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Kvach MV, Harjes S, Kurup HM, Jameson GB, Harjes E, Filichev VV. Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A. Beilstein J Org Chem 2024; 20:1088-1098. [PMID: 38774272 PMCID: PMC11106675 DOI: 10.3762/bjoc.20.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/26/2024] [Indexed: 05/24/2024] Open
Abstract
Nucleoside and polynucleotide cytidine deaminases (CDAs), such as CDA and APOBEC3, share a similar mechanism of cytosine to uracil conversion. In 1984, phosphapyrimidine riboside was characterised as the most potent inhibitor of human CDA, but the quick degradation in water limited the applicability as a potential therapeutic. To improve stability in water, we synthesised derivatives of phosphapyrimidine nucleoside having a CH2 group instead of the N3 atom in the nucleobase. A charge-neutral phosphinamide and a negatively charged phosphinic acid derivative had excellent stability in water at pH 7.4, but only the charge-neutral compound inhibited human CDA, similar to previously described 2'-deoxyzebularine (Ki = 8.0 ± 1.9 and 10.7 ± 0.5 µM, respectively). However, under basic conditions, the charge-neutral phosphinamide was unstable, which prevented the incorporation into DNA using conventional DNA chemistry. In contrast, the negatively charged phosphinic acid derivative was incorporated into DNA instead of the target 2'-deoxycytidine using an automated DNA synthesiser, but no inhibition of APOBEC3A was observed for modified DNAs. Although this shows that the negative charge is poorly accommodated in the active site of CDA and APOBEC3, the synthetic route reported here provides opportunities for the synthesis of other derivatives of phosphapyrimidine riboside for potential development of more potent CDA and APOBEC3 inhibitors.
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Affiliation(s)
- Maksim V Kvach
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Harikrishnan M Kurup
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Geoffrey B Jameson
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Food Technology and Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Thomas Building of the University of Auckland, Level 2, 3A Symonds Street, Auckland 1142, New Zealand
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2
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Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TR. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3997426. [PMID: 38496447 PMCID: PMC10942551 DOI: 10.21203/rs.3.rs-3997426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.
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Affiliation(s)
- Nicola J. Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- School of Biosciences, University of Kent, UK
| | - Ian Reddin
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Bio-R Bioinformatics Research Facility, Faculty of Medicine, University of Southampton, UK
| | - Paige Policelli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nur Zainal
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Emma Howes
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Jenkins
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ian Tracy
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Mark Edmond
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Sharpe
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Damian Amendra
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ke Zheng
- Department of Pathology, University of Cambridge, UK
| | | | - John Doorbar
- Department of Pathology, University of Cambridge, UK
| | - Anjali Rao
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Sangeetha Mahadevan
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Christopher Hanley
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Emma King
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Gareth J. Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim R. Fenton
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
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3
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Su N, Zhou E, Cui M, Li H, Wu S, Zhang Q, Cao Z. Role and molecular mechanism of APOBEC3B in the development and progression of gastric cancer. Heliyon 2024; 10:e24458. [PMID: 38312680 PMCID: PMC10835258 DOI: 10.1016/j.heliyon.2024.e24458] [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: 10/13/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/06/2024] Open
Abstract
Gastric cancer is a common malignant tumor with a high mortality rate. Abnormal APOBEC3B (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3B) expression increases tumor susceptibility. However, the exact molecular mechanism of APOBEC3B expression in the development of gastric cancer is still unknown. We investigated the effect of APOBEC3B on the malignant biological behavior of gastric cancer cells and discussed the role of APOBEC3B in the development and progression of gastric cancer. APOBEC3B protein levels were measured in 161 gastric cancer samples using western blotting and immunohistochemistry. Both in vitro and in vivo assays were performed, and molecules were analyzed using bioinformatics analysis and western blotting. APOBEC3B was overexpressed in gastric cancer. Moreover, APOBEC3B significantly enhanced cell proliferation in vitro and tumorigenicity in vivo. Regarding the underlying mechanism, APOBEC3B promoted the proliferation of gastric cancer cells by upregulating P53, MCM2 (minichromosome maintenance protein 2), and cyclin D1. Our results suggest that APOBEC3B is involved in cancer progression, providing a new theoretical basis for the prevention and treatment of gastric cancer.
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Affiliation(s)
- Nana Su
- Department of Pathology, Binzhou Medical University Hospital, Binzhou, 256603, China
| | - Erle Zhou
- Department of Pathology, Binzhou Medical University Hospital, Binzhou, 256603, China
| | - Min Cui
- Department of Pediatrics, Binzhou City People's Hospital, Binzhou, 256600, China
| | - Hong Li
- Department of Pathology, Binzhou Medical University Hospital, Binzhou, 256603, China
| | - Shuhua Wu
- Department of Pathology, Binzhou Medical University Hospital, Binzhou, 256603, China
| | - Qian Zhang
- Department of Pathology, Binzhou Medical University Hospital, Binzhou, 256603, China
| | - Zhang Cao
- Department of Pathology, Binzhou Medical University Hospital, Binzhou, 256603, China
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4
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Wei L, Wu X, Wang L, Chen L, Wu X, Song T, Wang Y, Chang W, Guo A, Niu Y, Huang H. Expression and prognostic value of APOBEC2 in gastric adenocarcinoma and its association with tumor-infiltrating immune cells. BMC Cancer 2024; 24:15. [PMID: 38166744 PMCID: PMC10763203 DOI: 10.1186/s12885-023-11769-3] [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: 07/16/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 2 (APOBEC2) is associated with nucleotide alterations in the transcripts of tumor-related genes which are contributed to carcinogenesis. Expression and prognosis value of APOBEC2 in stomach adenocarcinoma (STAD) remains unclear. METHODS The APOBEC2 gene alteration frequency of STAD and APOBEC2 gene expression in STAD and normal tissues were investigated in cBioportal and GEPIA, respectively. We detected expression of APOBEC2, infiltration of CD66b+ tumor-associated neutrophils and CD163+ tumor-associated macrophages in tissue microarrays by immunohistochemistry. APOBEC2 gene expression was explored by western blot and qRT-PCR. Relationships between APOBEC2 and CD66b, CD163, and other clinicopathological characteristics were investigated. Associations among APOBEC2 expression status and patient survival outcome were further analyzed. RESULTS APOBEC2 gene alteration frequency was 5%, and APOBEC2 gene was downexpressed in STAD compared to normal tissues (P < 0.05). APOBEC2 expression status were associated with the infiltration of CD66b+ TANs, differentiation grade, TNM stage, histological type and gender (all P < 0.05) in STAD. Little or no APOBEC2 expression was detected in STAD and adjacent normal tissues by western blot. We failed to show that APOBEC2 was an independent risk factor for OS (Hazard Ratio 0.816, 95%CI 0.574-1.161, P = 0.259) or DFS (Hazard Ratio 0.821, 95%CI 0.578-1.166, P = 0.270) in STAD by multivariate Cox regression analysis, but APOBEC2 negative subgroup has a worse OS and DFS among patients with adjuvant chemotherapy. CONCLUSIONS APOBEC2 correlates with CD66b, differentiation grade, TNM stages, histological classification, and gender in STAD. APOBEC2 is not an independent prognostic factor for STAD, our results suggest that patients with positive APOBEC2 can benefit from postoperative chemotherapy, and combination of APOBEC2 and CD66b is helpful to further stratify patients into different groups with distinct prognoses.
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Affiliation(s)
- Lipan Wei
- Department of Pathology, Second affiliated Hospital of Medical College of Shantou University, Shantou, China
| | - Xiuqian Wu
- Department of Interventional Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Lan Wang
- Department of Pathology, Second affiliated Hospital of Medical College of Shantou University, Shantou, China
| | - Ling Chen
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Xuejun Wu
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Tiantian Song
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Yuanyuan Wang
- Department of Pathology, Shantou Central Hospital, Shantou, China
| | - Wenjun Chang
- Department of Environmental Hygiene, Second Military Medical University, Shanghai, China
| | - Aizhen Guo
- Department of General Practice, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Yongdong Niu
- Department of Pharmacology, Shantou University Medical College, Shantou, China.
| | - Haihua Huang
- Department of Pathology, Second affiliated Hospital of Medical College of Shantou University, Shantou, China.
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5
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Castellano G, Giugliano F, Curigliano G, Marra A. Clinical utility of genomic signatures for the management of early and metastatic triple-negative breast cancer. Curr Opin Oncol 2023; 35:479-490. [PMID: 37621170 DOI: 10.1097/cco.0000000000000989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
PURPOSE OF REVIEW This comprehensive review aims to provide timely and relevant insights into the current therapeutic landscape for triple-negative breast cancer (TNBC) and the molecular features underlying this subtype. It emphasizes the need for more reliable biomarkers to refine prognostication and optimize therapy, considering the aggressive nature of TNBC and its limited targeted treatment options. RECENT FINDINGS The review explores the multidisciplinary management of early TNBC, which typically involves systemic chemotherapy, surgery, and radiotherapy. It highlights the emergence of immune checkpoint inhibitors (ICIs), poly(ADP-ribose) polymerase (PARP) inhibitors, and antibody-drug conjugates (ADCs) as promising therapeutic strategies for TNBC. Recent clinical trials investigating the use of ICIs in combination with chemotherapy and the approval of pembrolizumab and atezolizumab for PD-L1-positive metastatic TNBC are discussed. The efficacy of PARP inhibitors and ADCs in treating TNBC patients with specific genetic alterations is also highlighted. SUMMARY The findings discussed in this review have significant implications for clinical practice and research in TNBC. The identification of distinct molecular subtypes through gene expression profiling has enabled a better understanding of TNBC heterogeneity and its clinical implications. This knowledge has the potential to guide treatment decisions, as different subtypes display varying responses to neoadjuvant chemotherapy. Furthermore, the review emphasizes the importance of developing reliable genomic and transcriptomic signatures as biomarkers to refine patient prognostication and optimize therapy selection in TNBC. Integrating these signatures into clinical practice may lead to more personalized treatment approaches, improving outcomes for TNBC patients.
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Affiliation(s)
- Grazia Castellano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Federica Giugliano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Antonio Marra
- Division of New Drugs and Early Drug Development, European Institute of Oncology IRCCS
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6
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Zong C, Zhang Z, Gao L, He J, Wang Y, Li Q, Liu X, Yang J, Chen D, Huang R, Zheng G, Jin X, Wei W, Jia R, Shen J. APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors. Cell Death Dis 2023; 14:348. [PMID: 37270643 DOI: 10.1038/s41419-023-05867-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/05/2023]
Abstract
The cytidine deaminase, Apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B, herein termed A3B), is a critical mutation driver that induces genomic instability in cancer by catalyzing cytosine-to-thymine (C-to-T) conversion and promoting replication stress (RS). However, the detailed function of A3B in RS is not fully determined and it is not known whether the mechanism of A3B action can be exploited for cancer therapy. Here, we conducted an immunoprecipitation-mass spectrometry (IP-MS) study and identified A3B to be a novel binding component of R-loops, which are RNA:DNA hybrid structures. Mechanistically, overexpression of A3B exacerbated RS by promoting R-loop formation and altering the distribution of R-loops in the genome. This was rescued by the R-loop gatekeeper, Ribonuclease H1 (RNASEH1, herein termed RNH1). In addition, a high level of A3B conferred sensitivity to ATR/Chk1 inhibitors (ATRi/Chk1i) in melanoma cells, which was dependent on R-loop status. Together, our results provide novel insights into the mechanistic link between A3B and R-loops in the promotion of RS in cancer. This will inform the development of markers to predict the response of patients to ATRi/Chk1i.
