOI: 10.3389/fonc.2022.816706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
Introduction Tumor mutational burden (TMB) and APOBEC mutational signatures are potential prognostic markers in patients with advanced urothelial carcinoma (aUC). Their utility in predicting outcomes to specific therapies in aUC warrants additional study. Methods We retrospectively reviewed consecutive UC cases assessed with UCSF500, an institutional assay that uses hybrid capture enrichment of target DNA to interrogate 479 common cancer genes. Hypermutated tumors (HM), defined as having TMB ≥10 mutations/Mb, were also assessed for APOBEC mutational signatures, while non-HM (NHM) tumors were not assessed due to low TMB. The logrank test was used to determine if there were differences in overall survival (OS) and progression-free survival (PFS) among patient groups of interest. Results Among 75 aUC patients who had UCSF500 testing, 46 patients were evaluable for TMB, of which 19 patients (41%) had HM tumors and the rest had NHM tumors (27 patients). An additional 29 patients had unknown TMB status. Among 19 HM patients, all 16 patients who were evaluable for analysis had APOBEC signatures. HM patients (N=19) were compared with NHM patients (N=27) and had improved OS from diagnosis (125.3 months vs 35.7 months, p=0.06) but inferior OS for patients treated with chemotherapy (7.0 months vs 13.1 months, p=0.04). Patients with APOBEC (N=16) were compared with remaining 56 patients, comprised of 27 NHM patients and 29 patients with unknown TMB, showing APOBEC patients to have improved OS from diagnosis (125.3 months vs 44.5 months, p=0.05) but inferior OS for patients treated with chemotherapy (7.0 months vs 13.1 months, p=0.05). Neither APOBEC nor HM status were associated with response to immunotherapy. Conclusions In a large, single-institution aUC cohort assessed with UCSF500, an institutional NGS panel, HM tumors were common and all such tumors that were evaluated for mutational signature analysis had APOBEC signatures. APOBEC signatures and high TMB were prognostic of improved OS from diagnosis and both analyses also predicted inferior outcomes with chemotherapy treatment.
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Affiliation(s)
- Divya Natesan
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Li Zhang
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Henry J. Martell
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - Tanya Jindal
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Patrick Devine
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Bradley Stohr
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Carlos Espinosa-Mendez
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - James Grenert
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Jessica Van Ziffle
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Nancy Joseph
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Sarah Umetsu
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Courtney Onodera
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Michelle Turski
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Emily Chan
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Arpita Desai
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Rahul Aggarwal
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Anthony Wong
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Sima Porten
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Jonathan Chou
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Terence Friedlander
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Lawrence Fong
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Eric J. Small
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Alejandro Sweet-Cordero
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - Vadim S. Koshkin
- Helen Diller Family Cancer Center, University of California San Francisco, San Francisco, CA, United States
- *Correspondence: Vadim S. Koshkin,
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12
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Liu Y, Lan W, Wang C, Cao C. Two different kinds of interaction modes of deaminase APOBEC3A with single-stranded DNA in solution detected by nuclear magnetic resonance. Protein Sci 2022; 31:443-453. [PMID: 34792260 PMCID: PMC8819843 DOI: 10.1002/pro.4242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
APOBEC3A (A3A) deaminates deoxycytidine in target motif TC in a single-stranded DNA (we termed it as TC DNA), which mortally mutates viral pathogens and immunoglobulins, and leads to the diversification and lethality of cancers. The crystal structure of A3A-DNA revealed a unique U-shaped recognition mode of target base dC0 . However, when TC DNA was titrated into 15 N-labeled A3A solution, we observed two sets of 1 H-15 N cross-peaks of A3A in HSQC spectra, and two sets of 1 H-1 H cross-peaks of DNA in two-dimensional 13 C,15 N-filtered TOCSY spectra, indicating two different kinds of conformers of either A3A or TC DNA existing in solution. Here, mainly by NMR, we demonstrated that one DNA conformer interacted with one A3A conformer, forming a specific complex A3AS -DNAS in a way almost similar to that observed in the reported crystal A3A-DNA structure, where dC0 inserted into zinc ion binding center. While the other DNA conformer bound with another A3A conformer, but dC0 did not extend into the zinc-binding pocket, forming a nonspecific A3ANS -DNANS complex. The NMR solution structure implied three sites Asn61 , His182 and Arg189 were necessary to DNA recognition. These observations indicate a distinctive way from that reported in X-ray crystal structure, suggesting an unexpected mode of deaminase APOBEC3A to identify target motif TC in DNA in solution.
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Affiliation(s)
- Yaping Liu
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of ScienceBeijingChina
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product ChemistryCenter for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of ScienceBeijingChina
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Queiroz MM, de Souza ZS, Gongora ABL, de Galiza Barbosa F, Buchpiguel CA, de Castro MG, de Macedo MP, Coelho RF, Sokol ES, Camargo AA, Bastos DA. Emerging biomarkers in metastatic urothelial carcinoma: tumour mutational burden, PD-L1 expression and APOBEC polypeptide-like signature in a patient with complete response to anti-programmed cell death protein-1 inhibitor. Ecancermedicalscience 2021; 15:1306. [PMID: 34824629 PMCID: PMC8580725 DOI: 10.3332/ecancer.2021.1306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Indexed: 12/24/2022] Open
Abstract
Immunotherapy has recently been incorporated into the treatment guidelines for metastatic urothelial carcinoma. Nevertheless, the role of prognostic and predictive biomarkers in this setting is not completely defined. To date, PD-L1 expression and a high tumour mutational burden (TMB) seem to predict better responses to immune checkpoint inhibitors, but patients without these biomarkers may still respond to immunotherapy. There are some caveats regarding these biomarkers, such as lack of standardisation of techniques, tumour heterogeneity and other factors influencing the tumour microenvironment. Genomic signatures are other promising emerging strategies. We hereby discuss the management of a 70-year-old man with a metastatic recurrence of urothelial carcinoma within 1 year after neoadjuvant chemotherapy and radical cystectomy. Tumour next-generation sequencing showed a high TMB and a CD274 (PD-L1) amplification. The patient was treated with pembrolizumab and achieved a complete response.
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Affiliation(s)
- Marcello Moro Queiroz
- Oncology Center, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0001-5789-3397
| | - Zenaide Silva de Souza
- Oncology Center, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0002-9743-191X
| | - Aline Bobato Lara Gongora
- Oncology Center, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0002-2167-8166
| | - Felipe de Galiza Barbosa
- Department of Diagnostic Imaging and Nuclear Medicine, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0002-3986-1778
| | - Carlos Alberto Buchpiguel
- Department of Diagnostic Imaging and Nuclear Medicine, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0003-0956-2790
| | - Marilia Germanos de Castro
- Department of Pathology, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0001-8882-4650
| | - Mariana Petaccia de Macedo
- Department of Pathology, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0002-0434-7605
| | - Rafael Ferreira Coelho
- Instituto do Câncer do Estado de São Paulo, Av Dr Arnaldo, 251 - Cerqueira César, São Paulo, SP, 01246-000, Brazil
| | - Ethan Samuel Sokol
- Cancer Genomics Research, Foundation Medicine Inc., 150 Second St, Cambridge, MA 02141, USA
- https://orcid.org/0000-0002-2988-0537
| | - Anamaria Aranha Camargo
- Oncology Center, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0002-6076-9597
| | - Diogo Assed Bastos
- Oncology Center, Hospital Sírio-Libanês (HSL), Rua Dona Adma Jafet, 91, São Paulo, SP, 01308-050, Brazil
- https://orcid.org/0000-0003-2480-353X
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15
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Bussey KJ, Davies PCW. Reverting to single-cell biology: The predictions of the atavism theory of cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:49-55. [PMID: 34371024 PMCID: PMC8833046 DOI: 10.1016/j.pbiomolbio.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Cancer or cancer-like phenomena pervade multicellular life, implying deep evolutionary roots. Many of the hallmarks of cancer recapitulate unicellular modalities, suggesting that cancer initiation and progression represent a systematic reversion to simpler ancestral phenotypes in response to a stress or insult. This so-called atavism theory may be tested using phylostratigraphy, which can be used to assign ages to genes. Several research groups have confirmed that cancer cells tend to over-express evolutionary older genes, and rewire the architecture linking unicellular and multicellular gene networks. In addition, some of the elevated mutation rate - a well-known hallmark of cancer - is actually self-inflicted, driven by genes found to be homologs of the ancient SOS genes activated in stressed bacteria, and employed to evolve biological workarounds. These findings have obvious implications for therapy.
