1
|
Wiecek AJ, Jacobson DH, Lason W, Secrier M. Pan-Cancer Survey of Tumor Mass Dormancy and Underlying Mutational Processes. Front Cell Dev Biol 2021; 9:698659. [PMID: 34307377 PMCID: PMC8299471 DOI: 10.3389/fcell.2021.698659] [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: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Abstract
Tumor mass dormancy is the key intermediate step between immune surveillance and cancer progression, yet due to its transitory nature it has been difficult to capture and characterize. Little is understood of its prevalence across cancer types and of the mutational background that may favor such a state. While this balance is finely tuned internally by the equilibrium between cell proliferation and cell death, the main external factors contributing to tumor mass dormancy are immunological and angiogenic. To understand the genomic and cellular context in which tumor mass dormancy may develop, we comprehensively profiled signals of immune and angiogenic dormancy in 9,631 cancers from the Cancer Genome Atlas and linked them to tumor mutagenesis. We find evidence for immunological and angiogenic dormancy-like signals in 16.5% of bulk sequenced tumors, with a frequency of up to 33% in certain tissues. Mutations in the CASP8 and HRAS oncogenes were positively selected in dormant tumors, suggesting an evolutionary pressure for controlling cell growth/apoptosis signals. By surveying the mutational damage patterns left in the genome by known cancer risk factors, we found that aging-induced mutations were relatively depleted in these tumors, while patterns of smoking and defective base excision repair were linked with increased tumor mass dormancy. Furthermore, we identified a link between APOBEC mutagenesis and dormancy, which comes in conjunction with immune exhaustion and may partly depend on the expression of the angiogenesis regulator PLG as well as interferon and chemokine signals. Tumor mass dormancy also appeared to be impaired in hypoxic conditions in the majority of cancers. The microenvironment of dormant cancers was enriched in cytotoxic and regulatory T cells, as expected, but also in macrophages and showed a reduction in inflammatory Th17 signals. Finally, tumor mass dormancy was linked with improved patient survival outcomes. Our analysis sheds light onto the complex interplay between dormancy, exhaustion, APOBEC activity and hypoxia, and sets directions for future mechanistic explorations.
Collapse
Affiliation(s)
- Anna Julia Wiecek
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Daniel Hadar Jacobson
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom.,UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Wojciech Lason
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| |
Collapse
|
2
|
Prasad R, Yen TJ, Bellacosa A. Active DNA demethylation-The epigenetic gatekeeper of development, immunity, and cancer. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 2:e10033. [PMID: 36618446 PMCID: PMC9744510 DOI: 10.1002/ggn2.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/11/2023]
Abstract
DNA methylation is a critical process in the regulation of gene expression with dramatic effects in development and continually expanding roles in oncogenesis. 5-Methylcytosine was once considered to be an inherited and stably repressive epigenetic mark, which can be only removed by passive dilution during multiple rounds of DNA replication. However, in the past two decades, physiologically controlled DNA demethylation and deamination processes have been identified, thereby revealing the function of cytosine methylation as a highly regulated and complex state-not simply a static, inherited signature or binary on-off switch. Alongside these fundamental discoveries, clinical studies over the past decade have revealed the dramatic consequences of aberrant DNA demethylation. In this review we discuss DNA demethylation and deamination in the context of 5-methylcytosine as critical processes for physiological and physiopathological transitions within three states-development, immune maturation, and oncogenic transformation; and we describe the expanding role of DNA demethylating drugs as therapeutic agents in cancer.
Collapse
Affiliation(s)
- Rahul Prasad
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Timothy J. Yen
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| |
Collapse
|
3
|
Alternative splicing of APOBEC3D generates functional diversity and its role as a DNA mutator. Int J Hematol 2020; 112:395-408. [PMID: 32533515 DOI: 10.1007/s12185-020-02904-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/08/2020] [Accepted: 05/29/2020] [Indexed: 01/27/2023]
Abstract
The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) protein family members have cytidine deaminase activity and can induce cytosine to uracil transition in nucleic acid. The main function of APOBEC3 (A3) proteins is to trigger an innate immune response to viral infections. Recent reports have shown that several APOBEC family proteins such as A3B can induce somatic mutations into genomic DNA and thus promote cancer development. However, the role of A3D on somatic mutations is unclear. Here, we identified the alternative splicing of A3D, and investigated each splice variant's subcellular localization and role in DNA mutagenesis. We identified four A3D variants, which all have one or two cytidine deaminase domains. The full-length form of A3D (variant 1) and truncated forms of A3D (variant 2, 6, 7) showed the ability to induce C/G to T/A transitions in foreign DNA and genomic DNA and retained antiretroviral activity. Furthermore, we demonstrated that A3D and A3B could induce deletions that are possibly repaired by microhomology-mediated end joining (MMEJ). Taken together, our experiments illustrated that alternative splicing generates functional diversity of A3D, and some variants can act as DNA mutators in genomic DNA.