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Affiliation(s)
- Chunyan Zong
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Li Gao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jie He
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiran Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoting Liu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Di Chen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guopei Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
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7
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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: 0] [Impact Index Per Article: 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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8
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Roelofs PA, Martens JW, Harris RS, Span PN. Clinical Implications of APOBEC3-Mediated Mutagenesis in Breast Cancer. Clin Cancer Res 2023; 29:1658-1669. [PMID: 36478188 PMCID: PMC10159886 DOI: 10.1158/1078-0432.ccr-22-2861] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
Over recent years, members of the APOBEC3 family of cytosine deaminases have been implicated in increased cancer genome mutagenesis, thereby contributing to intratumor and intertumor genomic heterogeneity and therapy resistance in, among others, breast cancer. Understanding the available methods for clinical detection of these enzymes, the conditions required for their (dysregulated) expression, the clinical impact they have, and the clinical implications they may offer is crucial in understanding the current impact of APOBEC3-mediated mutagenesis in breast cancer. Here, we provide a comprehensive review of recent developments in the detection of APOBEC3-mediated mutagenesis and responsible APOBEC3 enzymes, summarize the pathways that control their expression, and explore the clinical ramifications and opportunities they pose. We propose that APOBEC3-mediated mutagenesis can function as a helpful predictive biomarker in several standard-of-care breast cancer treatment plans and may be a novel target for treatment.
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Affiliation(s)
- Pieter A. Roelofs
- Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - John W.M. Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul N. Span
- Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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9
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Roelofs PA, Timmermans MAM, Stefanovska B, den Boestert MA, van den Borne AWM, Balcioglu HE, Trapman AM, Harris RS, Martens JWM, Span PN. Aberrant APOBEC3B Expression in Breast Cancer Is Linked to Proliferation and Cell Cycle Phase. Cells 2023; 12:cells12081185. [PMID: 37190094 DOI: 10.3390/cells12081185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/15/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
APOBEC3B (A3B) is aberrantly overexpressed in a subset of breast cancers, where it associates with advanced disease, poor prognosis, and treatment resistance, yet the causes of A3B dysregulation in breast cancer remain unclear. Here, A3B mRNA and protein expression levels were quantified in different cell lines and breast tumors and related to cell cycle markers using RT-qPCR and multiplex immunofluorescence imaging. The inducibility of A3B expression during the cell cycle was additionally addressed after cell cycle synchronization with multiple methods. First, we found that A3B protein levels within cell lines and tumors are heterogeneous and associate strongly with the proliferation marker Cyclin B1 characteristic of the G2/M phase of the cell cycle. Second, in multiple breast cancer cell lines with high A3B, expression levels were observed to oscillate throughout the cell cycle and again associate with Cyclin B1. Third, induction of A3B expression is potently repressed throughout G0/early G1, likely by RB/E2F pathway effector proteins. Fourth, in cells with low A3B, induction of A3B through the PKC/ncNF-κB pathway occurs predominantly in actively proliferating cells and is largely absent in cells arrested in G0. Altogether, these results support a model in which dysregulated A3B overexpression in breast cancer is the cumulative result of proliferation-associated relief from repression with concomitant pathway activation during the G2/M phase of the cell cycle.
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Affiliation(s)
- Pieter A Roelofs
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mieke A M Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Bojana Stefanovska
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Myrthe A den Boestert
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Amber W M van den Borne
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Anita M Trapman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Paul N Span
- Radiotherapy & OncoImmunology Laboratory, Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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10
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Butler K, Banday AR. APOBEC3-mediated mutagenesis in cancer: causes, clinical significance and therapeutic potential. J Hematol Oncol 2023; 16:31. [PMID: 36978147 PMCID: PMC10044795 DOI: 10.1186/s13045-023-01425-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs) are cytosine deaminases involved in innate and adaptive immunity. However, some APOBEC family members can also deaminate host genomes to generate oncogenic mutations. The resulting mutations, primarily signatures 2 and 13, occur in many tumor types and are among the most common mutational signatures in cancer. This review summarizes the current evidence implicating APOBEC3s as major mutators and outlines the exogenous and endogenous triggers of APOBEC3 expression and mutational activity. The review also discusses how APOBEC3-mediated mutagenesis impacts tumor evolution through both mutagenic and non-mutagenic pathways, including by inducing driver mutations and modulating the tumor immune microenvironment. Moving from molecular biology to clinical outcomes, the review concludes by summarizing the divergent prognostic significance of APOBEC3s across cancer types and their therapeutic potential in the current and future clinical landscapes.
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Affiliation(s)
- Kelly Butler
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Rouf Banday
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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11
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de Sousa Pereira N, Vitiello GAF, Amarante MK. Involvement of APOBEC3A/B Deletion in Mouse Mammary Tumor Virus (MMTV)-like Positive Human Breast Cancer. Diagnostics (Basel) 2023; 13:diagnostics13061196. [PMID: 36980505 PMCID: PMC10047902 DOI: 10.3390/diagnostics13061196] [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: 02/06/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The association between mouse mammary tumor virus (MMTV)-like sequences and human breast cancer (BC) is largely documented in the literature, but further research is needed to determine how they influence carcinogenesis. APOBEC3 cytidine deaminases are viral restriction factors that have been implicated in cancer mutagenesis, and a germline deletion that results in the fusion of the APOBEC3A coding region with the APOBEC3B 3'-UTR has been linked to increased mutagenic potential, enhanced risk of BC development, and poor prognosis. However, little is known about factors influencing APOBEC3 family activation in cancer. Thus, we hypothesized that MMTV infection and APOBEC3-mediated mutagenesis may be linked in the pathogenesis of BC. We investigated APOBEC3A/B genotyping, MMTV-like positivity, and clinicopathological parameters of 209 BC patients. We show evidence for active APOBEC3-mediated mutagenesis in human-derived MMTV sequences and comparatively investigate the impact of APOBEC3A/B germline deletion in MMTV-like env positive and negative BC in a Brazilian cohort. In MMTV-like negative samples, APOBEC3A/B deletion was negatively correlated with tumor stage while being positively correlated with estrogen receptor expression. Although APOBEC3A/B was not associated with MMTV-like positivity, samples carrying both MMTV-like positivity and APOBEC3A/B deletion had the lowest age-at-diagnosis of all study groups, with all patients being less than 50 years old. These results indicate that APOBEC3 mutagenesis is active against MMTV-like sequences, and that APOBEC3A/B deletion might act along with the MMTV-like presence to predispose people to early-onset BC.
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Affiliation(s)
- Nathália de Sousa Pereira
- Oncology Laboratory, Department of Pathology, Clinical and Toxicological Analyses, Health Sciences Center, Londrina State University, Londrina 86057-970, PR, Brazil
| | | | - Marla Karine Amarante
- Oncology Laboratory, Department of Pathology, Clinical and Toxicological Analyses, Health Sciences Center, Londrina State University, Londrina 86057-970, PR, Brazil
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12
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Argyris PP, Naumann J, Jarvis MC, Wilkinson PE, Ho DP, Islam MN, Bhattacharyya I, Gopalakrishnan R, Li F, Koutlas IG, Giubellino A, Harris RS. Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B. Histopathology 2023; 82:608-621. [PMID: 36416305 PMCID: PMC10107945 DOI: 10.1111/his.14843] [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: 05/05/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022]
Abstract
AIMS Primary head/neck mucosal melanomas (MMs) are rare and exhibit aggressive biologic behaviour and elevated mutational loads. The molecular mechanisms responsible for high genomic instability observed in head/neck MMs remain elusive. The DNA cytosine deaminase APOBEC3B (A3B) constitutes a major endogenous source of mutation in human cancer. A3B-related mutations are identified through C-to-T/-G base substitutions in 5'-TCA/T motifs. Herein, we present immunohistochemical and genomic data supportive of a role for A3B in head/neck MMs. METHODS AND RESULTS A3B protein levels were assessed in oral (n = 13) and sinonasal (n = 13) melanomas, and oral melanocytic nevi (n = 13) by immunohistochemistry using a custom rabbit α-A3B mAb (5210-87-13). Heterogeneous, selective-to-diffuse, nuclear only, A3B immunopositivity was observed in 12 of 13 (92.3%) oral melanomas (H-score range = 9-72, median = 40) and 8 of 13 (62%) sinonasal melanomas (H-score range = 1-110, median = 24). Two cases negative for A3B showed prominent cytoplasmic staining consistent with A3G. A3B protein levels were significantly higher in oral and sinonasal MMs than intraoral melanocytic nevi (P < 0.0001 and P = 0.0022, respectively), which were A3B-negative (H-score range = 1-8, median = 4). A3B levels, however, did not differ significantly between oral and sinonasal tumours (P > 0.99). NGS performed in 10 sinonasal MMs revealed missense NRAS mutations in 50% of the studied cases and one each KIT and HRAS mutations. Publicly available whole-genome sequencing (WGS) data disclosed that the number of C-to-T mutations and APOBEC3 enrichment score were markedly elevated in head/neck MMs (n = 2). CONCLUSION The above data strongly indicate a possible role for the mutagenic enzyme A3B in head/neck melanomagenesis, but not benign melanocytic neoplasms.
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Affiliation(s)
- Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Jordan Naumann
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Peter E Wilkinson
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Dan P Ho
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Mohammed N Islam
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Indraneel Bhattacharyya
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Rajaram Gopalakrishnan
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Faqian Li
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Ioannis G Koutlas
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Alessio Giubellino
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
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13
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Poonia S, Goel A, Chawla S, Bhattacharya N, Rai P, Lee YF, Yap YS, West J, Bhagat AA, Tayal J, Mehta A, Ahuja G, Majumdar A, Ramalingam N, Sengupta D. Marker-free characterization of full-length transcriptomes of single live circulating tumor cells. Genome Res 2023; 33:80-95. [PMID: 36414416 PMCID: PMC9977151 DOI: 10.1101/gr.276600.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022]
Abstract
The identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor in the enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypes relative to the primary tumor. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from peripheral blood. Most CTC detection methods based on single-cell RNA sequencing (scRNA-seq) use a mix of size selection, marker-based white blood cell (WBC) depletion, and antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analyses. These include a novel method of scRNA-seq clustering, named deep dictionary learning using k-means clustering cost (DDLK), expression-based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell FX and Polaris workflow that works by the principles of size-based separation of CTCs and marker-based WBC depletion.
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Affiliation(s)
- Sarita Poonia
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Anurag Goel
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Department of Computer Science and Engineering, Delhi Technological University, New Delhi 110042, India
| | - Smriti Chawla
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Namrata Bhattacharya
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Priyadarshini Rai
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Yi Fang Lee
- Biolidics Limited, Singapore 118257, Singapore
| | - Yoon Sim Yap
- National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Jay West
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | | | - Juhi Tayal
- Department of Research, Rajiv Gandhi Cancer Institute and Research Centre-Delhi (RGCIRC-Delhi), New Delhi 110085, India
| | - Anurag Mehta
- Department of Laboratory Services and Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre-Delhi (RGCIRC-Delhi), New Delhi 110085, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | - Angshul Majumdar
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Department of Electronics & Communications Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
| | | | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India;,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), New Delhi 110020, India
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14
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High APOBEC3B mRNA Expression Is Associated with Human Papillomavirus Type 18 Infection in Cervical Cancer. Viruses 2022; 14:v14122653. [PMID: 36560657 PMCID: PMC9784603 DOI: 10.3390/v14122653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The APOBEC3 (A3) proteins are cytidine deaminases that exhibit the ability to insert mutations in DNA and/or RNA sequences. APOBEC3B (A3B) has been evidenced as a DNA mutagen with consistent high expression in several cancer types. Data concerning the A3B influence on HPV infection and cervical cancer are limited and controversial. We investigated the role of A3B expression levels in cervical cancer in affected women positive for infection by different HPV types. Tumor biopsies from cancerous uterine cervix were collected from 216 women registered at Hospital do Câncer II of Instituto Nacional de Câncer, and infecting HPV was typed. A3B expression levels were quantified from RNA samples extracted from cervical biopsies using real-time quantitative PCR. Median A3B expression levels were higher among HPV18+ samples when compared to HPV16+ counterparts and were also increased compared to samples positive for other HPV types. In squamous cell carcinoma, HPV18+ samples also showed increased median A3B expression when compared to HPV Alpha-9 species or only to HPV16+ samples. Our findings suggest that A3B expression is differentially upregulated in cervical cancer samples infected with HPV18. A3B could be potentially used as a biomarker for HPV infection and as a prognostic tool for clinical outcomes in the context of cervical cancer.