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Affiliation(s)
- Kimberly J Bussey
- Precision Medicine, Midwestern University, Glendale, AZ, USA; The BEYOND Center for Fundamental Concepts in Science, Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Paul C W Davies
- The BEYOND Center for Fundamental Concepts in Science, Department of Physics, Arizona State University, Tempe, AZ, USA.
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16
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Lin X, Hua Y, Gu S, Lv L, Li X, Chen P, Dai P, Hu Y, Liu A, Li J. kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing. BMC Genomics 2021; 22:440. [PMID: 34118871 PMCID: PMC8196519 DOI: 10.1186/s12864-021-07696-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations "violent storm", which is just what the Greek word "kataegis" means. RESULTS There are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package "kataegis" to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions. CONCLUSIONS The kataegis package is available on Bionconductor/Github ( https://github.com/flosalbizziae/kataegis ), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.
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Affiliation(s)
- Xue Lin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, 211166, Nanjing, People's Republic of China.
| | - Yingying Hua
- Traditional Chinese Medicine Department, Fuxing Hospital, Capital Medical University, 100038, Beijing, People's Republic of China
| | - Shuanglin Gu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China
| | - Li Lv
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China
| | - Xingyu Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China
| | - Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China
| | - Peng Dai
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, 211166, Nanjing, People's Republic of China
| | - Yunyun Hu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, 210096, Nanjing, People's Republic of China.
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17
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Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [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: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
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Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M. Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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18
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Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.
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Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
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19
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Biayna J, Garcia-Cao I, Álvarez MM, Salvadores M, Espinosa-Carrasco J, McCullough M, Supek F, Stracker TH. Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells. PLoS Biol 2021; 19:e3001176. [PMID: 33788831 PMCID: PMC8041192 DOI: 10.1371/journal.pbio.3001176] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 04/12/2021] [Accepted: 03/08/2021] [Indexed: 12/26/2022] Open
Abstract
Analysis of cancer mutagenic signatures provides information about the origin of mutations and can inform the use of clinical therapies, including immunotherapy. In particular, APOBEC3A (A3A) has emerged as a major driver of mutagenesis in cancer cells, and its expression results in DNA damage and susceptibility to treatment with inhibitors of the ATR and CHK1 checkpoint kinases. Here, we report the implementation of CRISPR/Cas-9 genetic screening to identify susceptibilities of multiple A3A-expressing lung adenocarcinoma (LUAD) cell lines. We identify HMCES, a protein recently linked to the protection of abasic sites, as a central protein for the tolerance of A3A expression. HMCES depletion results in synthetic lethality with A3A expression preferentially in a TP53-mutant background. Analysis of previous screening data reveals a strong association between A3A mutational signatures and sensitivity to HMCES loss and indicates that HMCES is specialized in protecting against a narrow spectrum of DNA damaging agents in addition to A3A. We experimentally show that both HMCES disruption and A3A expression increase susceptibility of cancer cells to ionizing radiation (IR), oxidative stress, and ATR inhibition, strategies that are often applied in tumor therapies. Overall, our results suggest that HMCES is an attractive target for selective treatment of A3A-expressing tumors.
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Affiliation(s)
- Josep Biayna
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Isabel Garcia-Cao
- Genomic Instability and Cancer, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Miguel M. Álvarez
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marina Salvadores
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jose Espinosa-Carrasco
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marcel McCullough
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- * E-mail: (FS); (THS)
| | - Travis H. Stracker
- Genomic Instability and Cancer, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- National Cancer Institute, Center for Cancer Research, Radiation Oncology Branch, Bethesda, Maryland, United States of America
- * E-mail: (FS); (THS)
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20
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Roufas C, Georgakopoulos-Soares I, Zaravinos A. Molecular correlates of immune cytolytic subgroups in colorectal cancer by integrated genomics analysis. NAR Cancer 2021; 3:zcab005. [PMID: 34316699 PMCID: PMC8210146 DOI: 10.1093/narcan/zcab005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
Although immune checkpoint inhibition (ICI) has shown promising results in metastatic dMMR/MSI-H colorectal cancer (CRC), the majority of pMMR/MSS patients do not respond to such therapies. To systematically evaluate the determinants of immune response in CRC, we explored whether patients with diverse levels of immune cytolytic activity (CYT) have different patterns of chromothripsis and kataegis. Analysis of CRC genomic data from the TCGA, indicated an excess of chromothriptic clusters among CYT-low colon adenocarcinomas, affecting known cancer drivers (APC, KRAS, BRAF, TP53 and FBXW7), immune checkpoints (CD274, PDCD1LG2, IDO1/2 and LAG3) and immune-related genes (ENTPD1, PRF1, NKG7, FAS, GZMA/B/H/K and CD73). CYT-high tumors were characterized by hypermutation, enrichment in APOBEC-associated mutations and kataegis events, as well as APOBEC activation. We also assessed differences in the most prevalent mutational signatures (SBS15, SBS20, SBS54 and DBS2) across cytolytic subgroups. Regarding the composition of immune cells in the tumor milieu, we found enrichment of M1 macrophages, CD8+ T cells and Tregs, as well as higher CD8+ T-cells/Tregs ratio among CYT-high tumors. CYT-high patients had higher immunophenoscores, which is predictive of their responsiveness if they were to be treated with anti-PD-1 alone or in combination with anti-CTLA-4 drugs. These results could have implications for patient responsiveness to immune checkpoint inhibitors.
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Affiliation(s)
- Constantinos Roufas
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus
| | - Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Apostolos Zaravinos
- Department of Basic Medical Sciences, College of Medicine, Member of QU Health, Qatar University, 2713 Doha, Qatar
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21
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Hu X, Xu Z, De S. Characteristics of mutational signatures of unknown etiology. NAR Cancer 2020; 2:zcaa026. [PMID: 33015626 PMCID: PMC7520824 DOI: 10.1093/narcan/zcaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/01/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022] Open
Abstract
Although not all somatic mutations are cancer drivers, their mutational signatures, i.e. the patterns of genomic alterations at a genome-wide scale, provide insights into past exposure to mutagens, DNA damage and repair processes. Computational deconvolution of somatic mutation patterns and expert curation pan-cancer studies have identified a number of mutational signatures associated with point mutations, dinucleotide substitutions, insertions and deletions, and rearrangements, and have established etiologies for a subset of these signatures. However, the mechanisms underlying nearly one-third of all mutational signatures are not yet understood. The signatures with established etiology and those with hitherto unknown origin appear to have some differences in strand bias, GC content and nucleotide context diversity. It is possible that some of the hitherto ‘unknown’ signatures predominantly occur outside gene regions. While nucleotide contexts might be adequate to establish etiologies of some mutational signatures, in other cases additional features, such as broader (epi)genomic contexts, including chromatin, replication timing, processivity and local mutational patterns, may help fully understand the underlying DNA damage and repair processes. Nonetheless, remarkable progress in characterization of mutational signatures has provided fundamental insights into the biology of cancer, informed disease etiology and opened up new opportunities for cancer prevention, risk management, and therapeutic decision making.