Collapse
|
4
|
Gassner FJ, Zaborsky N, Feldbacher D, Greil R, Geisberger R. RNA Editing Alters miRNA Function in Chronic Lymphocytic Leukemia. Cancers (Basel) 2020; 12:cancers12051159. [PMID: 32380696 PMCID: PMC7280959 DOI: 10.3390/cancers12051159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a high incidence B cell leukemia with a highly variable clinical course, leading to survival times ranging from months to several decades. MicroRNAs (miRNAs) are small non-coding RNAs that regulate the expression levels of genes by binding to the untranslated regions of transcripts. Although miRNAs have been previously shown to play a crucial role in CLL development, progression and treatment resistance, their further processing and diversification by RNA editing (specifically adenosine to inosine or cytosine to uracil deamination) has not been addressed so far. In this study, we analyzed next generation sequencing data to provide a detailed map of adenosine to inosine and cytosine to uracil changes in miRNAs from CLL and normal B cells. Our results reveal that in addition to a CLL-specific expression pattern, there is also specific RNA editing of many miRNAs, particularly miR-3157 and miR-6503, in CLL. Our data draw further light on how miRNAs and miRNA editing might be implicated in the pathogenesis of the disease.
Collapse
Affiliation(s)
- Franz J. Gassner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
| | - Daniel Feldbacher
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
- Department of Biosciences, University of Salzburg, Hellbrunner Strasse, 34, 5020 Salzburg, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
| | - Roland Geisberger
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Cancer Cluster Salzburg, Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (F.J.G.); (N.Z.); (D.F.); (R.G.)
- Correspondence: ; Tel.: +43-57255-25847; Fax: +43-57255-25998
| |
Collapse
|
5
|
Maura F, Degasperi A, Nadeu F, Leongamornlert D, Davies H, Moore L, Royo R, Ziccheddu B, Puente XS, Avet-Loiseau H, Campbell PJ, Nik-Zainal S, Campo E, Munshi N, Bolli N. A practical guide for mutational signature analysis in hematological malignancies. Nat Commun 2019; 10:2969. [PMID: 31278357 PMCID: PMC6611883 DOI: 10.1038/s41467-019-11037-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 06/10/2019] [Indexed: 02/08/2023] Open
Abstract
Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis and result interpretation. Using whole-genome sequencing of multiple myeloma (MM), chronic lymphocytic leukemia (CLL) and acute myeloid leukemia, we compare the performance of public signature analysis tools. We describe caveats and pitfalls of de novo signature extraction and fitting approaches, reporting on common inaccuracies: erroneous signature assignment, identification of localized hyper-mutational processes, overcalling of signatures. We provide reproducible solutions to solve these issues and use orthogonal approaches to validate our results. We show how a comprehensive mutational signature analysis may provide relevant biological insights, reporting evidence of c-AID activity among unmutated CLL cases or the absence of BRCA1/BRCA2-mediated homologous recombination deficiency in a MM cohort. Finally, we propose a general analysis framework to ensure production of accurate and reproducible mutational signature data.
Collapse
Affiliation(s)
- Francesco Maura
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, Milan, 20122, Italy.
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Andrea Degasperi
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Ferran Nadeu
- Patologia Molecular de Neoplàsies Limfoides, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Daniel Leongamornlert
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Helen Davies
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Luiza Moore
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, 08036, Barcelona, Spain
| | - Bachisio Ziccheddu
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Xose S Puente
- Unitat Hematopatologia, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Departamento de Bioquimica y Biologia Molecular, Instituto Universitario de Oncologia (IUOPA), Universidad de Oviedo, Oviedo, 33003, Spain
| | | | - Peter J Campbell
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Serena Nik-Zainal
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Elias Campo
- Patologia Molecular de Neoplàsies Limfoides, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, 08036, Barcelona, Spain
| | - Nikhil Munshi
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, MA, USA
- Veterans Administration Boston Healthcare System, West Roxbury, 02130, MA, USA
| | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, Milan, 20122, Italy.
