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Chi ZC. Progress in understanding of relationship between inflammation and tumors. Shijie Huaren Xiaohua Zazhi 2024; 32:23-40. [DOI: 10.11569/wcjd.v32.i1.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/05/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
Over the past decade, there has been clear evidence that inflammation plays a key role in tumorigenesis. Tumor extrinsic inflammation is caused by many factors, including bacterial and viral infections, autoimmune diseases, obesity, smoking, excessive alcohol consumption, etc., all of which can increase cancer risk and stimulate malignant progression. Conversely, inflammation inherent in cancer or caused by cancer can be triggered by cancer-initiating mutations and can promote malignant progression through recruitment and activation of inflammatory cells. Both exogenous and endogenous inflammation can lead to immunosuppression, thus providing a preferred opportunity for tumor development. Studies have confirmed that chronic inflammation is involved in various steps of tumorigenesis, including cell transformation, promotion, survival, prolifer-ation, invasion, angiogenesis, and metastasis. Recent research has shed new light on the molecular and cellular circuits between inflammation and cancer. Two pathways have been preliminarily identified: Intrinsic and extrinsic. In the intrinsic pathway, genetic events leading to tumors initiate the expression of inflammatory related programs and guide the construction of the inflammatory microenvironment. In the extrinsic pathway, inflammatory conditions promote the development of cancer. This article reviews the recent progress in the understanding of the relationship between inflammation and tumors.
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Affiliation(s)
- Zhao-Chun Chi
- Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao 266011, Shandong Province, China
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2
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Dananberg A, Striepen J, Rozowsky JS, Petljak M. APOBEC Mutagenesis in Cancer Development and Susceptibility. Cancers (Basel) 2024; 16:374. [PMID: 38254863 PMCID: PMC10814203 DOI: 10.3390/cancers16020374] [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: 12/20/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
APOBEC cytosine deaminases are prominent mutators in cancer, mediating mutations in over 50% of cancers. APOBEC mutagenesis has been linked to tumor heterogeneity, persistent cell evolution, and therapy responses. While emerging evidence supports the impact of APOBEC mutagenesis on cancer progression, the understanding of its contribution to cancer susceptibility and malignant transformation is limited. We examine the existing evidence for the role of APOBEC mutagenesis in carcinogenesis on the basis of the reported associations between germline polymorphisms in genes encoding APOBEC enzymes and cancer risk, insights into APOBEC activities from sequencing efforts of both malignant and non-malignant human tissues, and in vivo studies. We discuss key knowledge gaps and highlight possible ways to gain a deeper understanding of the contribution of APOBEC mutagenesis to cancer development.
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Affiliation(s)
- Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jacob S Rozowsky
- Medical Scientist Training Program, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mia Petljak
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA
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3
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Chai JW, Hu XW, Zhang MM, Dong YN. Seven chromatin regulators as immune cell infiltration characteristics, potential diagnostic biomarkers and drugs prediction in hepatocellular carcinoma. Sci Rep 2023; 13:18643. [PMID: 37903974 PMCID: PMC10616163 DOI: 10.1038/s41598-023-46107-x] [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: 07/27/2023] [Accepted: 10/27/2023] [Indexed: 11/01/2023] Open
Abstract
Treatment is challenging due to the heterogeneity of hepatocellular carcinoma (HCC). Chromatin regulators (CRs) are important in epigenetics and are closely associated with HCC. We obtained HCC-related expression data and relevant clinical data from The Cancer Genome Atlas (TCGA) databases. Then, we crossed the differentially expressed genes (DEGs), immune-related genes and CRs to obtain immune-related chromatin regulators differentially expressed genes (IRCR DEGs). Least absolute shrinkage and selection operator (LASSO) Cox regression analysis was performed to select the prognostic gene and construct a risk model for predicting prognosis in HCC, followed by a correlation analysis of risk scores with clinical characteristics. Finally, we also carried out immune microenvironment analysis and drug sensitivity analysis, the correlation between risk score and clinical characteristics was analyzed. In addition, we carried out immune microenvironment analysis and drug sensitivity analysis. Functional analysis suggested that IRCR DEGs was mainly enriched in chromatin-related biological processes. We identified and validated PPARGC1A, DUSP1, APOBEC3A, AIRE, HDAC11, HMGB2 and APOBEC3B as prognostic biomarkers for the risk model construction. The model was also related to immune cell infiltration, and the expression of CD48, CTLA4, HHLA2, TNFSF9 and TNFSF15 was higher in high-risk group. HCC patients in the high-risk group were more sensitive to Axitinib, Docetaxel, Erlotinib, and Metformin. In this study, we construct a prognostic model of immune-associated chromatin regulators, which provides new ideas and research directions for the accurate treatment of HCC.
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Affiliation(s)
- Jin-Wen Chai
- Department of Oncology, Laizhou Traditional Chinese Medicine Hospital, Laizhou, Shandong, China
| | - Xi-Wen Hu
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Miao-Miao Zhang
- Department of Oncology, Laizhou Traditional Chinese Medicine Hospital, Laizhou, Shandong, China
| | - Yu-Na Dong
- Department of Gastroenterology, Laizhou People's Hospital, No.1718 Wuli Street, Laizhou, Shandong, China.