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Affiliation(s)
- Xiaoju Hu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Zhuxuan Xu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
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22
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Saini N, Gordenin DA. Hypermutation in single-stranded DNA. DNA Repair (Amst) 2020; 91-92:102868. [PMID: 32438271 PMCID: PMC7234795 DOI: 10.1016/j.dnarep.2020.102868] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
Regions of genomic DNA can become single-stranded in the course of normal replication and transcription as well as during DNA repair. Abnormal repair and replication intermediates can contain large stretches of persistent single-stranded DNA, which is extremely vulnerable to DNA damaging agents and hypermutation. Since such single-stranded DNA spans only a fraction of the genome at a given instance, hypermutation in these regions leads to tightly-spaced mutation clusters. This phenomenon of hypermutation in single-stranded DNA has been documented in several experimental models as well as in cancer genomes. Recently, hypermutated single-stranded RNA viral genomes also have been documented. Moreover, indications of hypermutation in single-stranded DNA may also be found in the human germline. This review will summarize key current knowledge and the recent developments in understanding the diverse mechanisms and sources of ssDNA hypermutation.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.
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23
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Branton SA, Ghorbani A, Bolt BN, Fifield H, Berghuis LM, Larijani M. Activation-induced cytidine deaminase can target multiple topologies of double-stranded DNA in a transcription-independent manner. FASEB J 2020; 34:9245-9268. [PMID: 32437054 DOI: 10.1096/fj.201903036rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 12/30/2022]
Abstract
Activation-induced cytidine deaminase (AID) mutates immunoglobulin genes and acts genome-wide. AID targets robustly transcribed genes, and purified AID acts on single-stranded (ss) but not double-stranded (ds) DNA oligonucleotides. Thus, it is believed that transcription is the generator of ssDNA for AID. Previous cell-free studies examining the relationship between transcription and AID targeting have employed a bacterial colony count assay wherein AID reverts an antibiotic resistance stop codon in plasmid substrates, leading to colony formation. Here, we established a novel assay where kb-long dsDNA of varying topologies is incubated with AID, with or without transcription, followed by direct sequencing. This assay allows for an unselected and in-depth comparison of mutation frequency and pattern of AID targeting in the absence of transcription or across a range of transcription dynamics. We found that without transcription, AID targets breathing ssDNA in supercoiled and, to a lesser extent, in relaxed dsDNA. The most optimal transcription only modestly enhanced AID action on supercoiled dsDNA in a manner dependent on RNA polymerase speed. These data suggest that the correlation between transcription and AID targeting may reflect transcription leading to AID-accessible breathing ssDNA patches naturally occurring in de-chromatinized dsDNA, as much as being due to transcription directly generating ssDNA.
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Affiliation(s)
- Sarah A Branton
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Brittany N Bolt
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Heather Fifield
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Lesley M Berghuis
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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24
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Sui Y, Qi L, Zhang K, Saini N, Klimczak LJ, Sakofsky CJ, Gordenin DA, Petes TD, Zheng DQ. Analysis of APOBEC-induced mutations in yeast strains with low levels of replicative DNA polymerases. Proc Natl Acad Sci U S A 2020; 117:9440-9450. [PMID: 32277034 PMCID: PMC7196835 DOI: 10.1073/pnas.1922472117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Yeast strains with low levels of the replicative DNA polymerases (alpha, delta, and epsilon) have high levels of chromosome deletions, duplications, and translocations. By examining the patterns of mutations induced in strains with low levels of DNA polymerase by the human protein APOBEC3B (a protein that deaminates cytosine in single-stranded DNA), we show dramatically elevated amounts of single-stranded DNA relative to a wild-type strain. During DNA replication, one strand (defined as the leading strand) is replicated processively by DNA polymerase epsilon and the other (the lagging strand) is replicated as short fragments initiated by DNA polymerase alpha and extended by DNA polymerase delta. In the low DNA polymerase alpha and delta strains, the APOBEC-induced mutations are concentrated on the lagging-strand template, whereas in the low DNA polymerase epsilon strain, mutations occur on the leading- and lagging-strand templates with similar frequencies. In addition, for most genes, the transcribed strand is mutagenized more frequently than the nontranscribed strand. Lastly, some of the APOBEC-induced clusters in strains with low levels of DNA polymerase alpha or delta are greater than 10 kb in length.
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Affiliation(s)
- Yang Sui
- Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Lei Qi
- Ocean College, Zhejiang University, 316021 Zhoushan, China
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
| | - Ke Zhang
- Ocean College, Zhejiang University, 316021 Zhoushan, China
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Cynthia J Sakofsky
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710;
| | - Dao-Qiong Zheng
- Ocean College, Zhejiang University, 316021 Zhoushan, China;
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710
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25
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Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Brief Bioinform 2019; 19:1085-1101. [PMID: 28498882 DOI: 10.1093/bib/bbx049] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 12/22/2022] Open
Abstract
Cancer is a genetic disorder, meaning that a plethora of different mutations, whether somatic or germ line, underlie the etiology of the 'Emperor of Maladies'. Point mutations, chromosomal rearrangements and copy number changes, whether they have occurred spontaneously in predisposed individuals or have been induced by intrinsic or extrinsic (environmental) mutagens, lead to the activation of oncogenes and inactivation of tumor suppressor genes, thereby promoting malignancy. This scenario has now been recognized and experimentally confirmed in a wide range of different contexts. Over the past decade, a surge in available sequencing technologies has allowed the sequencing of whole genomes from liquid malignancies and solid tumors belonging to different types and stages of cancer, giving birth to the new field of cancer genomics. One of the most striking discoveries has been that cancer genomes are highly enriched with mutations of specific kinds. It has been suggested that these mutations can be classified into 'families' based on their mutational signatures. A mutational signature may be regarded as a type of base substitution (e.g. C:G to T:A) within a particular context of neighboring nucleotide sequence (the bases upstream and/or downstream of the mutation). These mutational signatures, supplemented by mutable motifs (a wider mutational context), promise to help us to understand the nature of the mutational processes that operate during tumor evolution because they represent the footprints of interactions between DNA, mutagens and the enzymes of the repair/replication/modification pathways.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Youri I Pavlov
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, USA
| | | | | | - Artem G Lada
- Department Microbiology and Molecular Genetics, University of California, Davis, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Institutes of Health, USA
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26
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Yan X, Lan W, Wang C, Cao C. Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA. Chem Asian J 2019; 14:2235-2241. [PMID: 31116511 DOI: 10.1002/asia.201900480] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/20/2019] [Indexed: 02/05/2023]
Abstract
Human APOBEC3G (A3G) inhibits the replication of human immunodeficiency virus-1 by deaminating cytidine at the 3'-end in the target motif 5'-CCC-3' in viral cDNA during reverse transcription. It in vitro deaminates two consecutive cytidines in a 3'->5' order. Although a crystal structure of the A3G catalytic domain (A3G-CD2) with DNA was reported, it is unknown why residues involved in enzymatic reaction are distributed widely. Here, we introduced an iodine atom into the C-5 position of cytidine (dC6 I ) in DNA 5'-ATTC4 C5 C6 I A7 ATT-3' (TCCC6 I ). It switches the deamination sequence preference from CCC to TCC, although small dC6 I deamination was observed. Solution structures of A3G-CD2 in complexes with products DNA TCUC6 I and TCUU6 I indicate that the substrate DNA binds A3G-CD2 in TCC and CCC modes. The dC6 deamination correlates with the 4th base type. The CCC mode favours dC6 deamination, while the TCC mode results in dC5 deamination. These studies present an extensive basis to design inhibitors to impede viral evolvability.