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15
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Maiti A, Hedger AK, Myint W, Balachandran V, Watts JK, Schiffer CA, Matsuo H. Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state. Nat Commun 2022; 13:7117. [PMID: 36402773 PMCID: PMC9675756 DOI: 10.1038/s41467-022-34752-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Abstract
APOBEC3 proteins (A3s) are enzymes that catalyze the deamination of cytidine to uridine in single-stranded DNA (ssDNA) substrates, thus playing a key role in innate antiviral immunity. However, the APOBEC3 family has also been linked to many mutational signatures in cancer cells, which has led to an intense interest to develop inhibitors of A3's catalytic activity as therapeutics as well as tools to study A3's biochemistry, structure, and cellular function. Recent studies have shown that ssDNA containing 2'-deoxy-zebularine (dZ-ssDNA) is an inhibitor of A3s such as A3A, A3B, and A3G, although the atomic determinants of this activity have remained unknown. To fill this knowledge gap, we determined a 1.5 Å resolution structure of a dZ-ssDNA inhibitor bound to active A3G. The crystal structure revealed that the activated dZ-H2O mimics the transition state by coordinating the active site Zn2+ and engaging in additional stabilizing interactions, such as the one with the catalytic residue E259. Therefore, this structure allowed us to capture a snapshot of the A3's transition state and suggests that developing transition-state mimicking inhibitors may provide a new opportunity to design more targeted molecules for A3s in the future.
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Affiliation(s)
- Atanu Maiti
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Adam K. Hedger
- grid.168645.80000 0001 0742 0364Institute for Drug Resistance, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Wazo Myint
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Vanivilasini Balachandran
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Jonathan K. Watts
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Celia A. Schiffer
- grid.168645.80000 0001 0742 0364Institute for Drug Resistance, University of Massachusetts Chan Medical School, Worcester, MA USA ,grid.168645.80000 0001 0742 0364Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Hiroshi Matsuo
- grid.418021.e0000 0004 0535 8394Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
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16
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Jafarpour S, Yazdi M, Nedaeinia R, Ghobakhloo S, Salehi R. Unfavorable prognosis and clinical consequences of APOBEC3B expression in breast and other cancers: A systematic review and meta-analysis. Tumour Biol 2022; 44:153-169. [DOI: 10.3233/tub-211577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION: Controversy exists regarding the association of apolipoprotein B mRNA editing enzyme catalytic subunit 3B APOBEC3B, (A3B) overexpression and poor prognosis, metastasis, and chemotherapy drug resistance in cancers. Here we conducted a systematic review and meta-analysis to determine its prognostic value and clinicopathological features in breast cancer and some other malignancies. MATERIALS AND METHODS: PubMed, Scopus, Cochrane Library, Web of Science, and EMBASE were searched up to Feb 2022 for the association of A3B with breast, ovarian, gastrointestinal and lung cancers. The pooled hazard ratios with 95% confidence interval (CI) were evaluated to assess disease-free survival (DFS), overall survival (OS), and recurrence-free survival (RFS) in cancers under study. RESULTS: Over 3700 patients were included in this meta-survey. Elevated levels of A3B were significantly related to low OS (pooled HR = 1.30; 95% CI:1.09–1.55, P < 0.01), poor DFS (pooled HR = 1.66; 95% CI:1.17–2.35, P < 0.01) and poor RFS (HR = 1.51, 95% CI:1.11–2.04, P = 0.01). Subgroup analysis revealed that high A3B expression was associated with poor OS in lung (HR = 1.85, 95% CI: 1.40–2.45), and breast cancers (HR = 1.38, 95% CI: 1.00–1.89). High expression of A3B did not display any significant association with clinicopathologic features. CONCLUSION: APOBEC3B overexpression is related to poor OS, DFS and RFS only in some cancer types and no generalized role could be predicted for all cancers.
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Affiliation(s)
- Sima Jafarpour
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Yazdi
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Reza Nedaeinia
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sepideh Ghobakhloo
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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17
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Wu R, Oshi M, Asaoka M, Huyser MR, Tokumaru Y, Yamada A, Yan L, Endo I, Ishikawa T, Takabe K. APOBEC3F expression in triple-negative breast cancer is associated with tumor microenvironment infiltration and activation of cancer immunity and improved survival. Am J Cancer Res 2022; 12:744-762. [PMID: 35261799 PMCID: PMC8899983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 06/14/2023] Open
Abstract
The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) causes a point mutation from cytidine to uracil in DNA and/or RNA. The role of APOBEC3A and APOBEC3B in breast cancer has been well described, whereas that of APOBEC3F remains unknown. To investigate the clinical relevance of APOBEC3F expression, we analyzed a total of 3000 breast cancer cases from multiple independent large patient cohorts including METABRIC, TCGA, GSE75688, and GSE114725. High expression of APOBEC3F was associated with improved disease-specific and overall survival in triple negative breast cancer (TNBC). APOBEC3F is not usually a reflection of cancer cell biology in TNBC or luminal breast cancer, except for homologous recombination deficiency in TNBC. In the TNBC homologous recombination deficiency group, APOBEC3F expression was not consistently associated with intratumor heterogeneity, mutation rates, or neoantigens. APOBEC3F expression did not correlate with response to any of the drugs tested in breast cancer cell lines in vitro. However, high APOBEC3F expression was associated with enrichment of several immune-related gene sets and immune activity. High APOBEC3F expression also accompanied higher infiltration of anti-cancer immune cell infiltration in TNBC. However, in luminal breast cancer, high APOBEC3F tumor significantly enriched not only immune-related gene sets, but also cell proliferation-, metastasis-, and apoptosis-related gene sets. Analysis of single-cell transcriptomes showed APOBEC3F exclusively expressed in immune cells and significantly associated with cytolytic activity of the immune cells, immune response, and immune cell proliferation. Expression of immune checkpoint genes was uniformly elevated in APOBEC3F-high tumors. We conclude that APOBEC3F is exclusively expressed in immune cells and this expression is associated with enhanced anti-cancer immune response as well as improved survival in TNBC.
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Affiliation(s)
- Rongrong Wu
- Department of Surgical Oncology, Roswell Park Cancer InstituteBuffalo, NY, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Cancer InstituteBuffalo, NY, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa, Japan
| | - Mariko Asaoka
- Department of Surgical Oncology, Roswell Park Cancer InstituteBuffalo, NY, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
| | - Michelle R Huyser
- Department of Surgical Oncology, Roswell Park Cancer InstituteBuffalo, NY, USA
| | - Yoshihisa Tokumaru
- Department of Surgical Oncology, Roswell Park Cancer InstituteBuffalo, NY, USA
- Department of Surgical Oncology, Graduate School of Medicine, Gifu UniversityGifu, Japan
| | - Akimitsu Yamada
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa, Japan
| | - Li Yan
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer InstituteBuffalo, NY, USA
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Cancer InstituteBuffalo, NY, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of MedicineYokohama, Kanagawa, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, NY, USA
- Department of Surgery, Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
- Department of Breast Surgery, Fukushima Medical UniversityFukushima, Japan
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18
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Zhang Y, Chen X, Cao Y, Yang Z. Roles of APOBEC3 in hepatitis B virus (HBV) infection and hepatocarcinogenesis. Bioengineered 2021; 12:2074-2086. [PMID: 34043485 PMCID: PMC8806738 DOI: 10.1080/21655979.2021.1931640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 02/08/2023] Open
Abstract
APOBEC3 (A3) cytidine deaminases inhibit hepatitis B virus (HBV) infection and play vital roles in maintaining a variety of biochemical processes, including the regulation of protein expression and innate immunity. Emerging evidence indicates that the deaminated deoxycytidine biochemical activity of A3 proteins in single-stranded DNA makes them a double-edged sword. These enzymes can cause cellular genetic mutations at replication forks or within transcription bubbles, depending on the physiological state of the cell and the phase of the cell cycle. Under pathological conditions, aberrant expression of A3 genes with improper deaminase activity regulation may threaten genomic stability and eventually lead to cancer development. This review attempted to summarize the antiviral activities and underlying mechanisms of A3 editing enzymes in HBV infections. Moreover, the correlations between A3 genes and hepatocarcinogenesis were also elucidated.
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Affiliation(s)
- Yuan Zhang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaorong Chen
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yajuan Cao
- Central Laboratory, Shanghai Pulmonary HospitalSchool of Medicine, Tongji University School of Medicine, Shanghai, China
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zongguo Yang
- Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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19
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Asaoka M, Patnaik SK, Ishikawa T, Takabe K. Different members of the APOBEC3 family of DNA mutators have opposing associations with the landscape of breast cancer. Am J Cancer Res 2021; 11:5111-5125. [PMID: 34765315 PMCID: PMC8569370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023] Open
Abstract
APOBEC enzymes are strong mutagenic factors. In breast cancer, expression of APOBEC3B is increased and associated with mutation load and poor outcome. Other APOBEC3s can also mutate DNA but their clinical significance in breast cancer and its underpinnings have not been comprehensively studied. In our examination of 1,091 breast carcinoma cases, high expression of APOBEC3A or APOBEC3B genes was associated with greater tumor burden of mutations and other genomic aberrations. Expression of none of the five APOBEC3C-H genes had any correlation with these features, including T[C-T/G]W mutations, but their high expression levels indicated a robust anti-cancer immune response within tumors, with elevated CD8+ T cell abundance, T cell receptor diversity, and immune cytolytic activity. Concordantly, survival analyses of this and two other cohorts with > 3,000 patients each showed favorable prognostic benefit of high APOBEC3C-H expression for both cancer progression and mortality. A detrimental prognostic value was observed for APOBEC3A and APOBEC3B. Single-cell data revealed cancer epithelial and stromal immune cells as major sources of APOBEC3B and APOBEC3C-H expression in tumors, respectively. These observations on opposing associations with breast cancer of different APOBEC3s highlight the contrasting roles of these enzymes, promoting cancer through mutagenesis while antagonizing it through immune response.
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Affiliation(s)
- Mariko Asaoka
- Department of Breast Surgery, Roswell Park Comprehensive Cancer CenterBuffalo, New York, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
| | - Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Comprehensive Cancer CenterBuffalo, New York, USA
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, New York, USA
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
| | - Kazuaki Takabe
- Department of Breast Surgery, Roswell Park Comprehensive Cancer CenterBuffalo, New York, USA
- Department of Breast Surgery and Oncology, Tokyo Medical UniversityTokyo, Japan
- Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, State University of New YorkBuffalo, New York, USA
- Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
- Department of Surgery, Yokohama City UniversityYokohama, Japan
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20
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Xia S, Gu Y, Zhang H, Fei Y, Cao Y, Fang H, Wang J, Lin C, Zhang H, Li H, He H, Xu J, Li R, Liu H, Zhang W. Immune inactivation by APOBEC3B enrichment predicts response to chemotherapy and survival in gastric cancer. Oncoimmunology 2021; 10:1975386. [PMID: 34552824 PMCID: PMC8451457 DOI: 10.1080/2162402x.2021.1975386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Apolipoprotein B mRNA editing enzyme catalytic polypeptide 3B (APOBEC3B) plays an important role in tumor mutagenesis. However, its clinical significance in gastric cancer (GC) remains largely unknown. We enrolled a total of 482 GC patients from Zhongshan Hospital, Fudan University for immunohistochemistry (IHC) staining to evaluate the prognostic and predictive values of APOBEC3B. Genomic and phenotypic datasets from the Cancer Genome Atlas (TCGA) and Asian Cancer Research Group (ACRG) cohort were downloaded for external validation and complementary bioinformatic analysis. Fresh specimens of additional 60 patients from Zhongshan Hospital, Fudan University were collected to detect CD8+ T cell phenotype with flow cytometry (FCM). The high expression of APOBEC3B indicated inferior overall survival (OS, P < .001 and P = .003) and disease-free survival (DFS, P < .001 and P < .001), yet superior therapeutic responsiveness to fluorouracil-based adjuvant chemotherapy (ACT) in TNM stage II patients. The tumor microenvironment (TME) of APOBEC3B-enriched tumors was characterized by reduced infiltration of tumor reactive CD8+ T cells expressing both effector molecules and immune checkpoints. APOBEC3B high CD8+ T cell high GC patients were most likely to benefit from ACT and PD-1 blockade. Our study demonstrates that APOBEC3B was an independent prognostic and predictive factor in GC. The potential interplay between APOBEC3B and CD8+ T cells merited further investigations.