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy.
| |
Collapse
|
6
|
Du Y, Tao X, Wu J, Yu H, Yu Y, Zhao H. APOBEC3B up-regulation independently predicts ovarian cancer prognosis: a cohort study. Cancer Cell Int 2018; 18:78. [PMID: 29853799 PMCID: PMC5975489 DOI: 10.1186/s12935-018-0572-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/23/2018] [Indexed: 01/22/2023] Open
Abstract
Background Ovarian cancer is a heterogeneous disease with a high degree of genomic instability, pro-/antitumor immunity and inflammation, and remains the most lethal gynecologic cancer worldwide. APOBEC3B, a member of the AID/APOBEC family, is part of the innate immune system which plays a key role in combating exogenous infection especially viral infection. Studies have shown that APOBEC3B expression is elevated in a variety of cancer tissues and cell lines, and plays a prominent role in the genesis and evolution of various cancers. However, the clinical relevance of APOBEC3B in ovarian cancer needs to be further investigated. The current study aimed to evaluate the predictive value of APOBEC3B in ovarian cancer clinical outcome, and to explore possible molecular mechanisms contributing to ovarian cancer progression. Methods The expression of APOBEC3B in biopsy tissue specimens from 88 ovarian cancer patients was examined using immunohistochemistry. In addition, ovarian cancer cell lines were transfected with APOBEC3B siRNA or pLenti-APOBEC3B construct. Western blotting and SRB assay were performed to explore the role of APOBEC3B in ovarian cancer. Results Patients were followed for a median of 74.77 months following the time of surgery. Forty-two patients had died, 5 had relapsed but were still alive at the end of study, and 41 patients remained alive and had no recurrence. Over-expression of APOBEC3B was associated with advanced FIGO stage and elevated CA125 (both p< 0.05). Univariate analysis result showed that histological subtype, FIGO stage, intravascular tumor thrombus, CA125 and APOBEC3B expression were associated with overall survival and disease-free survival of ovarian cancer patients. Multivariate analysis result showed that higher APOBEC3B expression were an independent prognostic factor to predict both worse overall survival (hazard ratio: 5.18, 95% confidence interval: 1.40–11.95, p= 0.003) and disease-free survival (hazard ratio: 4.23, 95% confidence interval: 1.60–11.17, p= 0.004) of ovarian cancer patients. Furthermore, knockdown of APOBEC3B expression in ovarian cancer cells caused an decrease in cell line viability. Conclusions APOBEC3B expression is an independent prognostic factor in ovarian cancer patients. Knockdown of APOBEC3B expression affects ovarian cancer viability.
Collapse
Affiliation(s)
- Yan Du
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,2The Academy of Integrative Medicine of Fudan University, 200011 Shanghai, People's Republic of China
| | - Xiang Tao
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Jing Wu
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Huandi Yu
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Yinhua Yu
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Hongbo Zhao
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| |
Collapse
|
7
|
Nikkilä J, Kumar R, Campbell J, Brandsma I, Pemberton HN, Wallberg F, Nagy K, Scheer I, Vertessy BG, Serebrenik AA, Monni V, Harris RS, Pettitt SJ, Ashworth A, Lord CJ. Elevated APOBEC3B expression drives a kataegic-like mutation signature and replication stress-related therapeutic vulnerabilities in p53-defective cells. Br J Cancer 2017; 117:113-123. [PMID: 28535155 PMCID: PMC5520199 DOI: 10.1038/bjc.2017.133] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system. METHODS We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing. In vitro small-molecule inhibitor sensitivity profiling was used to identify candidate therapeutic vulnerabilities. RESULTS Although APOBEC3B expression increased the incorporation of genomic uracil, invoked DDR biomarkers and caused cell cycle arrest, inactivation of p53 circumvented APOBEC3B-induced cell cycle arrest without reversing the increase in genomic uracil or DDR biomarkers. The continued expression of APOBEC3B in p53-defective cells not only caused a kataegic mutational signature but also caused hypersensitivity to small-molecule DDR inhibitors (ATR, CHEK1, CHEK2, PARP, WEE1 inhibitors) as well as cisplatin/ATR inhibitor and ATR/PARP inhibitor combinations. CONCLUSIONS Although loss of p53 might allow tumour cells to tolerate elevated APOBEC3B expression, continued expression of this enzyme might impart a number of therapeutic vulnerabilities upon tumour cells.