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Affiliation(s)
- Xiaoxuan Yan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, 345 Lingling Road, Shanghai, 200032, China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China
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27
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Yamazaki H, Shirakawa K, Matsumoto T, Hirabayashi S, Murakawa Y, Kobayashi M, Sarca AD, Kazuma Y, Matsui H, Maruyama W, Fukuda H, Shirakawa R, Shindo K, Ri M, Iida S, Takaori-Kondo A. Endogenous APOBEC3B Overexpression Constitutively Generates DNA Substitutions and Deletions in Myeloma Cells. Sci Rep 2019; 9:7122. [PMID: 31073151 PMCID: PMC6509214 DOI: 10.1038/s41598-019-43575-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/26/2019] [Indexed: 02/07/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) DNA cytosine deaminases have emerged as potential genomic mutators in various cancers. Multiple myeloma accumulates APOBEC signature mutations as it progresses; however, the mechanisms underlying APOBEC signature acquisition and its consequences remain elusive. In this study, we examined the significance and clinical impact of APOBEC3B (A3B) activity in multiple myeloma. Among APOBECs, only highly expressed A3B was associated with poor prognosis in myeloma patients, independent of other known poor prognostic factors. Quantitative PCR revealed that CD138-positive primary myeloma cells and myeloma cell lines exhibited remarkably high A3B expression levels. Interestingly, lentiviral A3B knockdown prevented the generation of deletion and loss-of-function mutations in exogenous DNA, whereas in control cells, these mutations accumulated with time. A3B knockdown also decreased the basal levels of γ-H2AX foci, suggesting that A3B promotes constitutive DNA double-strand breaks in myeloma cells. Importantly, among control shRNA-transduced cells, we observed the generation of clones that harboured diverse mutations in exogenous genes and several endogenous genes frequently mutated in myeloma, including TP53. Taken together, the results suggest that A3B constitutively mutates the tumour genome beyond the protection of the DNA repair system, which may lead to clonal evolution and genomic instability in myeloma.
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Affiliation(s)
- Hiroyuki Yamazaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Tadahiko Matsumoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Shigeki Hirabayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.,RIKEN-HMC Clinical Omics Unit, RIKEN Baton Zone Program, Kanagawa, 230-0045, Japan
| | - Yasuhiro Murakawa
- RIKEN-HMC Clinical Omics Unit, RIKEN Baton Zone Program, Kanagawa, 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Kanagawa, 230-0045, Japan
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Anamaria Daniela Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Wataru Maruyama
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Hirofumi Fukuda
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Keisuke Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Masaki Ri
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.
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28
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Shapiro JA. No genome is an island: toward a 21st century agenda for evolution. Ann N Y Acad Sci 2019; 1447:21-52. [DOI: 10.1111/nyas.14044] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 12/21/2022]
Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular BiologyUniversity of Chicago Chicago Illinois
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29
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Boichard A, Pham TV, Yeerna H, Goodman A, Tamayo P, Lippman S, Frampton GM, Tsigelny IF, Kurzrock R. APOBEC-related mutagenesis and neo-peptide hydrophobicity: implications for response to immunotherapy. Oncoimmunology 2018; 8:1550341. [PMID: 30723579 PMCID: PMC6350681 DOI: 10.1080/2162402x.2018.1550341] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/11/2018] [Accepted: 11/10/2018] [Indexed: 01/07/2023] Open
Abstract
Tumor-associated neo-antigens are mutated peptides that allow the immune system to recognize the affected cell as foreign. Cells carrying excessive mutation load often develop mechanisms of tolerance. PD-L1/PD-1 checkpoint immunotherapy is a highly promising approach to overcome these protective signals and induce tumor shrinkage. Yet, the nature of the neo-antigens driving those beneficial responses remains unclear. Here, we show that APOBEC-related mutagenesis - a mechanism at the crossroads between anti-viral immunity and endogenous nucleic acid editing - increases neo-peptide hydrophobicity (a feature of immunogenicity), as demonstrated by in silico computation and in the TCGA pan-cancer cohort, where APOBEC-related mutagenesis was also strongly associated with immune marker expression. Moreover, APOBEC-related mutagenesis correlated with immunotherapy response in a cohort of 99 patients with diverse cancers, and this correlation was independent of the tumor mutation burden (TMB). Combining APOBEC-related mutagenesis estimate and TMB resulted in greater predictive ability than either parameter alone. Based on these results, further investigation of APOBEC-related mutagenesis as a marker of response to anti-cancer checkpoint blockade is warranted.
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Affiliation(s)
- Amélie Boichard
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
| | | | - Huwate Yeerna
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
| | - Aaron Goodman
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA.,Division of Blood and Marrow Transplantation, University of California, Moores Cancer Center, La Jolla, CA, USA
| | - Pablo Tamayo
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA.,Division of Medical Genetics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Scott Lippman
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
| | | | - Igor F Tsigelny
- CureMatch Inc., San Diego, CA, USA.,San Diego Supercomputer Center and Neuroscience Department, University of California San Diego, La Jolla, CA, USA
| | - Razelle Kurzrock
- Department of Medicine, Division of Hematology/Oncology, and Center for Personalized Cancer Therapy, University of California, Moores Cancer Center, La Jolla, CA, USA
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30
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Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res 2018; 28:1747-1756. [PMID: 30341162 PMCID: PMC6211645 DOI: 10.1101/gr.239244.118] [Citation(s) in RCA: 2590] [Impact Index Per Article: 431.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022]
Abstract
Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types. However, the downstream analysis of data from somatic mutations entails a number of computational and statistical approaches, requiring usage of independent software and numerous tools. Here, we describe an R Bioconductor package, Maftools, which offers a multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools only requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files. With the implementation of well-established statistical and computational methods, Maftools facilitates data-driven research and comparative analysis to discover novel results from publicly available data sets. In the present study, using three of the well-annotated cohorts from The Cancer Genome Atlas (TCGA), we describe the application of Maftools to reproduce known results. More importantly, we show that Maftools can also be used to uncover novel findings through integrative analysis.