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Affiliation(s)
- Siyu Xia
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yun Gu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuchao Fei
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yifan Cao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hanji Fang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jieti Wang
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Chao Lin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Heng Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - He Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hongyong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ruochen Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weijuan Zhang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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21
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Vile RG, Melcher A, Pandha H, Harrington KJ, Pulido JS. APOBEC and Cancer Viroimmunotherapy: Thinking the Unthinkable. Clin Cancer Res 2021; 27:3280-3290. [PMID: 33558423 PMCID: PMC8281496 DOI: 10.1158/1078-0432.ccr-20-1888] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/25/2020] [Accepted: 01/19/2021] [Indexed: 01/21/2023]
Abstract
The apolipoprotein B mRNA editing enzyme catalytic polypeptide (APOBEC) family protects against infection by degrading incoming viral genomes through cytosine deamination. Here, we review how the potential to unleash these potent DNA mutagens comes at a price as APOBEC DNA mutagenesis can contribute to development of multiple types of cancer. In addition, because viral infection induces its expression, APOBEC is seen as the enemy of oncolytic virotherapy through mutation of the viral genome and by generating virotherapy-resistant tumors. Therefore, overall APOBEC in cancer has received very poor press. However, we also speculate how there may be silver linings to the storm clouds (kataegis) associated with APOBEC activity. Thus, although mutagenic genomic chaos promotes emergence of ever more aggressive subclones, it also provides significant opportunity for cytotoxic and immune therapies. In particular, the superpower of cancer immunotherapy derives in part from mutation, wherein generation of tumor neoantigens-neoantigenesis-exposes tumor cells to functional T-cell repertoires, and susceptibility to immune checkpoint blockade. Moreover, APOBECs may be able to induce suprathreshold levels of cellular mutation leading to mitotic catastrophe and direct tumor cell killing. Finally, we discuss the possibility that linking predictable APOBEC-induced mutation with escape from specific frontline therapies could identify mutated molecules/pathways that can be targeted with small molecules and/or immunotherapies in a Trap and Ambush strategy. Together, these considerations lead to the counterintuitive hypothesis that, instead of attempting to expunge and excoriate APOBEC activity in cancer therapy, it might be exploited-and even, counterintuitively, encouraged.
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Affiliation(s)
- Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota.
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - Alan Melcher
- The Institute of Cancer Research/Royal Marsden, National Institute for Health Research Biomedical Research Centre, London, United Kingdom
| | - Hardev Pandha
- Surrey Cancer Research Institute, Faculty of Health and Medical Sciences, University of Surrey Guildford, Surrey, United Kingdom
| | - Kevin J Harrington
- The Institute of Cancer Research/Royal Marsden, National Institute for Health Research Biomedical Research Centre, London, United Kingdom
| | - Jose S Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
- Will's Eye Hospital, Philadelphia, Pennsylvania
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22
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Udquim KI, Zettelmeyer C, Banday AR, Lin SHY, Prokunina-Olsson L. APOBEC3B expression in breast cancer cell lines and tumors depends on the estrogen receptor status. Carcinogenesis 2021; 41:1030-1037. [PMID: 31930332 DOI: 10.1093/carcin/bgaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/17/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Increased exposure to estrogen is associated with an elevated risk of breast cancer. Considering estrogen as a possible mutagen, we hypothesized that exposure to estrogen alone or in combination with the DNA-damaging chemotherapy drug, cisplatin, could induce expression of genes encoding enzymes involved in APOBEC-mediated mutagenesis. To test this hypothesis, we measured the expression of APOBEC3A (A3A) and APOBEC3B (A3B) genes in two breast cancer cell lines treated with estradiol, cisplatin or their combination. These cell lines, T-47D (ER+) and MDA-MB-231 (ER-), differed by the status of the estrogen receptor (ER). Expression of A3A was not detectable in any conditions tested, while A3B expression was induced by treatment with cisplatin and estradiol in ER+ cells but was not affected by estradiol in ER- cells. In The Cancer Genome Atlas, expression of A3B was significantly associated with genotypes of a regulatory germline variant rs17000526 upstream of the APOBEC3 cluster in 116 ER- breast tumors (P = 0.006) but not in 387 ER+ tumors (P = 0.48). In conclusion, we show that in breast cancer cell lines, A3B expression was induced by estradiol in ER+ cells and by cisplatin regardless of ER status. In ER+ breast tumors, the effect of estrogen may be masking the association of rs17000526 with A3B expression, which was apparent in ER- tumors. Our results provide new insights into the differential etiology of ER+ and ER- breast cancer and the possible role of A3B in this process through a mitogenic rather than the mutagenic activity of estrogen.
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Affiliation(s)
- Krizia-Ivana Udquim
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara Zettelmeyer
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Seraph Han-Yin Lin
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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23
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Pan JW, Zabidi MMA, Chong BK, Meng MY, Ng PS, Hasan SN, Sandey B, Bahnu S, Rajadurai P, Yip CH, Rueda OM, Caldas C, Chin SF, Teo SH. Germline APOBEC3B deletion increases somatic hypermutation in Asian breast cancer that is associated with Her2 subtype, PIK3CA mutations and immune activation. Int J Cancer 2021; 148:2489-2501. [PMID: 33423300 DOI: 10.1002/ijc.33463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022]
Abstract
A 30-kb deletion that eliminates the coding region of APOBEC3B (A3B) is >5 times more common in women of Asian descent compared to European descent. This polymorphism creates a chimera with the APOBEC3A (A3A) coding region and A3B 3'UTR, and it is associated with an increased risk for breast cancer in Asian women. Here, we explored the relationship between the A3B deletion polymorphism with tumour characteristics in Asian women. Using whole exome and whole transcriptome sequencing data of 527 breast tumours, we report that germline A3B deletion polymorphism leads to expression of the A3A-B hybrid isoform and increased APOBEC-associated somatic hypermutation. Hypermutated tumours, regardless of A3B germline status, were associated with the Her2 molecular subtype and PIK3CA mutations. Compared to nonhypermutated tumours, hypermutated tumours also had higher neoantigen burden, tumour heterogeneity and immune activation. Taken together, our results suggest that the germline A3B deletion polymorphism, via the A3A-B hybrid isoform, contributes to APOBEC mutagenesis in a significant proportion of Asian breast cancers. In addition, APOBEC somatic hypermutation, regardless of A3B background, may be an important clinical biomarker for Asian breast cancers.
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Affiliation(s)
- Jia-Wern Pan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | - Boon-Keat Chong
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Mei-Yee Meng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Pei-Sze Ng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Siti Norhidayu Hasan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Bethan Sandey
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Saira Bahnu
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | | | - Cheng-Har Yip
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
- Cambridge Breast Cancer Research Unit, CRUK Cambridge Cancer Centre, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Soo-Hwang Teo
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
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24
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Perez-Bercoff D, Laude H, Lemaire M, Hunewald O, Thiers V, Vignuzzi M, Blanc H, Poli A, Amoura Z, Caval V, Suspène R, Hafezi F, Mathian A, Vartanian JP, Wain-Hobson S. Sustained high expression of multiple APOBEC3 cytidine deaminases in systemic lupus erythematosus. Sci Rep 2021; 11:7893. [PMID: 33846459 PMCID: PMC8041901 DOI: 10.1038/s41598-021-87024-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
APOBEC3 (A3) enzymes are best known for their role as antiviral restriction factors and as mutagens in cancer. Although four of them, A3A, A3B, A3F and A3G, are induced by type-1-interferon (IFN-I), their role in inflammatory conditions is unknown. We thus investigated the expression of A3, and particularly A3A and A3B because of their ability to edit cellular DNA, in Systemic Lupus Erythematosus (SLE), a chronic inflammatory disease characterized by high IFN-α serum levels. In a cohort of 57 SLE patients, A3A and A3B, but also A3C and A3G, were upregulated ~ 10 to 15-fold (> 1000-fold for A3B) compared to healthy controls, particularly in patients with flares and elevated serum IFN-α levels. Hydroxychloroquine, corticosteroids and immunosuppressive treatment did not reverse A3 levels. The A3AΔ3B polymorphism, which potentiates A3A, was detected in 14.9% of patients and in 10% of controls, and was associated with higher A3A mRNA expression. A3A and A3B mRNA levels, but not A3C or A3G, were correlated positively with dsDNA breaks and negatively with lymphopenia. Exposure of SLE PBMCs to IFN-α in culture induced massive and sustained A3A levels by 4 h and led to massive cell death. Furthermore, the rs2853669 A > G polymorphism in the telomerase reverse transcriptase (TERT) promoter, which disrupts an Ets-TCF-binding site and influences certain cancers, was highly prevalent in SLE patients, possibly contributing to lymphopenia. Taken together, these findings suggest that high baseline A3A and A3B levels may contribute to cell frailty, lymphopenia and to the generation of neoantigens in SLE patients. Targeting A3 expression could be a strategy to reverse cell death and the generation of neoantigens.
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Affiliation(s)
- Danielle Perez-Bercoff
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg.
| | - Hélène Laude
- ICAReB Platform, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Morgane Lemaire
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Valérie Thiers
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Aurélie Poli
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Zahir Amoura
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre D'Immunologie Et Des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Vincent Caval
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Rodolphe Suspène
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - François Hafezi
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Alexis Mathian
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre D'Immunologie Et Des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
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25
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Ben X, Tian D, Liang J, Wu M, Xie F, Zheng J, Chen J, Fei Q, Guo X, Weng X, Liu S, Xie X, Ying Y, Qiao G, Jing C. APOBEC3B deletion polymorphism and lung cancer risk in the southern Chinese population. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:656. [PMID: 33987354 PMCID: PMC8105993 DOI: 10.21037/atm-21-989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Approximately 80–85% of lung cancer is the non-small cell lung cancer (NSCLC) subtype, which ranks as the leading cause of cancer deaths worldwide. APOBEC3B (A3B) was reported to be a key source of mutations in NSCLC. However, the role of the A3B deletion polymorphism in the etiology of NSCLC has not been well-documented. Methods A case-control study with 317 NSCLC patients and 334 healthy controls was conducted to explore the association between the A3B deletion polymorphism and the risk of NSCLC. The unconditional logistic regression model was performed to calculate the odds ratio (OR) and the 95% confidence interval (CI), and the confounding factors were adjusted, including age, gender, and smoking status, to estimate the risk. An analysis of gene-environment interactions was performed using multifactor dimensionality reduction (MDR) software. Results We found that the del/del genotype of A3B deletion significantly increased NSCLC risk. Compared with individuals carrying the ins/ins genotype of A3B deletion, individuals with the del/del genotype had a 2.36 times increased risk of developing NSCLC after adjusting for confounding factors (OR =2.71, 95% CI: 1.67–4.42, P<0.001). A 3-factor gene-environment (A3B deletion, gender, and smoking) interaction model was found for NSCLC (OR =4.407, 95% CI: 1.174–16.549, P=0.028). Conclusions We propose that the A3B deletion polymorphism can increase the risk of developing NSCLC, and their interactions with gender and smoking may contribute to the risk of NSCLC in the southern Chinese population.