Collapse
Affiliation(s)
- Jenni Nikkilä
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Rahul Kumar
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Inger Brandsma
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Helen N Pemberton
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Fredrik Wallberg
- FACS Facility, The Institute of Cancer Research, London SW3 6JB, UK
| | - Kinga Nagy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp 3, Budapest H-1111, Hungary
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, Budapest H-1117, Hungary
| | - Ildikó Scheer
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp 3, Budapest H-1111, Hungary
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, Budapest H-1117, Hungary
| | - Beata G Vertessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp 3, Budapest H-1111, Hungary
| | - Artur A Serebrenik
- Howard Hughes Medical Institute, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Valentina Monni
- Howard Hughes Medical Institute, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Reuben S Harris
- Howard Hughes Medical Institute, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Alan Ashworth
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Greil R, Hutterer E, Hartmann TN, Pleyer L. Reactivation of dormant anti-tumor immunity - a clinical perspective of therapeutic immune checkpoint modulation. Cell Commun Signal 2017; 15:5. [PMID: 28100240 PMCID: PMC5244547 DOI: 10.1186/s12964-016-0155-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/06/2016] [Indexed: 12/17/2022] Open
Abstract
In favor of their outgrowth, cancer cells must resist immune surveillance and edit the immune response. Cancer immunoediting is characterized by fundamental changes in the cellular composition and the inflammatory cytokine profiles in the microenvironment of the primary tumor and metastatic niches, with an ever increasing complexity of interactions between tumor cells and the immune system. Recent data suggest that genetic instability and immunoediting are not necessarily disparate processes. Increasing mutational load may be associated with multiple neoepitopes expressed by the tumor cells and thus increased chances for the immune system to recognize and combat these cells. At the same time the immune system is more and more suppressed and exhausted by this process. Consequently, immune checkpoint modulation may have the potential to be most successful in genetically highly altered and usually extremely unfavorable types of cancer. Moreover, the fact that epitopes recognized by the immune system are preferentially encoded by passenger gene mutations opens windows of synergy in targeting cancer-specific signaling pathways by small molecules simultaneously with antibodies modifying T-cell activation or exhaustion. This review covers some aspects of the current understanding of the immunological basis necessary to understand the rapidly developing therapeutic endeavours in cancer treatment, the clinical achievements made, and raises some burning questions for translational research in this field.
Collapse
Affiliation(s)
- Richard Greil
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria. .,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria. .,Arbeitsgemeinschaft Medikamentöse Tumortherapie (AGMT) Study Group, Salzburg, Austria. .,Cancer Cluster Salzburg (CCS), Salzburg, Austria.
| | - Evelyn Hutterer
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria.,Cancer Cluster Salzburg (CCS), Salzburg, Austria
| | - Tanja Nicole Hartmann
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria.,Cancer Cluster Salzburg (CCS), Salzburg, Austria
| | - Lisa Pleyer
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria.,Arbeitsgemeinschaft Medikamentöse Tumortherapie (AGMT) Study Group, Salzburg, Austria.,Cancer Cluster Salzburg (CCS), Salzburg, Austria
| |
Collapse
|
10
|
Land AM, Wang J, Law EK, Aberle R, Kirmaier A, Krupp A, Johnson WE, Harris RS. Degradation of the cancer genomic DNA deaminase APOBEC3B by SIV Vif. Oncotarget 2016; 6:39969-79. [PMID: 26544511 PMCID: PMC4741873 DOI: 10.18632/oncotarget.5483] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 10/19/2015] [Indexed: 12/17/2022] Open
Abstract
APOBEC3B is a newly identified source of mutation in many cancers, including breast, head/neck, lung, bladder, cervical, and ovarian. APOBEC3B is a member of the APOBEC3 family of enzymes that deaminate DNA cytosine to produce the pro-mutagenic lesion, uracil. Several APOBEC3 family members function to restrict virus replication. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H combine to restrict HIV-1 in human lymphocytes. HIV-1 counteracts these APOBEC3s with the viral protein Vif, which targets the relevant APOBEC3s for proteasomal degradation. While APOBEC3B does not restrict HIV-1 and is not targeted by HIV-1 Vif in CD4-positive T cells, we asked whether related lentiviral Vif proteins could degrade APOBEC3B. Interestingly, several SIV Vif proteins are capable of promoting APOBEC3B degradation, with SIVmac239 Vif proving the most potent. This likely occurs through the canonical polyubiquitination mechanism as APOBEC3B protein levels are restored by MG132 treatment and by altering a conserved E3 ligase-binding motif. We further show that SIVmac239 Vif can prevent APOBEC3B mediated geno/cytotoxicity and degrade endogenous APOBEC3B in several cancer cell lines. Our data indicate that the APOBEC3B degradation potential of SIV Vif is an effective tool for neutralizing the cancer genomic DNA deaminase APOBEC3B. Further optimization of this natural APOBEC3 antagonist may benefit cancer therapy.