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Affiliation(s)
- Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.,Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Yassen Assenov
- Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Christoph Plass
- Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA.,National University Cancer Institute, National University Hospital, 119074, Singapore
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31
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Fujiki Y, Yamamoto Y, Sueta A, Yamamoto-Ibusuki M, Goto-Yamaguchi L, Tomiguchi M, Takeshita T, Iwase H. APOBEC3B gene expression as a novel predictive factor for pathological complete response to neoadjuvant chemotherapy in breast cancer. Oncotarget 2018; 9:30513-30526. [PMID: 30093965 PMCID: PMC6078135 DOI: 10.18632/oncotarget.25495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 05/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3B (APOBEC3B) is a gene editing enzyme with cytidine deaminase activity and high expression of its mRNA in breast tumors have been shown to be associated with progressive cases and poor prognosis. In this study, we aimed to examine the relationship between the expression of APOBEC3B and the effect of neoadjuvant chemotherapy (NAC) using pretreatment biopsy tissue, and examined whether the expression of APOBEC3B influenced chemotherapy efficacy. Methods We retrospectively selected a total of 274 patients with primary breast cancer who received NAC in more than 4 courses and underwent surgery at our institute. We assessed the expression of APOBEC3B mRNA using pretreatment biopsy specimens of NAC by quantitative real-time PCR (qRT-PCR) and examined the relationship between APOBEC3B mRNA expression and sensitivity to chemotherapy using pathological complete response (pCR) as an indicator. Further, we assessed the prognostic value of APOBEC3B in the patients receiving NAC. Results APOBEC3B mRNA expression levels were successfully assessed in 173 (63.1%) of the 274 specimens. The total pCR rate was 36.4% (n = 63). An association between APOBEC3B expression levels and pCR was observed (Wilcoxon test, P ≤ 0.0001). The patients were divided into two groups, low (n = 66) and high (n = 107), according to the APOBEC3B expression levels, using the cut-off value calculated by the receiver operating characteristics (ROC) curve for pCR. The rate of pCR was significantly higher among the patients in the high group than among those in the low group (47.7% vs 18.2%, P ≤ 0.0001). High APOBEC3B expression was significantly associated with high nuclear grade (P = 0.0078), high Ki-67 labeling index (P = 0.0087), estrogen receptor (ER) negativity (P ≤ 0.0001) and human epidermal growth factor receptor 2 (HER2) negativity (P = 0.032). Tumor size (P = 0.011), ER (P ≤ 0.0001), HER2 (P = 0.0013) and APOBEC3B expression (P = 0.037) were independent predictive factors for pCR in multivariate analysis. However, there was no association between APOBEC3B expression and prognosis. Conclusions Our study showed that APOBEC3B mRNA expression correlated with sensitivity to NAC in breast cancer patients. In contrast to previous studies, APOBEC3B mRNA expression was not associated with breast cancer prognosis in patients receiving NAC.
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Affiliation(s)
- Yoshitaka Fujiki
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Yutaka Yamamoto
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Aiko Sueta
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Mutsuko Yamamoto-Ibusuki
- Department of Molecular-Targeting Therapy for Breast Cancer, Kumamoto University Hospital, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Lisa Goto-Yamaguchi
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Mai Tomiguchi
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Takashi Takeshita
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
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Sun R, Hu Z, Curtis C. Big Bang Tumor Growth and Clonal Evolution. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a028381. [PMID: 28710260 DOI: 10.1101/cshperspect.a028381] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution. Although first noted in colorectal tumors, effective neutrality may be relatively common. Additionally, punctuated evolution resulting from mutational bursts and cataclysmic genomic alterations have been described. In this review, we contrast these findings with the conventional gradualist view of clonal evolution and describe potential clinical and therapeutic implications of different evolutionary modes and tempos.
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Affiliation(s)
- Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, California 94305.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Zheng Hu
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, California 94305.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, California 94305.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305
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De S, Ganesan S. Looking beyond drivers and passengers in cancer genome sequencing data. Ann Oncol 2018; 28:938-945. [PMID: 27998972 DOI: 10.1093/annonc/mdw677] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cancer arises as a result of acquired changes in the DNA sequence of the genome of somatic cells. A subset of the genetic changes, dubbed driver mutations, propels tumor growth, and the remaining changes are passengers, apparently inconsequential for neoplastic transformation. Massive genome sequencing of thousands of tumors from all major cancer types has enabled cataloging of the so-called driver and passenger mutations, and facilitated molecular classification of cancer, guiding precision medicine approach for the patients. Nonetheless, innovative analyses of cancer genomics data has led to novel, sometimes serendipitous findings that have aided to our understanding of other aspects of the biology of the disease and opened up new frontiers. For instance, emerging findings show that mutational patterns in cancer genomes can help detect signatures of known and novel DNA damage and repair processes, provide a likely chronological account of genomic changes in cancer genomes, and allow revisiting the models of cancer evolution. These findings have stimulated original approaches to identify disease etiology, stratify patients, target the disease, and monitor patient responses, complementing driver-mutation centric approaches. In this review, we discuss these emerging approaches and unexpected breakthroughs, and their implications for basic cancer research and clinical practices.
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Affiliation(s)
- S De
- Center for Cancer Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, New Brunswick, USA
| | - S Ganesan
- Center for Cancer Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, New Brunswick, USA
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34
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Glaser AP, Fantini D, Wang Y, Yu Y, Rimar KJ, Podojil JR, Miller SD, Meeks JJ. APOBEC-mediated mutagenesis in urothelial carcinoma is associated with improved survival, mutations in DNA damage response genes, and immune response. Oncotarget 2017; 9:4537-4548. [PMID: 29435122 PMCID: PMC5796993 DOI: 10.18632/oncotarget.23344] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/26/2017] [Indexed: 12/20/2022] Open
Abstract
APOBEC enzymes are responsible for a mutation signature (TCW>T/G) implicated in a wide variety of tumors. We explore the APOBEC mutational signature in bladder cancer and the relationship with specific mutations, molecular subtype, gene expression, and survival using sequencing data from The Cancer Genome Atlas (n = 395), Beijing Genomics Institute (n = 99), and Cancer Cell Line Encyclopedia. Tumors were split into “APOBEC-high” and “APOBEC-low” based on APOBEC enrichment. Patients with APOBEC-high tumors have better overall survival compared to those with APOBEC-low tumors (38.2 vs. 18.5 months, p = 0.005). APOBEC-high tumors are more likely to have mutations in DNA damage response genes (TP53, ATR, BRCA2) and chromatin regulatory genes (ARID1A, MLL, MLL3), while APOBEC-low tumors are more likely to have mutations in FGFR3 and KRAS. APOBEC3A and APOBEC3B expression correlates with mutation burden, regardless of bladder tumor molecular subtype. APOBEC mutagenesis is associated with increased expression of immune signatures, including interferon signaling, and expression of APOBEC3B is increased after stimulation of APOBEC-high bladder cancer cell lines with IFNγ. In summary, APOBEC-high tumors are more likely to have mutations in DNA damage response and chromatin regulatory genes, potentially providing more substrate for APOBEC enzymes, leading to a hypermutational phenotype and the subsequent enhanced immune response.
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Affiliation(s)
- Alexander P Glaser
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Damiano Fantini
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Yiduo Wang
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Yanni Yu
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Kalen J Rimar
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Joseph R Podojil
- Interdepartmental Immunobiology Center, Department of Microbiology-Immunology, Northwestern University, Chicago, IL, USA
| | - Stephen D Miller
- Interdepartmental Immunobiology Center, Department of Microbiology-Immunology, Northwestern University, Chicago, IL, USA
| | - Joshua J Meeks
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
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35
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Lada AG, Stepchenkova EI, Zhuk AS, Kliver SF, Rogozin IB, Polev DE, Dhar A, Pavlov YI. Recombination Is Responsible for the Increased Recovery of Drug-Resistant Mutants with Hypermutated Genomes in Resting Yeast Diploids Expressing APOBEC Deaminases. Front Genet 2017; 8:202. [PMID: 29312434 PMCID: PMC5733079 DOI: 10.3389/fgene.2017.00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/22/2017] [Indexed: 12/11/2022] Open
Abstract
DNA editing deaminases (APOBECs) are implicated in generation of mutations in somatic cells during tumorigenesis. APOBEC-dependent mutagenesis is thought to occur during transient exposure of unprotected single-stranded DNA. Mutations frequently occur in clusters (kataegis). We investigated mechanisms of mutant generation in growing and resting diploid yeast expressing APOBEC from sea lamprey, PmCDA1, whose kataegistic effect was previously shown to be associated with transcription. We have found that the frequency of canavanine-resistant mutants kept raising after growth cessation, while the profile of transcription remained unchanged. Surprisingly, the overall number of mutations in the genomes did not elevate in resting cells. Thus, mutations were accumulated during vigorous growth stage with both intense replication and transcription. We found that the elevated recovery of can1 mutant clones in non-growing cells is the result of loss of heterozygosity (LOH) leading to clusters of homozygous mutations in the chromosomal regions distal to the reporter gene. We confirmed that recombination frequency in resting cells was elevated by orders of magnitude, suggesting that cells were transiently committed to meiotic levels of recombination, a process referred to in yeast genetics as return-to-growth. In its extreme, on day 6 of starvation, a few mutant clones were haploid, likely resulting from completed meiosis. Distribution of mutations along chromosomes indicated that PmCDA1 was active during ongoing recombination events and sometimes produced characteristic kataegis near initial breakpoints. AID and APOBEC1 behaved similar to PmCDA1. We conclude that replication, transcription, and mitotic recombination contribute to the recovered APOBEC-induced mutations in resting diploids. The mechanism is relevant to the initial stages of oncogenic transformation in terminally differentiated cells, when recombination may lead to the LOH exposing recessive mutations induced by APOBECs in cell's history and to acquisition of new mutations near original break.