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Affiliation(s)
- Xiaosong Ben
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dan Tian
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiayu Liang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Min Wu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Fan Xie
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Jinlong Zheng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Jingmin Chen
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Qiaoyuan Fei
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xinrong Guo
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xueqiong Weng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Shan Liu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xin Xie
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Yuting Ying
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Guibin Qiao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chunxia Jing
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China.,Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, China
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26
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Kottke T, Tonne J, Evgin L, Driscoll CB, van Vloten J, Jennings VA, Huff AL, Zell B, Thompson JM, Wongthida P, Pulido J, Schuelke MR, Samson A, Selby P, Ilett E, McNiven M, Roberts LR, Borad MJ, Pandha H, Harrington K, Melcher A, Vile RG. Oncolytic virotherapy induced CSDE1 neo-antigenesis restricts VSV replication but can be targeted by immunotherapy. Nat Commun 2021; 12:1930. [PMID: 33772027 PMCID: PMC7997928 DOI: 10.1038/s41467-021-22115-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/25/2021] [Indexed: 01/06/2023] Open
Abstract
In our clinical trials of oncolytic vesicular stomatitis virus expressing interferon beta (VSV-IFNβ), several patients achieved initial responses followed by aggressive relapse. We show here that VSV-IFNβ-escape tumors predictably express a point-mutated CSDE1P5S form of the RNA-binding Cold Shock Domain-containing E1 protein, which promotes escape as an inhibitor of VSV replication by disrupting viral transcription. Given time, VSV-IFNβ evolves a compensatory mutation in the P/M Inter-Genic Region which rescues replication in CSDE1P5S cells. These data show that CSDE1 is a major cellular co-factor for VSV replication. However, CSDE1P5S also generates a neo-epitope recognized by non-tolerized T cells. We exploit this predictable neo-antigenesis to drive, and trap, tumors into an escape phenotype, which can be ambushed by vaccination against CSDE1P5S, preventing tumor escape. Combining frontline therapy with escape-targeting immunotherapy will be applicable across multiple therapies which drive tumor mutation/evolution and simultaneously generate novel, targetable immunopeptidomes associated with acquired treatment resistance.
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Affiliation(s)
- Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jason Tonne
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura Evgin
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jacob van Vloten
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Victoria A Jennings
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Amanda L Huff
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brady Zell
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jill M Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jose Pulido
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Adel Samson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Peter Selby
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Elizabeth Ilett
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Mark McNiven
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Mitesh J Borad
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ, USA
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Kevin Harrington
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Alan Melcher
- Chester Beatty Laboratories, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
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27
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Law EK, Levin-Klein R, Jarvis MC, Kim H, Argyris PP, Carpenter MA, Starrett GJ, Temiz NA, Larson LK, Durfee C, Burns MB, Vogel RI, Stavrou S, Aguilera AN, Wagner S, Largaespada DA, Starr TK, Ross SR, Harris RS. APOBEC3A catalyzes mutation and drives carcinogenesis in vivo. J Exp Med 2021; 217:152061. [PMID: 32870257 PMCID: PMC7953736 DOI: 10.1084/jem.20200261] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/08/2020] [Accepted: 07/22/2020] [Indexed: 12/24/2022] Open
Abstract
The APOBEC3 family of antiviral DNA cytosine deaminases is implicated as the second largest source of mutation in cancer. This mutational process may be a causal driver or inconsequential passenger to the overall tumor phenotype. We show that human APOBEC3A expression in murine colon and liver tissues increases tumorigenesis. All other APOBEC3 family members, including APOBEC3B, fail to promote liver tumor formation. Tumor DNA sequences from APOBEC3A-expressing animals display hallmark APOBEC signature mutations in TCA/T motifs. Bioinformatic comparisons of the observed APOBEC3A mutation signature in murine tumors, previously reported APOBEC3A and APOBEC3B mutation signatures in yeast, and reanalyzed APOBEC mutation signatures in human tumor datasets support cause-and-effect relationships for APOBEC3A-catalyzed deamination and mutagenesis in driving multiple human cancers.
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Affiliation(s)
- Emily K Law
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Rena Levin-Klein
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Matthew C Jarvis
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Hyoung Kim
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Prokopios P Argyris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Division of Oral and Maxillofacial Pathology, School of Dentistry, University of Minnesota, Minneapolis, MN
| | - Michael A Carpenter
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Gabriel J Starrett
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Health Informatics, University of Minnesota, Minneapolis, MN
| | - Lindsay K Larson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Cameron Durfee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
| | - Michael B Burns
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN.,Department of Biology, Loyola University, Chicago, IL
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN
| | - Spyridon Stavrou
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Sandra Wagner
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Timothy K Starr
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Department of Obstetrics, Gynecology, and Women's Health, University of Minnesota, Minneapolis, MN
| | - Susan R Ross
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN
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Hirabayashi S, Shirakawa K, Horisawa Y, Matsumoto T, Matsui H, Yamazaki H, Sarca AD, Kazuma Y, Nomura R, Konishi Y, Takeuchi S, Stanford E, Kawaji H, Murakawa Y, Takaori-Kondo A. APOBEC3B is preferentially expressed at the G2/M phase of cell cycle. Biochem Biophys Res Commun 2021; 546:178-184. [PMID: 33592502 DOI: 10.1016/j.bbrc.2021.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
APOBEC3B (A3B) is a cytosine deaminase that converts cytosine to uracil in single-stranded DNA. Cytosine-to-thymine and cytosine-to-guanine base substitution mutations in trinucleotide motifs (APOBEC mutational signatures) were found in various cancers including lymphoid hematological malignancies such as multiple myeloma and A3B has been shown to be an enzymatic source of mutations in those cancers. Although the importance of A3B is being increasingly recognized, it is unclear how A3B expression is regulated in cancer cells as well as normal cells. To answer these fundamental questions, we analyzed 1276 primary myeloma cells using single-cell RNA-sequencing (scRNA-seq) and found that A3B was preferentially expressed at the G2/M phase, in sharp contrast to the expression patterns of other APOBEC3 genes. Consistently, we demonstrated that A3B protein was preferentially expressed at the G2/M phase in myeloma cells by cell sorting. We also demonstrated that normal blood cells expressing A3B were also enriched in G2/M-phase cells by analyzing scRNA-seq data from 86,493 normal bone marrow mononuclear cells. Furthermore, we revealed that A3B was expressed mainly in plasma cells, CD10+ B cells and erythroid cells, but not in granulocyte-macrophage progenitors. A3B expression profiling in normal blood cells may contribute to understanding the defense mechanism of A3B against viruses, and partially explain the bias of APOBEC mutational signatures in lymphoid but not myeloid malignancies. This study identified the cells and cellular phase in which A3B is highly expressed, which may help reveal the mechanisms behind carcinogenesis and cancer heterogeneity, as well as the biological functions of A3B in normal blood cells.
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Affiliation(s)
- Shigeki Hirabayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihito Horisawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadahiko Matsumoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Yamazaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Anamaria Daniela Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Nomura
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshinobu Konishi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Suguru Takeuchi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Emani Stanford
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy; Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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29
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Progression to Metastasis of Solid Cancer. Cancers (Basel) 2021; 13:cancers13040717. [PMID: 33578666 PMCID: PMC7916396 DOI: 10.3390/cancers13040717] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 12/26/2022] Open
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30
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Endogenous APOBEC3B overexpression characterizes HPV-positive and HPV-negative oral epithelial dysplasias and head and neck cancers. Mod Pathol 2021; 34:280-290. [PMID: 32632179 PMCID: PMC8261524 DOI: 10.1038/s41379-020-0617-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022]
Abstract
The DNA cytosine deaminase APOBEC3B (A3B) is a newly recognized endogenous source of mutations in a range of human tumors, including head/neck cancer. A3B inflicts C-to-T and C-to-G base substitutions in 5'-TCA/T trinucleotide motifs, contributes to accelerated rates of tumor development, and affects clinical outcomes in a variety of cancer types. High-risk human papillomavirus (HPV) infection causes A3B overexpression, and HPV-positive cervical and head/neck cancers are among tumor types with the highest degree of APOBEC signature mutations. A3B overexpression in HPV-positive tumor types is caused by the viral E6/E7 oncoproteins and may be an early off-to-on switch in tumorigenesis. In comparison, less is known about the molecular mechanisms responsible for A3B overexpression in HPV-negative head/neck cancers. Here, we utilize an immunohistochemical approach to determine whether A3B is turned from off-to-on or if it undergoes a more gradual transition to overexpression in HPV-negative head/neck cancers. As positive controls, almost all HPV-positive oral epithelial dysplasias and oropharyngeal cancers showed high levels of nuclear A3B staining regardless of diagnosis. As negative controls, A3B levels were low in phenotypically normal epithelium adjacent to cancer and oral epithelial hyperplasias. Interestingly, HPV-negative and low-grade oral epithelial dysplasias showed intermediate A3B levels, while high-grade oral dysplasias showed high A3B levels similar to oral squamous cell carcinomas. A3B levels were highest in grade 2 and grade 3 oral squamous cell carcinomas. In addition, a strong positive association was found between nuclear A3B and Ki67 scores suggesting a linkage to the cell cycle. Overall, these results support a model in which gradual activation of A3B expression occurs during HPV-negative tumor development and suggest that A3B overexpression may provide a marker for advanced grade oral dysplasia and cancer.
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31
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Kim S, Shin D, Min A, Kim M, Na D, Lee HB, Ryu HS, Yang Y, Woo GU, Lee KH, Lee DW, Kim TY, Lee C, Im SA, Kim JI. Genomic profile of metastatic breast cancer patient-derived xenografts established using percutaneous biopsy. J Transl Med 2021; 19:7. [PMID: 33407601 PMCID: PMC7789010 DOI: 10.1186/s12967-020-02607-2] [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: 05/04/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022] Open
Abstract
Background Metastatic breast cancer (mBC) is a complex and life-threatening disease and although it is difficult to cure, patients can benefit from sequential anticancer treatment, including endocrine therapy, targeted therapy and cytotoxic chemotherapy. The patient-derived xenograft (PDX) model is suggested as a practical tool to predict the clinical outcome of this disease as well as to screen novel drugs. This study aimed to establish PDX models in Korean patients and analyze their genomic profiles and utility for translational research. Methods Percutaneous core needle biopsy or punch biopsy samples were used for xenotransplantation. Whole exome sequencing and transcriptome analysis were performed to assess the genomic and RNA expression profiles, respectively. Copy number variation and mutational burden were analyzed and compared with other metastatic breast cancer genomic results. Mutational signatures were also analyzed. The antitumor effect of an ATR inhibitor was tested in the relevant PDX model. Results Of the 151 cases studied, 40 (26%) PDX models were established. Notably, the take rate of all subtypes, including the hormone receptor-positive (HR +) subtype, exceeded 20%. The PDX model had genomic fidelity and copy number variation that represented the pattern of its donor sample. TP53, PIK3CA, ESR1, and GATA3 mutations were frequently found in our samples, with TP53 being the most frequently mutated, and the somatic mutations in these genes strengthened their frequency in the PDX model. The ESR1 mutation, CCND1 amplification, and the APOBEC signature were significant features in our HR + HER2- PDX model. Fulvestrant in combination with palbociclib showed a partial response to the relevant patient’s tumor harboring the ESR1 mutation, and CCND1 amplification was found in the PDX model. AZD6738, an ATR inhibitor, delayed tumor growth in a relevant PDX model. Conclusions Our PDX model was established using core needle biopsy samples from primary and metastatic tissues. Genomic profiles of the samples reflected their original tissue characteristics and could be used for the interpretation of clinical outcomes.