Collapse
Affiliation(s)
- Allison M Land
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.,Present address: Department of Biological Sciences, Minnesota State University Mankato, Mankato, Minnesota, USA
| | - Jiayi Wang
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ryan Aberle
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrea Kirmaier
- Department of Biology, Boston College, Boston, Massachusetts, USA
| | - Annabel Krupp
- Department of Biology, Boston College, Boston, Massachusetts, USA.,Present address: Biogen Idec, Cambridge, Massachusetts, USA
| | - Welkin E Johnson
- Department of Biology, Boston College, Boston, Massachusetts, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
11
|
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.
Collapse
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; ,
| |
Collapse
|
12
|
Kasar S, Kim J, Improgo R, Tiao G, Polak P, Haradhvala N, Lawrence MS, Kiezun A, Fernandes SM, Bahl S, Sougnez C, Gabriel S, Lander ES, Kim HT, Getz G, Brown JR. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nat Commun 2015; 6:8866. [PMID: 26638776 PMCID: PMC4686820 DOI: 10.1038/ncomms9866] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/08/2015] [Indexed: 12/17/2022] Open
Abstract
Patients with chromosome 13q deletion or normal cytogenetics represent the majority of chronic lymphocytic leukaemia (CLL) cases, yet have relatively few driver mutations. To better understand their genomic landscape, here we perform whole-genome sequencing on a cohort of patients enriched with these cytogenetic characteristics. Mutations in known CLL drivers are seen in only 33% of this cohort, and associated with normal cytogenetics and unmutated IGHV. The most commonly mutated gene in our cohort, IGLL5, shows a mutational pattern suggestive of activation-induced cytidine deaminase (AID) activity. Unsupervised analysis of mutational signatures demonstrates the activities of canonical AID (c-AID), leading to clustered mutations near active transcriptional start sites; non-canonical AID (nc-AID), leading to genome-wide non-clustered mutations, and an ageing signature responsible for most mutations. Using mutation clonality to infer time of onset, we find that while ageing and c-AID activities are ongoing, nc-AID-associated mutations likely occur earlier in tumour evolution. The oncogenic events driving indolent chronic lymphocytic leukaemia are relatively unknown. Here, the authors perform whole genome sequencing on 30 such tumours and identify recurrent mutations in IGLL5 and two activation induced cytidine deaminase signatures that are operative at different stages of CLL evolution.
Collapse
Affiliation(s)
- S Kasar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - J Kim
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - R Improgo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - G Tiao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - P Polak
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - N Haradhvala
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - M S Lawrence
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - A Kiezun
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - S M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - S Bahl
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - C Sougnez
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - S Gabriel
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - E S Lander
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - H T Kim
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - G Getz
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Department of Pathology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - J R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| |
Collapse
|
13
|
Swanton C, McGranahan N, Starrett GJ, Harris RS. APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity. Cancer Discov 2015; 5:704-12. [PMID: 26091828 PMCID: PMC4497973 DOI: 10.1158/2159-8290.cd-15-0344] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/14/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED Deep sequencing technologies are revealing the complexities of cancer evolution, casting light on mutational processes fueling tumor adaptation, immune escape, and treatment resistance. Understanding mechanisms driving cancer diversity is a critical step toward developing strategies to attenuate tumor evolution and adaptation. One emerging mechanism fueling tumor diversity and subclonal evolution is genomic DNA cytosine deamination catalyzed by APOBEC3B and at least one other APOBEC family member. Deregulation of APOBEC3 enzymes causes a general mutator phenotype that manifests as diverse and heterogeneous tumor subclones. Here, we summarize knowledge of the APOBEC DNA deaminase family in cancer, and their role as driving forces for intratumor heterogeneity and a therapeutic target to limit tumor adaptation. SIGNIFICANCE APOBEC mutational signatures may be enriched in tumor subclones, suggesting APOBEC cytosine deaminases fuel subclonal expansions and intratumor heterogeneity. APOBEC family members might represent a new class of drug target aimed at limiting tumor evolution, adaptation, and drug resistance.