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Affiliation(s)
- Artem G Lada
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Elena I Stepchenkova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Anna S Zhuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Sergei F Kliver
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.,Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitrii E Polev
- Research Resource Center "Biobank", Research Park, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Alok Dhar
- Department of Genetics, Cell Biology and Anatomy and Vice Chancellor of Research Core, University of Nebraska Medical Center, Omaha, NE, United States
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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36
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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37
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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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38
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Boehm T, Hirano M, Holland SJ, Das S, Schorpp M, Cooper MD. Evolution of Alternative Adaptive Immune Systems in Vertebrates. Annu Rev Immunol 2017; 36:19-42. [PMID: 29144837 DOI: 10.1146/annurev-immunol-042617-053028] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive immunity in jawless fishes is based on antigen recognition by three types of variable lymphocyte receptors (VLRs) composed of variable leucine-rich repeats, which are differentially expressed by two T-like lymphocyte lineages and one B-like lymphocyte lineage. The T-like cells express either VLRAs or VLRCs of yet undefined antigen specificity, whereas the VLRB antibodies secreted by B-like cells bind proteinaceous and carbohydrate antigens. The incomplete VLR germline genes are assembled into functional units by a gene conversion-like mechanism that employs flanking variable leucine-rich repeat sequences as templates in association with lineage-specific expression of cytidine deaminases. B-like cells develop in the hematopoietic typhlosole and kidneys, whereas T-like cells develop in the thymoid, a thymus-equivalent region at the gill fold tips. Thus, the dichotomy between T-like and B-like cells and the presence of dedicated lymphopoietic tissues emerge as ancestral vertebrate features, whereas the somatic diversification of structurally distinct antigen receptor genes evolved independently in jawless and jawed vertebrates.
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Affiliation(s)
- Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; , ,
| | - Masayuki Hirano
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA; , ,
| | - Stephen J Holland
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; , ,
| | - Sabyasachi Das
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA; , ,
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; , ,
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia 30322, USA; , ,
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39
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Schutsky EK, Nabel CS, Davis A, DeNizio JE, Kohli RM. APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA. Nucleic Acids Res 2017; 45:7655-7665. [PMID: 28472485 PMCID: PMC5570014 DOI: 10.1093/nar/gkx345] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/18/2017] [Indexed: 12/21/2022] Open
Abstract
AID/APOBEC family enzymes are best known for deaminating cytosine bases to uracil in single-stranded DNA, with characteristic sequence preferences that can produce mutational signatures in targets such as retroviral and cancer cell genomes. These deaminases have also been proposed to function in DNA demethylation via deamination of either 5-methylcytosine (mC) or TET-oxidized mC bases (ox-mCs), which include 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. One specific family member, APOBEC3A (A3A), has been shown to readily deaminate mC, raising the prospect of broader activity on ox-mCs. To investigate this claim, we developed a novel assay that allows for parallel profiling of activity on all modified cytosines. Our steady-state kinetic analysis reveals that A3A discriminates against all ox-mCs by >3700-fold, arguing that ox-mC deamination does not contribute substantially to demethylation. A3A is, by contrast, highly proficient at C/mC deamination. Under conditions of excess enzyme, C/mC bases can be deaminated to completion in long DNA segments, regardless of sequence context. Interestingly, under limiting A3A, the sequence preferences observed with targeting unmodified cytosine are further exaggerated when deaminating mC. Our study informs how methylation, oxidation, and deamination can interplay in the genome and suggests A3A's potential utility as a biotechnological tool to discriminate between cytosine modification states.
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Affiliation(s)
- Emily K. Schutsky
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher S. Nabel
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy K. F. Davis
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie E. DeNizio
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
- To whom correspondence should be addressed. Tel: +1 215 573 7523; Fax: +1 215 348 5111;
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40
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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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41
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Esser D, Holze N, Haag J, Schreiber S, Krüger S, Warneke V, Rosenstiel P, Röcken C. Interpreting whole genome and exome sequencing data of individual gastric cancer samples. BMC Genomics 2017; 18:517. [PMID: 28683819 PMCID: PMC5501078 DOI: 10.1186/s12864-017-3895-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 06/22/2017] [Indexed: 01/18/2023] Open
Abstract
Background Gastric cancer is the fourth most common cancer and the second leading cause of cancer death worldwide. In order to understand the genetic background, we sequenced the whole exome and the whole genome of one microsatellite stable as well as one microsatellite unstable tumor and the matched healthy tissue on two different NGS platforms. We here aimed to provide a comparative approach for individual clinical tumor sequencing and annotation using different sequencing technologies and mutation calling algorithms. Results We applied a population-based whole genome resource as a novel pathway-based filter for interpretation of genomic alterations from single nucleotide variations (SNV), indels, and large structural variations. In addition to a comparison with tumor genome database resources and a filtering approach using data from the 1000 Genomes Project, we performed pyrosequencing analysis and immunohistochemistry in a large cohort of 428 independent gastric cancer cases. Conclusion We here provide an example comparing the usefulness and potential pitfalls of different technologies for a clinical interpretation of genomic sequence data of individual gastric cancer samples. Using different filtering approaches, we identified a multitude of novel potentially damaging mutations and could show a validated association between a mutation in GNAS and gastric cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3895-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniela Esser
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany.,Institute for Experimental Medicine, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Niklas Holze
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, Haus 14, D-24105, Kiel, Germany
| | - Jochen Haag
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, Haus 14, D-24105, Kiel, Germany
| | - Stefan Schreiber
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany.,Department of General Internal Medicine, University Hospital Schleswig-Holstein, 24105, Kiel, Germany
| | - Sandra Krüger
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, Haus 14, D-24105, Kiel, Germany
| | - Viktoria Warneke
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, Haus 14, D-24105, Kiel, Germany
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Christoph Röcken
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, Haus 14, D-24105, Kiel, Germany.