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Affiliation(s)
- Seongyeong Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Dongjin Shin
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Ahrum Min
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Minjung Kim
- Medical Research Center, Genomic Medicine Institute (GMI), Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Deukchae Na
- Ewha Institute of Convergence Medicine, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Han-Byeol Lee
- Department of General Surgery, Seoul National University Hospital, Seoul, Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Yaewon Yang
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Translational Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Internal Medicine, Chungbuk University Hospital, Cheong-Ju, Korea
| | - Go-Un Woo
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Kyung-Hun Lee
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Dae-Won Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Tae-Yong Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Charles Lee
- Department of Life Science, Ewha Womans University, Seoul, Korea.,The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Seock-Ah Im
- Cancer Research Institute, Seoul National University, Seoul, Korea. .,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea. .,Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
| | - Jong-Il Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea. .,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea. .,Medical Research Center, Genomic Medicine Institute (GMI), Seoul National University, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
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32
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Granadillo Rodríguez M, Flath B, Chelico L. The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead. Open Biol 2020; 10:200188. [PMID: 33292100 PMCID: PMC7776566 DOI: 10.1098/rsob.200188] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. While these enzymes normally act as an intrinsic immune defence against viruses, they can also catalyse 'off-target' cytidine deamination in genomic single-stranded DNA intermediates. The deamination of cytosine forms uracil, which is promutagenic in DNA. Key factors to trigger the APOBEC 'off-target' activity are overexpression in a non-normal cell type, nuclear localization and replication stress. The resulting uracil-induced mutations contribute to genomic variation, which may result in neutral, beneficial or harmful consequences for the cancer. This review summarizes the functional and biochemical basis of the APOBEC3 enzyme activity and highlights their relationship with the most well-studied cancers in this particular context such as breast, lung, bladder, and human papillomavirus-associated cancers. We focus on APOBEC3A, APOBEC3B and APOBEC3H haplotype I because they are the leading candidates as sources of somatic mutations in these and other cancers. Also, we discuss the prognostic value of the APOBEC3 expression in drug resistance and response to therapies.
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Affiliation(s)
| | | | - Linda Chelico
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Hix MA, Wong L, Flath B, Chelico L, Cisneros GA. Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer. NAR Cancer 2020; 2:zcaa023. [PMID: 32984821 PMCID: PMC7503452 DOI: 10.1093/narcan/zcaa023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022] Open
Abstract
A number of APOBEC family DNA cytosine deaminases can induce mutations in tumor cells. APOBEC3H haplotype I is one of the deaminases that has been proposed to cause mutations in lung cancer. Here, we confirmed that APOBEC3H haplotype I can cause uracil-induced DNA damage in lung cancer cells that results in γH2AX foci. Interestingly, the database of cancer biomarkers in DNA repair genes (DNArCdb) identified a single-nucleotide polymorphism (rs139298) of APOBEC3H haplotype I that is involved in lung cancer. While we thought this may increase the activity of APOBEC3H haplotype I, instead we found through computational modeling and cell-based experiments that this single-nucleotide polymorphism causes the destabilization of APOBEC3H Haplotype I. Computational analysis suggests that the resulting K121E change affects the structure of APOBEC3H leading to active site disruption and destabilization of the RNA-mediated dimer interface. A K117E mutation in a K121E background stabilized the APOBEC3H haplotype I, thus enabling biochemical study. Subsequent analysis showed that K121E affected catalytic activity, single-stranded DNA binding and oligomerization on single-stranded DNA. The destabilization of a DNA mutator associated with lung cancer supports the model that too much APOBEC3-induced mutation could result in immune recognition or death of tumor cells.
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Affiliation(s)
- Mark A Hix
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - Lai Wong
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Ben Flath
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
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GATA3 and APOBEC3B are prognostic markers in adrenocortical carcinoma and APOBEC3B is directly transcriptionally regulated by GATA3. Oncotarget 2020; 11:3354-3370. [PMID: 32934779 PMCID: PMC7486697 DOI: 10.18632/oncotarget.27703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/14/2020] [Indexed: 02/01/2023] Open
Abstract
Recent evidence has implicated APOBEC3B (Apolipoprotein B mRNA editing enzyme catalytic subunit 3B) as a source of mutations in breast, bladder, cervical, lung, head, and neck cancers. However, the role of APOBEC3B in adrenocortical carcinoma (ACC) and the mechanisms through which its expression is regulated in cancer are not fully understood. Here, we report that APOBEC3B is overexpressed in ACC and it regulates cell proliferation by inducing S phase arrest. We show high APOBEC3B expression is associated with a higher copy number gain/loss at chromosome 4 and 8 and TP53 mutation rate in ACC. GATA3 was identified as a positive regulator of APOBEC3B expression and directly binds the APOBEC3B promoter region. Both GATA3 and APOBEC3B expression levels were associated with patient survival. Our study provides novel insights into the function and regulation of APOBEC3B expression in addition to its known mutagenic ability.
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35
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Kim SH, Ahn S, Suh KJ, Kim YJ, Park SY, Kang E, Kim EK, Kim IA, Chae S, Choi M, Kim JH. Identifying germline APOBEC3B deletion and immune phenotype in Korean patients with operable breast cancer. Breast Cancer Res Treat 2020; 183:697-704. [PMID: 32715441 DOI: 10.1007/s10549-020-05811-2] [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: 04/19/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3B (APOBEC3B) is implicated in anti-viral immune response and cancer mutagenesis. Germline APOBEC3B deletion is associated with increased susceptibility to breast cancer. We aimed to evaluate the association between germline APOBEC3B deletion and clinical phenotypes of breast cancer in Korean patients with operable breast cancer. METHODS Mononuclear blood cell DNA of 103 patients with operable breast cancer was collected at Seoul National University Bundang Hospital in 2009. The DNA was sequenced to analyze APOBEC3B deletion status. Further, tumor-infiltrating lymphocytes (TILs) and programmed cell death-ligand 1 (PD-L1) expression in tumor cells were measured using immunohistochemistry. RESULTS Median age of breast cancer diagnosis was 46 (25-72). In APOBEC3B deletion analysis, 10 (9.7%), 36 (35.0%), and 57 (55.3%) patients were identified as two-copy deletion (A3Bdel/del), one-one copy deletion (A3Bdel/wt), and no deletion (A3Bwt/wt), respectively. For other cancer susceptibility gene alterations, 9 (8.7%) patients were identified as pathogenic variants: RAD51D (n = 1), GJB2 (n = 1), BRCA1 (n = 1), BRCA2 (n = 2), ATM (n = 1), USH2A (n = 1), RET (n = 1), BARD1 (n = 1). We observed no significant association between germline APOBEC3B deletion with any clinicopathologic features of breast cancer, such as age, family history of cancer, and bilateral breast cancer. Further, according to follow-up observations, APOBEC3B deletion was not predictive of disease-free survival. In ER+ subtype, a trend toward better survival was observed in patients with A3Bdel/del genotype as compared to patients with A3Bdel/wt and A3Bwt/wt genotype (log-rank, P = 0.25). In patients with sufficient tumor samples for the assessment of TIL (n = 63) and PD-L1 (n = 71), the A3Bdel/del genotype was significantly associated with high TILs (> 10%) than other tumor genotypes (6/7 patients in A3Bdel/del vs. 13/24 in A3Bdel/wt vs. 15/32 in A3Bwt/wt: Fisher's exact test, P = 0.029). However, PD-L1 expression was not associated with APOBEC3B deletion status (1/7 patients > 1% PD-L1 in A3Bdel/del vs. 4/26 in A3Bdel/wt vs. 8/38 in A3Bwt/wt: P = 0.901). CONCLUSION We identified germline APOBEC3B deletion in 9.7% of Korean patients with operable breast cancer. The relationship between A3Bdel/del genotype and high TILs suggests that patients carrying this genotype could be potential candidates for immunotherapy.
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Affiliation(s)
- Se Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - Soomin Ahn
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - Koung Jin Suh
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - Yu Jung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - Eunyoung Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - Eun-Kyu Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - In Ah Kim
- Department of Radiation Oncology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea
| | - Sumin Chae
- Department of Surgery, Kyung Hee University School of Medicine, Kyung Hee University Medical Center, Seoul, Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Songnam, Korea. .,Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 82 Gumi-ro 173 beon-gil, Bundang-gu, Songnam, 13620, Korea.
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36
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Germline APOBEC3B deletion influences clinicopathological parameters in luminal-A breast cancer: evidences from a southern Brazilian cohort. J Cancer Res Clin Oncol 2020; 146:1523-1532. [PMID: 32285256 DOI: 10.1007/s00432-020-03208-8] [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: 02/19/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE APOBEC3A and APOBEC3B cytidine deaminases have been implicated in the pathogenesis of multiple cancers, including breast cancer (BC). A germline deletion linking APOBEC3A and APOBEC3B loci (A3A/B) has been associated with higher APOBEC-mediated mutational burden, but its association with BC risk have been controversial. Therefore, this study investigated the association between A3A/B and BC susceptibility and clinical presentation in a Brazilian cohort. METHODS A3A/B deletion was evaluated through allele-specific PCR in 341 BC patients and 397 women without familial or personal history of neoplasia from Brazil and associations with susceptibility to BC subtypes were tested through age-adjusted logistic models while correlations with clinicopathological parameters were tested using Kendall's tests. RESULTS No association was found between A3A/B and BC susceptibility; however, in Luminal-A BCs, it was positively correlated with tumor size (Tau-c = 0.125) and Ki67 (Tau-c = 0.116) and negatively correlated with lymph node metastasis (LNM) (Tau-c = - 0.162). The negative association between A3A/B with LNM in Luminal-A BCs remained significant even after adjusting for tumor size and Ki67 in logistic models (OR = 0.22; p = 0.008). CONCLUSION These results show that although A3A/B may not modify BC susceptibility in Brazilian population, it may affect clinicopathological features in BC subtypes, promoting tumor cell proliferation while being negatively associated with LNM in Luminal-A BCs.
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Mao Y, Lv M, Zhang Y, Nie G, Cui J, Wang Y, Wang Y, Cao W, Liu X, Wang X, Wang H. APOBEC3B expression and its prognostic potential in breast cancer. Oncol Lett 2020; 19:3205-3214. [PMID: 32256817 PMCID: PMC7074638 DOI: 10.3892/ol.2020.11433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/03/2020] [Indexed: 12/24/2022] Open
Abstract
Apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) mRNA expression is associated with the poor prognosis of estrogen receptor positive (ER+) breast cancer. However, the clinical relevance of APOBEC3B protein expression in patients with breast cancer remains unclear. The present study evaluated the association of APOBEC3B protein expression with clinicopathological features, as well as survival outcomes of patients with breast cancer. Furthermore, the association between APOBEC3B protein expression and tumor infiltrating lymphocytes (TILs) was investigated. APOBEC3B protein expression in 120 patients with breast cancer was evaluated via immunohistochemistry, using a constructed tumor microarray, and TILs were analyzed by hematoxylin and eosin staining. The relevance of APOBEC3B mRNA expression in breast cancer was assessed using a Kaplan-Meier Plotter online tool, as well as the Tumor Immune Estimation Response and The Cancer Genome Atlas databases. The present study assessed APOBEC3B expression in 116 patients with breast cancer and demonstrated that protein expression was significantly associated with ER and progesterone receptor expression, as well as different subtypes of breast cancer. Notably, APOEBC3B protein expression was significantly associated with TILs. Overall, high expression levels of APOBEC3B protein and high levels of TILs were indicative of longer disease-free survival rate. High APOBEC3B mRNA expression was associated with poor relapse-free survival rate, overall survival rate and distant metastasis-free survival rate in patients with breast cancer, particularly for the Luminal A subtype. APOBEC3B mRNA expression was also indicated to be associated with the immune status of patients with breast cancer. Overall, the results of the present study demonstrated that APOBEC3B mRNA and protein expression levels presented different prognostic values in the survival of patients with breast cancer. However, both APOBEC3B mRNA and protein expression levels were associated with TILs in breast cancer. Therefore, APOBEC3B may be a prognostic biomarker for breast cancer.