Collapse
Affiliation(s)
- Charles Swanton
- The Francis Crick Institute, London, United Kingdom. UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, London, United Kingdom.
| | - Nicholas McGranahan
- The Francis Crick Institute, London, United Kingdom. Centre for Mathematics & Physics in the Life Sciences & Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.
| |
Collapse
|
14
|
Rebhandl S, Huemer M, Greil R, Geisberger R. AID/APOBEC deaminases and cancer. Oncoscience 2015; 2:320-33. [PMID: 26097867 PMCID: PMC4468319 DOI: 10.18632/oncoscience.155] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/01/2015] [Indexed: 02/06/2023] Open
Abstract
Mutations are the basis for evolution and the development of genetic diseases. Especially in cancer, somatic mutations in oncogenes and tumor suppressor genes alongside the occurrence of passenger mutations have been observed by recent deep-sequencing approaches. While mutations have long been considered random events induced by DNA-replication errors or by DNA damaging agents, genome sequencing led to the discovery of non-random mutation signatures in many human cancer. Common non-random mutations comprise DNA strand-biased mutation showers and mutations restricted to certain DNA motifs, which recently have become attributed to the activity of the AID/APOBEC family of DNA deaminases. Hence, APOBEC enzymes, which have evolved as key players in natural and adaptive immunity, have been proposed to contribute to cancer development and clonal evolution of cancer by inducing collateral genomic damage due to their DNA deaminating activity. This review focuses on how mutagenic events through AID/APOBEC deaminases may contribute to cancer development.
Collapse
Affiliation(s)
- Stefan Rebhandl
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Michael Huemer
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Richard Greil
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Roland Geisberger
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| |
Collapse
|
15
|
Henderson S, Fenton T. APOBEC3 genes: retroviral restriction factors to cancer drivers. Trends Mol Med 2015; 21:274-84. [PMID: 25820175 DOI: 10.1016/j.molmed.2015.02.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 02/09/2015] [Accepted: 02/19/2015] [Indexed: 12/31/2022]
Abstract
The APOBEC3 cytosine deaminases play key roles in innate immunity through their ability to mutagenize viral DNA and restrict viral replication. Recent advances in cancer genomics, together with biochemical characterization of the APOBEC3 enzymes, have now implicated at least two family members in somatic mutagenesis during tumor development. We review the evidence linking these enzymes to carcinogenesis and highlight key questions, including the potential mechanisms that misdirect APOBEC3 activity to the host genome, the links to viral infection, and the association between a common APOBEC3 polymorphism and cancer risk.
Collapse
Affiliation(s)
- Stephen Henderson
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tim Fenton
- Department of Oncology, University College London Cancer Institute, London, UK.
| |
Collapse
|
16
|
Huemer M, Rebhandl S, Zaborsky N, Gassner FJ, Hainzl S, Weiss L, Hebenstreit D, Greil R, Geisberger R. AID induces intraclonal diversity and genomic damage in CD86(+) chronic lymphocytic leukemia cells. Eur J Immunol 2014; 44:3747-57. [PMID: 25179679 PMCID: PMC4276288 DOI: 10.1002/eji.201344421] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 08/01/2014] [Accepted: 08/29/2014] [Indexed: 02/04/2023]
Abstract
The activation-induced cytidine deaminase (AID) mediates somatic hypermutation and class switch recombination of the Ig genes by directly deaminating cytosines to uracils. As AID causes a substantial amount of off-target mutations, its activity has been associated with lymphomagenesis and clonal evolution of B-cell malignancies. Although it has been shown that AID is expressed in B-cell chronic lymphocytic leukemia (CLL), a clear analysis of in vivo AID activity in this B-cell malignancy remained elusive. In this study performed on primary human CLL samples, we report that, despite the presence of a dominant VDJ heavy chain region, a substantial intraclonal diversity was observed at VDJ as well as at IgM switch regions (Sμ), showing ongoing AID activity in vivo during disease progression. This AID-mediated heterogeneity was higher in CLL subclones expressing CD86, which we identified as the proliferative CLL fraction. Finally, CD86 expression correlated with shortened time to first treatment and increased γ-H2AX focus formation. Our data demonstrate that AID is active in CLL in vivo and thus, AID likely contributes to clonal evolution of CLL.
Collapse
Affiliation(s)
- Michael Huemer
- Laboratory for Immunological and Molecular Cancer Research, Department of Internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|