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42
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Chen Z, Eggerman TL, Bocharov AV, Baranova IN, Vishnyakova TG, Kurlander R, Patterson AP. Heat shock proteins stimulate APOBEC-3-mediated cytidine deamination in the hepatitis B virus. J Biol Chem 2017. [PMID: 28637869 DOI: 10.1074/jbc.m116.760637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic subunit 3 (APOBEC-3) enzymes are cytidine deaminases that are broadly and constitutively expressed. They are often up-regulated during carcinogenesis and candidate genes for causing the major single-base substitution in cancer-associated DNA mutations. Moreover, APOBEC-3s are involved in host innate immunity against many viruses. However, how APOBEC-3 mutational activity is regulated in normal and pathological conditions remains largely unknown. Heat shock protein levels are often elevated in both carcinogenesis and viral infection and are associated with DNA mutations. Here, using mutational analyses of hepatitis B virus (HBV), we found that Hsp90 stimulates deamination activity of APOBEC-3G (A3G), A3B, and A3C during co-expression in human liver HepG2 cells. Hsp90 directly stimulated A3G deamination activity when the purified proteins were used in in vitro reactions. Hsp40, -60, and -70 also had variable stimulatory effects in the cellular assay, but not in vitro Sequencing analyses further demonstrated that Hsp90 increased both A3G cytosine mutation efficiency on HBV DNA and total HBV mutation frequency. In addition, Hsp90 shifted A3G's cytosine region selection in HBV DNA and increased A3G's 5' nucleoside preference for deoxycytidine (5'-CC). Furthermore, the Hsp90 inhibitor 17-N-allylamino-17-demethoxygeldanamycin dose dependently inhibited A3G and A3B mutational activity on HBV viral DNA. Hsp90 knockdown by siRNA or by Hsp90 active-site mutation also decreased A3G activity. These results indicate that heat shock proteins, in particular Hsp90, stimulate APOBEC-3-mediated DNA deamination activity, suggesting a potential physiological role in carcinogenesis and viral innate immunity.
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Affiliation(s)
- Zhigang Chen
- From the Department of Laboratory Medicine, Clinical Center
| | - Thomas L Eggerman
- From the Department of Laboratory Medicine, Clinical Center.,the Division of Diabetes, Endocrinology, and Metabolic Diseases, NIDDK, and
| | | | | | | | | | - Amy P Patterson
- From the Department of Laboratory Medicine, Clinical Center, .,NHLBI, National Institutes of Health, Bethesda, Maryland 20892
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43
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Green AM, Landry S, Budagyan K, Avgousti DC, Shalhout S, Bhagwat AS, Weitzman MD. APOBEC3A damages the cellular genome during DNA replication. Cell Cycle 2017; 15:998-1008. [PMID: 26918916 DOI: 10.1080/15384101.2016.1152426] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The human APOBEC3 family of DNA-cytosine deaminases comprises 7 members (A3A-A3H) that act on single-stranded DNA (ssDNA). The APOBEC3 proteins function within the innate immune system by mutating DNA of viral genomes and retroelements to restrict infection and retrotransposition. Recent evidence suggests that APOBEC3 enzymes can also cause damage to the cellular genome. Mutational patterns consistent with APOBEC3 activity have been identified by bioinformatic analysis of tumor genome sequences. These mutational signatures include clusters of base substitutions that are proposed to occur due to APOBEC3 deamination. It has been suggested that transiently exposed ssDNA segments provide substrate for APOBEC3 deamination leading to mutation signatures within the genome. However, the mechanisms that produce single-stranded substrates for APOBEC3 deamination in mammalian cells have not been demonstrated. We investigated ssDNA at replication forks as a substrate for APOBEC3 deamination. We found that APOBEC3A (A3A) expression leads to DNA damage in replicating cells but this is reduced in quiescent cells. Upon A3A expression, cycling cells activate the DNA replication checkpoint and undergo cell cycle arrest. Additionally, we find that replication stress leaves cells vulnerable to A3A-induced DNA damage. We propose a model to explain A3A-induced damage to the cellular genome in which cytosine deamination at replication forks and other ssDNA substrates results in mutations and DNA breaks. This model highlights the risk of mutagenesis by A3A expression in replicating progenitor cells, and supports the emerging hypothesis that APOBEC3 enzymes contribute to genome instability in human tumors.
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Affiliation(s)
- Abby M Green
- a Division of Oncology , Department of Pediatrics , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA.,b Center for Childhood Cancer Research, Children's Hospital of Philadelphia , Philadelphia , PA , USA
| | - Sébastien Landry
- c Faculty of Pharmacy, Université de Montréal , Montréal , QC , Canada
| | - Konstantin Budagyan
- d Division of Cancer Pathobiology , Department of Pathology and Laboratory Medicine , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Daphne C Avgousti
- d Division of Cancer Pathobiology , Department of Pathology and Laboratory Medicine , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Sophia Shalhout
- e Department of Chemistry , Wayne State University , Detroit , MI , USA
| | - Ashok S Bhagwat
- e Department of Chemistry , Wayne State University , Detroit , MI , USA.,f Department of Immunology and Microbiology , Wayne State University School of Medicine , Detroit , MI , USA
| | - Matthew D Weitzman
- b Center for Childhood Cancer Research, Children's Hospital of Philadelphia , Philadelphia , PA , USA.,d Division of Cancer Pathobiology , Department of Pathology and Laboratory Medicine , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
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44
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Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity. Genes (Basel) 2017; 8:genes8010046. [PMID: 28117753 PMCID: PMC5295039 DOI: 10.3390/genes8010046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.
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45
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Johnson MD, Reeder JE, O'Connell M. APOBEC3B expression in human leptomeninges and meningiomas. Oncol Lett 2017; 12:5344-5348. [PMID: 28101245 DOI: 10.3892/ol.2016.5377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 09/15/2016] [Indexed: 11/06/2022] Open
Abstract
Nucleic acid-editing enzymes of the apolipoprotein B mRNA-editing enzyme (APOBEC) family have been associated with somatic mutation in cancer. However, the role of APOBEC catalytic subunit 3B (APOBEC3B) editing in the pathogenesis of base substitutions in meningiomas is unknown. In the present study, the expression of APOBEC3B was examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analyses in five fetal and one adult human leptomeninges and 38 meningiomas. Genomic DNA was sequenced using the Illumina Tru-Seq Cancer Panel. Three meningioma primary cultures were also established and treated with cerebrospinal fluid form patients without neurological disease or platelet-derived growth factor-BB (PDGF-BB), prior to evaluation of APOBEC3B expression. By western blotting, APOBEC3B was revealed to be present in 100% of the fetal leptomeninges, and in 88% of World Health Organization grade I, 100% of grade II and 83% of grade III meningiomas tested, but was not different between grades. RT-qPCR revealed no difference in the mRNA expression of APOBEC3B between grades. Sequencing revealed no elevated levels of the C>T mutations that are characteristic of APOBEC3B editing of genomic DNA. Treatment with cerebrospinal fluid and PDGF-BB had no effect on APOBEC3B protein expression in the leptomeningeal or meningioma cells. These findings suggest that the mutations associated with increased APOBEC3B expression may not be central to the pathogenesis of meningiomas.
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Affiliation(s)
- Mahlon D Johnson
- Department of Pathology, Division of Neuropathology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14623, USA
| | - Jay E Reeder
- Department of Urology, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, NY 14623, USA
| | - Mary O'Connell
- Department of Pathology, Division of Neuropathology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14623, USA
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Sapoznik S, Bahar-Shany K, Brand H, Pinto Y, Gabay O, Glick-Saar E, Dor C, Zadok O, Barshack I, Zundelevich A, Gal-Yam EN, Yung Y, Hourvitz A, Korach J, Beiner M, Jacob J, Levanon EY, Barak M, Aviel-Ronen S, Levanon K. Activation-Induced Cytidine Deaminase Links Ovulation-Induced Inflammation and Serous Carcinogenesis. Neoplasia 2016; 18:90-9. [PMID: 26936395 PMCID: PMC5005261 DOI: 10.1016/j.neo.2015.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 12/10/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022] Open
Abstract
In recent years, the notion that ovarian carcinoma results from ovulation-induced inflammation of the fallopian tube epithelial cells (FTECs) has gained evidence. However, the mechanistic pathway for this process has not been revealed yet. In the current study, we propose the mutator protein activation-induced cytidine deaminase (AID) as a link between ovulation-induced inflammation in FTECs and genotoxic damage leading to ovarian carcinogenesis. We show that AID, previously shown to be functional only in B lymphocytes, is expressed in FTECs under physiological conditions, and is induced in vitro upon ovulatory-like stimulation and in vivo in carcinoma-associated FTECs. We also report that AID activity results in epigenetic, genetic and genomic damage in FTECs. Overall, our data provides new insights into the etiology of ovarian carcinogenesis and may set the ground for innovative approaches aimed at prevention and early detection.