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Affiliation(s)
- Yan Mao
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Meng Lv
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yuzi Zhang
- 3D Medicines Inc., Shanghai 200025, P.R. China
| | - Gang Nie
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Jian Cui
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yongmei Wang
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Yuanyuan Wang
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Weihong Cao
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Xiaoyi Liu
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Xingang Wang
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Haibo Wang
- Breast Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
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Kim YS, Sun DS, Yoon JS, Ko YH, Won HS, Kim JS. Clinical implications of APOBEC3A and 3B expression in patients with breast cancer. PLoS One 2020; 15:e0230261. [PMID: 32176735 PMCID: PMC7075570 DOI: 10.1371/journal.pone.0230261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
Background We aimed to evaluate the expression of APOBEC3A (A3A), 3B (A3B) mRNA, and germline APOBEC3A/B deletion polymorphism in patients with breast cancers and to investigate the correlation between their expressions and clinicopathological characteristics. Methods RNA and DNA samples were extracted from 138 breast cancer tissues and adjacent normal breast tissues. The levels of A3A and A3B mRNA transcripts were determined using quantitative real-time polymerase chain reaction. Insertion and deletion PCR assays were performed to detect the A3B deletion allele. The serum concentrations of soluble programmed death-ligand 1 (sPD-L1) and interferon gamma were determined using enzyme-linked immunosorbent assays. Results A3B mRNA expression levels were significantly higher in triple-negative breast cancers compared to hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancers. Older age of the patient and high ki-67 expression were associated with increased expression levels of A3A and A3B mRNA. Advanced tumor stage, presence of lymph node involvement, and high histological grade were associated with increased expression levels of A3A mRNA. The APOBEC3A/B deletion allele was found in 77 (55.8%) patients. TP53 and PIK3CA mutations were detected in 62 (44.9%) and 31 (22.5%) patients, respectively. The presence of a PIK3CA mutation was associated with lower A3A mRNA expression levels. There was a weak positive relationship between A3A mRNA expression levels and serum sPD-L1 levels. Conclusions There was a difference in A3B mRNA expression levels according to breast cancer subtypes, and high levels of A3A and A3B mRNA expressions were associated with an aggressive phenotype. There was a high incidence of APOBEC3A/B deletion allele. Further studies are needed to identify the clinical significance of APOBEC in Asian patients with breast cancer.
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Affiliation(s)
- Yong-seok Kim
- Department of Surgery, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Der Sheng Sun
- Division of Medical Oncology, Department of Internal Medicine, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung-sook Yoon
- Clinical Research Laboratory, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon Ho Ko
- Division of Medical Oncology, Department of Internal Medicine, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hye Sung Won
- Division of Medical Oncology, Department of Internal Medicine, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- * E-mail: (JSK); (HSW)
| | - Jeong Soo Kim
- Department of Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- * E-mail: (JSK); (HSW)
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Shen B, Chapman JH, Custance MF, Tricola GM, Jones CE, Furano AV. Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations. eLife 2020; 9:e51605. [PMID: 31904337 PMCID: PMC6961979 DOI: 10.7554/elife.51605] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
Abundant APOBEC3 (A3) deaminase-mediated mutations can dominate the mutational landscape ('mutator phenotype') of some cancers, however, the basis of this sporadic vulnerability is unknown. We show here that elevated expression of the bifunctional DNA glycosylase, NEIL2, sensitizes breast cancer cells to A3B-mediated mutations and double-strand breaks (DSBs) by perturbing canonical base excision repair (BER). NEIL2 usurps the canonical lyase, APE1, at abasic sites in a purified BER system, rendering them poor substrates for polymerase β. However, the nicked NEIL2 product can serve as an entry site for Exo1 in vitro to generate single-stranded DNA, which would be susceptible to both A3B and DSBs. As NEIL2 or Exo1 depletion mitigates the DNA damage caused by A3B expression, we suggest that aberrant NEIL2 expression can explain certain instances of A3B-mediated mutations.
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Affiliation(s)
- Birong Shen
- Section on Genomic Structure and Function, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Disease, National Institutes of HealthBethesdaUnited States
| | - Joseph H Chapman
- Section on Genomic Structure and Function, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Disease, National Institutes of HealthBethesdaUnited States
| | - Michael F Custance
- Section on Genomic Structure and Function, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Disease, National Institutes of HealthBethesdaUnited States
| | - Gianna M Tricola
- Section on Genomic Structure and Function, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Disease, National Institutes of HealthBethesdaUnited States
| | - Charles E Jones
- Section on Genomic Structure and Function, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Disease, National Institutes of HealthBethesdaUnited States
| | - Anthony V Furano
- Section on Genomic Structure and Function, Laboratory of Cell and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Disease, National Institutes of HealthBethesdaUnited States
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Zhu B, Tse LA, Wang D, Koka H, Zhang T, Abubakar M, Lee P, Wang F, Wu C, Tsang KH, Chan WC, Law SH, Li M, Li W, Wu S, Liu Z, Huang B, Zhang H, Tang E, Kan Z, Lee S, Park YH, Nam SJ, Wang M, Sun X, Jones K, Zhu B, Hutchinson A, Hicks B, Prokunina-Olsson L, Shi J, Garcia-Closas M, Chanock S, Yang XR. Immune gene expression profiling reveals heterogeneity in luminal breast tumors. Breast Cancer Res 2019; 21:147. [PMID: 31856876 PMCID: PMC6924001 DOI: 10.1186/s13058-019-1218-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/18/2019] [Indexed: 12/24/2022] Open
Abstract
Background Heterogeneity of immune gene expression patterns of luminal breast cancer (BC), which is clinically heterogeneous and overall considered as low immunogenic, has not been well studied especially in non-European populations. Here, we aimed at characterizing the immune gene expression profile of luminal BC in an Asian population and associating it with patient characteristics and tumor genomic features. Methods We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 luminal BC patients from Hong Kong using RNA-sequencing data and used unsupervised consensus clustering to stratify tumors. We then used luminal patients from The Cancer Genome Atlas (TCGA, N = 564) and a Korean breast cancer study (KBC, N = 112) as replication datasets. Results Based on the expression of 130 immune-related genes, luminal tumors were stratified into three distinct immune subtypes. Tumors in one subtype showed higher level of tumor-infiltrating lymphocytes (TILs), characterized by T cell gene activation, higher expression of immune checkpoint genes, higher nonsynonymous mutation burden, and higher APOBEC-signature mutations, compared with other luminal tumors. The high-TIL subtype was also associated with lower ESR1/ESR2 expression ratio and increasing body mass index. The comparison of the immune profile in tumor and matched normal tissue suggested a tumor-derived activation of specific immune responses, which was only seen in high-TIL patients. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in TCGA and KBC, although the pattern was more similar in Asian populations. The germline APOBEC3B deletion polymorphism, which is prevalent in East Asian populations and was previously linked to immune activation, was not associated with immune subtypes in our study. This result does not support the hypothesis that the germline APOBEC3B deletion polymorphism is the driving force for immune activation in breast tumors in Asian populations. Conclusion Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification and a subset of luminal BC patients may benefit from checkpoint immunotherapy, at least in Asian populations.
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Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lap Ah Tse
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China.
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Priscilla Lee
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Cherry Wu
- North District Hospital, Hong Kong, China
| | | | | | | | - Mengjie Li
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China.,Vanderbilt University, Nashville, TN, USA
| | - Wentao Li
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Suyang Wu
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhiguang Liu
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Bixia Huang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Eric Tang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Zhengyan Kan
- Pfizer Oncology Research, San Diego, CA, 92121, USA
| | | | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea
| | - Seok Jin Nam
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, South Korea
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xuezheng Sun
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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Chen Z, Wen W, Bao J, Kuhs KL, Cai Q, Long J, Shu XO, Zheng W, Guo X. Integrative genomic analyses of APOBEC-mutational signature, expression and germline deletion of APOBEC3 genes, and immunogenicity in multiple cancer types. BMC Med Genomics 2019; 12:131. [PMID: 31533728 PMCID: PMC6751822 DOI: 10.1186/s12920-019-0579-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Although APOBEC-mutational signature is found in tumor tissues of multiple cancers, how a common germline APOBEC3A/B deletion affects the mutational signature remains unclear. METHODS Using data from 10 cancer types generated as part of TCGA, we performed integrative genomic and association analyses to assess inter-relationship of expressions for isoforms APOBEC3A and APOBEC3B, APOBEC-mutational signature, germline APOBEC3A/B deletions, neoantigen loads, and tumor infiltration lymphocytes (TILs). RESULTS We found that expression level of the isoform uc011aoc transcribed from the APOBEC3A/B chimera was associated with a greater burden of APOBEC-mutational signature only in breast cancer, while germline APOBEC3A/B deletion led to an increased expression level of uc011aoc in multiple cancer types. Furthermore, we found that the deletion was associated with elevated APOBEC-mutational signature, neoantigen loads and relative composition of T cells (CD8+) in TILs only in breast cancer. Additionally, we also found that APOBEC-mutational signature significantly contributed to neoantigen loads and certain immune cell abundances in TILs across cancer types. CONCLUSIONS These findings reveal new insights into understanding the genetic, biological and immunological mechanisms through which APOBEC genes may be involved in carcinogenesis, and provide potential genetic biomarker for the development of disease prevention and cancer immunotherapy.
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Affiliation(s)
- Zhishan Chen
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Wanqing Wen
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Jiandong Bao
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Krystle L. Kuhs
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Qiuyin Cai
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Jirong Long
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Xiao-ou Shu
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Wei Zheng
- 0000 0004 1936 9916grid.412807.8Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203 USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
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McCann JL, Klein MM, Leland EM, Law EK, Brown WL, Salamango DJ, Harris RS. The DNA deaminase APOBEC3B interacts with the cell-cycle protein CDK4 and disrupts CDK4-mediated nuclear import of Cyclin D1. J Biol Chem 2019; 294:12099-12111. [PMID: 31217276 PMCID: PMC6690700 DOI: 10.1074/jbc.ra119.008443] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/27/2019] [Indexed: 12/13/2022] Open
Abstract
Apolipoprotein B mRNA editing enzyme catalytic subunit-like protein 3B (APOBEC3B or A3B), as other APOBEC3 members, is a single-stranded (ss)DNA cytosine deaminase with antiviral activity. A3B is also overexpressed in multiple tumor types, such as carcinomas of the bladder, cervix, lung, head/neck, and breast. A3B generates both dispersed and clustered C-to-T and C-to-G mutations in intrinsically preferred trinucleotide motifs (TCA/TCG/TCT). A3B-catalyzed mutations are likely to promote tumor evolution and cancer progression and, as such, are associated with poor clinical outcomes. However, little is known about cellular processes that regulate A3B. Here, we used a proteomics approach involving affinity purification coupled to MS with human 293T cells to identify cellular proteins that interact with A3B. This approach revealed a specific interaction with cyclin-dependent kinase 4 (CDK4). We validated and mapped this interaction by co-immunoprecipitation experiments. Functional studies and immunofluorescence microscopy experiments in multiple cell lines revealed that A3B is not a substrate for CDK4-Cyclin D1 phosphorylation nor is its deaminase activity modulated. Instead, we found that A3B is capable of disrupting the CDK4-dependent nuclear import of Cyclin D1. We propose that this interaction may favor a more potent antiviral response and simultaneously facilitate cancer mutagenesis.
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Affiliation(s)
- Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Madeline M Klein
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Evelyn M Leland
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455.
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455; Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455.
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Wojtowicz D, Sason I, Huang X, Kim YA, Leiserson MDM, Przytycka TM, Sharan R. Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer. Genome Med 2019; 11:49. [PMID: 31349863 PMCID: PMC6660659 DOI: 10.1186/s13073-019-0659-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/12/2019] [Indexed: 12/19/2022] Open
Abstract
Knowing the activity of the mutational processes shaping a cancer genome may provide insight into tumorigenesis and personalized therapy. It is thus important to characterize the signatures of active mutational processes in patients from their patterns of single base substitutions. However, mutational processes do not act uniformly on the genome, leading to statistical dependencies among neighboring mutations. To account for such dependencies, we develop the first sequence-dependent model, SigMa, for mutation signatures. We apply SigMa to characterize genomic and other factors that influence the activity of mutation signatures in breast cancer. We show that SigMa outperforms previous approaches, revealing novel insights on signature etiology. The source code for SigMa is publicly available at https://github.com/lrgr/sigma.
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Affiliation(s)
- Damian Wojtowicz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA
| | - Itay Sason
- School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Xiaoqing Huang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA
| | - Yoo-Ah Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA
| | - Mark D M Leiserson
- Center for Bioinformatics and Computational Biology, University of Maryland, 8125 Paint Branch Dr, College Park, 20740, USA.
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, 20894, USA.
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel.