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Affiliation(s)
- Stav Sapoznik
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Keren Bahar-Shany
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Hadar Brand
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Israel
| | - Yishay Pinto
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Orshay Gabay
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Efrat Glick-Saar
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Chen Dor
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Oranit Zadok
- Department of Pathology, Chaim Sheba Medical Center, Ramat-Gan 52621, Israel
| | - Iris Barshack
- Department of Pathology, Chaim Sheba Medical Center, Ramat-Gan 52621, Israel
| | - Adi Zundelevich
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Einav Nili Gal-Yam
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel; The Talpiot Medical Leadership Program, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Yuval Yung
- IVF Unit and Reproduction Lab, Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Ramat-Gan, 52621, Israel
| | - Ariel Hourvitz
- IVF Unit and Reproduction Lab, Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Ramat-Gan, 52621, Israel
| | - Jacob Korach
- Department of Gynecologic Oncology, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Mario Beiner
- Department of Gynecologic Oncology, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Jasmine Jacob
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Michal Barak
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Sarit Aviel-Ronen
- Department of Pathology, Chaim Sheba Medical Center, Ramat-Gan 52621, Israel; The Talpiot Medical Leadership Program, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel
| | - Keren Levanon
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Israel; The Talpiot Medical Leadership Program, Chaim Sheba Medical Center, Ramat Gan, 52621, Israel.
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47
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Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Sci Rep 2016; 6:38133. [PMID: 27924834 PMCID: PMC5141443 DOI: 10.1038/srep38133] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/07/2016] [Indexed: 01/12/2023] Open
Abstract
Follicular lymphoma (FL) is an uncurable cancer characterized by progressive severity of relapses. We analyzed sequence context specificity of mutations in the B cells from a large cohort of FL patients. We revealed substantial excess of mutations within a novel hybrid nucleotide motif: the signature of somatic hypermutation (SHM) enzyme, Activation Induced Deaminase (AID), which overlaps the CpG methylation site. This finding implies that in FL the SHM machinery acts at genomic sites containing methylated cytosine. We identified the prevalence of this hybrid mutational signature in many other types of human cancer, suggesting that AID-mediated, CpG-methylation dependent mutagenesis is a common feature of tumorigenesis.
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48
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Abstract
It has been long understood that mutation distribution is not completely random across genomic space and in time. Indeed, recent surprising discoveries identified multiple simultaneous mutations occurring in tiny regions within chromosomes while the rest of the genome remains relatively mutation-free. Mechanistic elucidation of these phenomena, called mutation showers, mutation clusters, or kataegis, in parallel with findings of abundant clustered mutagenesis in cancer genomes, is ongoing. So far, the combination of factors most important for clustered mutagenesis is the induction of DNA lesions within unusually long and persistent single-strand DNA intermediates. In addition to being a fascinating phenomenon, clustered mutagenesis also became an indispensable tool for identifying a previously unrecognized major source of mutation in cancer, APOBEC cytidine deaminases. Future research on clustered mutagenesis may shed light onto important mechanistic details of genome maintenance, with potentially profound implications for human health.
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Affiliation(s)
- Kin Chan
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
| | - Dmitry A Gordenin
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
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49
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AID/APOBEC-network reconstruction identifies pathways associated with survival in ovarian cancer. BMC Genomics 2016; 17:643. [PMID: 27527602 PMCID: PMC4986275 DOI: 10.1186/s12864-016-3001-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/08/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Building up of pathway-/disease-relevant signatures provides a persuasive tool for understanding the functional relevance of gene alterations and gene network associations in multifactorial human diseases. Ovarian cancer is a highly complex heterogeneous malignancy in respect of tumor anatomy, tumor microenvironment including pro-/antitumor immunity and inflammation; still, it is generally treated as single disease. Thus, further approaches to investigate novel aspects of ovarian cancer pathogenesis aiming to provide a personalized strategy to clinical decision making are of high priority. Herein we assessed the contribution of the AID/APOBEC family and their associated genes given the remarkable ability of AID and APOBECs to edit DNA/RNA, and as such, providing tools for genetic and epigenetic alterations potentially leading to reprogramming of tumor cells, stroma and immune cells. RESULTS We structured the study by three consecutive analytical modules, which include the multigene-based expression profiling in a cohort of patients with primary serous ovarian cancer using a self-created AID/APOBEC-associated gene signature, building up of multivariable survival models with high predictive accuracy and nomination of top-ranked candidate/target genes according to their prognostic impact, and systems biology-based reconstruction of the AID/APOBEC-driven disease-relevant mechanisms using transcriptomics data from ovarian cancer samples. We demonstrated that inclusion of the AID/APOBEC signature-based variables significantly improves the clinicopathological variables-based survival prognostication allowing significant patient stratification. Furthermore, several of the profiling-derived variables such as ID3, PTPRC/CD45, AID, APOBEC3G, and ID2 exceed the prognostic impact of some clinicopathological variables. We next extended the signature-/modeling-based knowledge by extracting top genes co-regulated with target molecules in ovarian cancer tissues and dissected potential networks/pathways/regulators contributing to pathomechanisms. We thereby revealed that the AID/APOBEC-related network in ovarian cancer is particularly associated with remodeling/fibrotic pathways, altered immune response, and autoimmune disorders with inflammatory background. CONCLUSIONS The herein study is, to our knowledge, the first one linking expression of entire AID/APOBECs and interacting genes with clinical outcome with respect to survival of cancer patients. Overall, data propose a novel AID/APOBEC-derived survival model for patient risk assessment and reconstitute mapping to molecular pathways. The established study algorithm can be applied further for any biologically relevant signature and any type of diseased tissue.
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50
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Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF. Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification. DNA Repair (Amst) 2016; 43:48-56. [PMID: 27258794 DOI: 10.1016/j.dnarep.2016.05.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 12/18/2022]
Abstract
Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) and class-switch recombination (CSR) by deaminating C→U during transcription of Ig-variable (V) and Ig-switch (S) region DNA, which is essential to produce high-affinity antibodies. Here we report the crystal structure of a soluble human AID variant at 2.8Å resolution that favors targeting WRC motifs (W=A/T, R=A/G) in vitro, and executes Ig V SHM in Ramos B-cells. A specificity loop extending away from the active site to accommodate two purine bases next to C, differs significantly in sequence, length, and conformation from APOBEC proteins Apo3A and Apo3G, which strongly favor pyrimidines at -1 and -2 positions. Individual amino acid contributions to specificity and processivity were measured in relation to a proposed ssDNA binding cleft. This study provides a structural basis for residue contributions to DNA scanning properties unique to AID, and for disease mutations in human HIGM-2 syndrome.
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Affiliation(s)
- Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States
| | - Samir A Afif
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan; Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan
| | - Nobuo Sakaguchi
- World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, United States
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States.
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