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Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. Determinants of Oligonucleotide Selectivity of APOBEC3B. J Chem Inf Model 2019; 59:2264-2273. [PMID: 30130104 PMCID: PMC6644697 DOI: 10.1021/acs.jcim.8b00427] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
APOBEC3B (A3B) is a prominent source of mutation in many cancers. To date, it has been difficult to capture the native protein-DNA interactions that confer A3B's substrate specificity by crystallography due to the highly dynamic nature of wild-type A3B active site. We use computational tools to restore a recent crystal structure of a DNA-bound A3B C-terminal domain mutant construct to its wild type sequence, and run molecular dynamics simulations to study its substrate recognition mechanisms. Analysis of these simulations reveal dynamics of the native A3Bctd-oligonucleotide interactions, including the experimentally inaccessible loop 1-oligonucleotide interactions. A second series of simulations in which the target cytosine nucleotide was computationally mutated from a deoxyribose to a ribose show a change in sugar ring pucker, leading to a rearrangement of the binding site and revealing a potential intermediate in the binding pathway. Finally, apo simulations of A3B, starting from the DNA-bound open state, experience a rapid and consistent closure of the binding site, reaching conformations incompatible with substrate binding. This study reveals a more realistic and dynamic view of the wild type A3B binding site and provides novel insights for structure-guided design efforts for A3B.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Özlem Demir
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Daniel A Harki
- Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Masonic Cancer Center , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Institute for Molecular Virology , University of Minnesota , Minneapolis , Minnesota 55455 , United States
- Howard Hughes Medical Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093-0340 , United States
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45
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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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46
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Smith NJ, Fenton TR. The APOBEC3 genes and their role in cancer: insights from human papillomavirus. J Mol Endocrinol 2019; 62:R269-R287. [PMID: 30870810 DOI: 10.1530/jme-19-0011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022]
Abstract
The interaction between human papillomaviruses (HPV) and the apolipoprotein-B mRNA-editing catalytic polypeptide-like (APOBEC)3 (A3) genes has garnered increasing attention in recent years, with considerable efforts focused on understanding their apparent roles in both viral editing and in HPV-driven carcinogenesis. Here, we review these developments and highlight several outstanding questions in the field. We consider whether editing of the virus and mutagenesis of the host are linked or whether both are essentially separate events, coincidentally mediated by a common or distinct A3 enzymes. We discuss the viral mechanisms and cellular signalling pathways implicated in A3 induction in virally infected cells and examine which of the A3 enzymes might play the major role in HPV-associated carcinogenesis and in the development of therapeutic resistance. We consider the parallels between A3 induction in HPV-infected cells and what might be causing aberrant A3 activity in HPV-independent cancers such as those arising in the bladder, lung and breast. Finally, we discuss the implications of ongoing A3 activity in tumours under treatment and the therapeutic opportunities that this may present.
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Affiliation(s)
- Nicola J Smith
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, Kent, UK
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47
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Evgin L, Huff AL, Kottke T, Thompson J, Molan AM, Driscoll CB, Schuelke M, Shim KG, Wongthida P, Ilett EJ, Smith KK, Harris RS, Coffey M, Pulido JS, Pandha H, Selby PJ, Harrington KJ, Melcher A, Vile RG. Suboptimal T-cell Therapy Drives a Tumor Cell Mutator Phenotype That Promotes Escape from First-Line Treatment. Cancer Immunol Res 2019; 7:828-840. [PMID: 30940643 PMCID: PMC7003288 DOI: 10.1158/2326-6066.cir-18-0013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/14/2018] [Accepted: 03/27/2019] [Indexed: 12/19/2022]
Abstract
Antitumor T-cell responses raised by first-line therapies such as chemotherapy, radiation, tumor cell vaccines, and viroimmunotherapy tend to be weak, both quantitatively (low frequency) and qualitatively (low affinity). We show here that T cells that recognize tumor-associated antigens can directly kill tumor cells if used at high effector-to-target ratios. However, when these tumor-reactive T cells were present at suboptimal ratios, direct T-cell-mediated tumor cell killing was reduced and the ability of tumor cells to evolve away from a coapplied therapy (oncolytic or suicide gene therapy) was promoted. This T-cell-mediated increase in therapeutic resistance was associated with C to T transition mutations that are characteristic of APOBEC3 cytosine deaminase activity and was induced through a TNFα and protein kinase C-dependent pathway. Short hairpin RNA inhibition of endogenous APOBEC3 reduced rates of tumor escape from oncolytic virus or suicide gene therapy to those seen in the absence of antitumor T-cell coculture. Conversely, overexpression of human APOBEC3B in tumor cells enhanced escape from suicide gene therapy and oncolytic virus therapy both in vitro and in vivo Our data suggest that weak affinity or low frequency T-cell responses against tumor antigens may contribute to the ability of tumor cells to evolve away from first-line therapies. We conclude that immunotherapies need to be optimized as early as possible so that, if they do not kill the tumor completely, they do not promote treatment resistance.
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Affiliation(s)
- Laura Evgin
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amanda L Huff
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Timothy Kottke
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jill Thompson
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Amy M Molan
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | | | | | - Kevin G Shim
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | | | - Elizabeth J Ilett
- Leeds Institute of Cancer and Pathology, St. James' University Hospital, Leeds, United Kingdom
| | | | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Matt Coffey
- Oncolytics Biotech Incorporated, Calgary, Canada
| | - Jose S Pulido
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Peter J Selby
- Leeds Institute of Cancer and Pathology, St. James' University Hospital, Leeds, United Kingdom
| | | | - Alan Melcher
- Institute of Cancer Research, London, United Kingdom
| | - Richard G Vile
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota.
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
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48
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Ng JCF, Quist J, Grigoriadis A, Malim MH, Fraternali F. Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases. Nucleic Acids Res 2019; 47:1178-1194. [PMID: 30624727 PMCID: PMC6379723 DOI: 10.1093/nar/gky1316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/19/2018] [Accepted: 01/04/2019] [Indexed: 12/25/2022] Open
Abstract
APOBEC3 cytidine deaminases are largely known for their innate immune protection from viral infections. Recently, members of the family have been associated with a distinct mutational activity in some cancer types. We report a pan-tissue, pan-cancer analysis of RNA-seq data specific to the APOBEC3 genes in 8,951 tumours, 786 cancer cell lines and 6,119 normal tissues. By deconvolution of levels of different cell types in tumour admixtures, we demonstrate that APOBEC3B (A3B), the primary candidate as a cancer mutagen, shows little association with immune cell types compared to its paralogues. We present a pipeline called RESPECTEx (REconstituting SPecific Cell-Type Expression) and use it to deconvolute cell-type specific expression levels in a given cohort of tumour samples. We functionally annotate APOBEC3 co-expressing genes, and create an interactive visualization tool which 'barcodes' the functional enrichment (http://fraternalilab.kcl.ac.uk/apobec-barcodes/). These analyses reveal that A3B expression correlates with cell cycle and DNA repair genes, whereas the other APOBEC3 members display specificity for immune processes and immune cell populations. We offer molecular insights into the functions of individual APOBEC3 proteins in antiviral and proliferative contexts, and demonstrate the diversification this family of enzymes displays at the transcriptomic level, despite their high similarity in protein sequences and structures.
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Affiliation(s)
- Joseph C F Ng
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Jelmar Quist
- Cancer Bioinformatics, School of Cancer and Pharmaceutical Sciences, CRUK King's Health Partners Centre, Breast Cancer Now Research Unit, King's College London, London, UK
| | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer and Pharmaceutical Sciences, CRUK King's Health Partners Centre, Breast Cancer Now Research Unit, King's College London, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
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49
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Polyomavirus T Antigen Induces APOBEC3B Expression Using an LXCXE-Dependent and TP53-Independent Mechanism. mBio 2019; 10:mBio.02690-18. [PMID: 30723127 PMCID: PMC6428753 DOI: 10.1128/mbio.02690-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
APOBEC3B is a single-stranded DNA cytosine deaminase with beneficial innate antiviral functions. However, misregulated APOBEC3B can also be detrimental by inflicting APOBEC signature C-to-T and C-to-G mutations in genomic DNA of multiple cancer types. Polyomavirus and papillomavirus oncoproteins induce APOBEC3B overexpression, perhaps to their own benefit, but little is known about the cellular mechanisms hijacked by these viruses to do so. Here we investigate the molecular mechanism of APOBEC3B upregulation by the polyomavirus large T antigen. First, we demonstrate that the upregulated APOBEC3B enzyme is strongly nuclear and partially localized to virus replication centers. Second, truncated T antigen (truncT) is sufficient for APOBEC3B upregulation, and the RB-interacting motif (LXCXE), but not the p53-binding domain, is required. Third, genetic knockdown of RB1 alone or in combination with RBL1 and/or RBL2 is insufficient to suppress truncT-mediated induction of APOBEC3B Fourth, CDK4/6 inhibition by palbociclib is also insufficient to suppress truncT-mediated induction of APOBEC3B Last, global gene expression analyses in a wide range of human cancers show significant associations between expression of APOBEC3B and other genes known to be regulated by the RB/E2F axis. These experiments combine to implicate the RB/E2F axis in promoting APOBEC3B transcription, yet they also suggest that the polyomavirus RB-binding motif has at least one additional function in addition to RB inactivation for triggering APOBEC3B upregulation in virus-infected cells.IMPORTANCE The APOBEC3B DNA cytosine deaminase is overexpressed in many different cancers and correlates with elevated frequencies of C-to-T and C-to-G mutations in 5'-TC motifs, oncogene activation, acquired drug resistance, and poor clinical outcomes. The mechanisms responsible for APOBEC3B overexpression are not fully understood. Here, we show that the polyomavirus truncated T antigen (truncT) triggers APOBEC3B overexpression through its RB-interacting motif, LXCXE, which in turn likely modulates the binding of E2F family transcription factors to promote APOBEC3B expression. This work strengthens the mechanistic linkage between active cell cycling, APOBEC3B overexpression, and cancer mutagenesis. Although this mutational mechanism damages cellular genomes, viruses may leverage it to promote evolution, immune escape, and pathogenesis. The cellular portion of the mechanism may also be relevant to nonviral cancers, where genetic mechanisms often activate the RB/E2F axis and APOBEC3B mutagenesis contributes to tumor evolution.
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50
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Ma W, Ho DWH, Sze KMF, Tsui YM, Chan LK, Lee JMF, Ng IOL. APOBEC3B promotes hepatocarcinogenesis and metastasis through novel deaminase-independent activity. Mol Carcinog 2019; 58:643-653. [PMID: 30575099 DOI: 10.1002/mc.22956] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/04/2018] [Accepted: 12/15/2018] [Indexed: 01/31/2023]
Abstract
Cytidine deaminase APOBEC3B (A3B) is known to play important roles in creating de novo genomic C-to-T mutations in cancers and contribute to induction of genomic instability. Our study evaluated the roles of A3B in the progression and metastasis of human hepatocellular carcinoma (HCC). Using whole-transcriptome and whole-exome sequencing, and quantitative PCR, we found that A3B was overexpressed in human HCCs and A3B expression was significantly correlated with the proportion of genomic C-to-A and G-to-T mutations. Upon clinicopathological correlation, higher A3B expression was associated with more aggressive tumor behavior. Wild-type A3B (wt-A3B) overexpression in HCC cells promoted cell proliferation, and cell migratory and invasive abilities in vitro, and tumorigenicity and metastasis in vivo. On the other hand, knockdown of A3B suppressed cell proliferation, migratory, and invasive abilities of HCC cells with high endogenous A3B level. However, to our surprise, overexpression of A3B deaminase-dead double mutant (E68A/E255Q) led to similar results as wt-A3B in HCC. Furthermore, overexpression of wt-A3B and mutant A3B both enhanced cell cycle progression in HCC cells. Altogether, our data demonstrated a novel deaminase-independent role of A3B in contributing to HCC tumorigenesis and metastasis.
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Affiliation(s)
- Wei Ma
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Daniel W-H Ho
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Karen M-F Sze
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yu-Man Tsui
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Lo-Kong Chan
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Joyce M-F Lee
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
| | - Irene O-L Ng
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory for Liver Research, The University of Hong Kong, Pokfulam, Hong Kong
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