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4
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Opeyemi Bello R, Willis-Powell L, James O, Sharma A, Marsh E, Ellis L, Gaston K, Siddiqui Y. Does Human Papillomavirus Play a Causative Role in Prostate Cancer? A Systematic Review Using Bradford Hill's Criteria. Cancers (Basel) 2023; 15:3897. [PMID: 37568712 PMCID: PMC10416874 DOI: 10.3390/cancers15153897] [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: 05/30/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 08/13/2023] Open
Abstract
Globally, prostate cancer is the fifth most common cause of cancer-related death among men, and metastatic castration-resistant prostate cancer has a high cancer-related mortality rate. However, the aetiology of this disease is not yet fully understood. While human papillomavirus (HPV) has been associated with several types of cancer, including cervical, anal, and oropharyngeal cancers, studies investigating the relationship between HPV and prostate cancer have shown mixed results. This systematic review aimed to evaluate the causative association between HPV and prostate cancer using Bradford Hill's criteria. A comprehensive search of PubMed was conducted, and 60 out of 482 studies were included in the review. The included studies were evaluated based on nine Bradford Hill criteria, and information on the identification and transmission of the virus and potential oncogenic mechanisms was also extracted. The strength of association criterion was not met, and other criteria, such as consistency and coherence, were not fulfilled. However, biological plausibility was supported, and potential oncogenic mechanisms were identified. While some studies have reported the presence of HPV in prostate cancer tissues, the overall quality of evidence remains low, and the association between HPV and prostate cancer is weak. Nevertheless, the prostate is a potential reservoir for the transmission of HPV, and the HPV E6 and E7 oncoproteins and inflammation are likely to be involved in any oncogenic mechanisms. Further studies with a higher level of evidence are needed to establish a definitive link between HPV and prostate cancer.
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Affiliation(s)
- Ridwan Opeyemi Bello
- School of Human Sciences, College of Science and Engineering, University of Derby, Derby DE22 1GB, UK; (R.O.B.); (E.M.)
| | - Lily Willis-Powell
- School of Medicine, University of Nottingham, Nottingham NG7 2QL, UK (K.G.)
| | - Olivia James
- School of Medicine, University of Nottingham, Nottingham NG7 2QL, UK (K.G.)
| | - Avyay Sharma
- School of Medicine, University of Nottingham, Nottingham NG7 2QL, UK (K.G.)
| | - Elizabeth Marsh
- School of Human Sciences, College of Science and Engineering, University of Derby, Derby DE22 1GB, UK; (R.O.B.); (E.M.)
| | - Libby Ellis
- School of Medicine, University of Nottingham, Nottingham NG7 2QL, UK (K.G.)
| | - Kevin Gaston
- School of Medicine, University of Nottingham, Nottingham NG7 2QL, UK (K.G.)
| | - Yusra Siddiqui
- School of Human Sciences, College of Science and Engineering, University of Derby, Derby DE22 1GB, UK; (R.O.B.); (E.M.)
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5
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Liu L, Zhang Y, Hu X, Zhang H, Jiang C, Guo Y, Cang S. MiR-138-5p inhibits prostate cancer cell proliferation and chemoresistance by targeting APOBEC3B. Transl Oncol 2023; 35:101723. [PMID: 37364333 DOI: 10.1016/j.tranon.2023.101723] [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: 04/08/2023] [Revised: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023] Open
Abstract
Docetaxel is one of the most commonly used drugs in prostate cancer (PCa) chemotherapy, but its therapeutic effect in PCa is usually limited due to its drug resistance. APOBEC3B is a DNA cytosine deaminase that can alter biological processes, including chemoresistance. APOBEC3B is upregulated in various cancers. However, the biological function and underlying regulation of APOBEC3B in PCa remain unclear. In this study, we explored the role of APOBEC3B in PCa chemoresistance and the molecular mechanism of its dysregulated expression. Our results revealed that APOBEC3B was upregulated in PCa docetaxel-resistant cells, while its knockdown significantly repressed cell proliferation and docetaxel resistance of PCa cells. Bioinformatics and luciferase report analysis showed that miR-138-5p targeted APOBEC3B. In addition, miR-138-5p overexpression impeded cell proliferation and docetaxel resistance in PCa, while miR-138-5p inhibitors reversed this process. Further studies showed that upregulation of APOBEC3B expression in docetaxel-resistant cells overexpressing miR-138-5p could desensitize PCa cells to docetaxel treatment. Taken together, miR-138-5p regulates PCa cell proliferation and chemoresistance by targeting the 3'-UTR of APOBEC3B, which may provide novel insights and therapeutic targets for the treatment of PCa.
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Affiliation(s)
- Lina Liu
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Henan University People's Hospital and Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yan Zhang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Henan University People's Hospital and Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Xi Hu
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Henan University People's Hospital and Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Hui Zhang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Henan University People's Hospital and Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Chenyang Jiang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Henan University People's Hospital and Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yan Guo
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Henan University People's Hospital and Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Shundong Cang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Henan University People's Hospital and Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China.
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6
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Castilha EP, Curti RRDJ, de Oliveira JN, Vitiello GAF, Guembarovski RL, Couto-Filho JD, Oliveira KBD. APOBEC3A/B Polymorphism Is Not Associated with Human Papillomavirus Infection and Cervical Carcinogenesis. Pathogens 2023; 12:pathogens12050636. [PMID: 37242306 DOI: 10.3390/pathogens12050636] [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: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The persistence of a high-risk Human papillomavirus (HPV-HR) infection of the cervix results in different manifestations of lesions depending on the immunologic capacity of the host. Variations in apolipoprotein B mRNA editing enzyme catalytic polypeptide (APOBEC)-like genes, such as the APOBEC3A/B deletion hybrid polymorphism (A3A/B), may contribute to cervical malignancy in the presence of HPV. The aim of this study was to investigate the association between the A3A/B polymorphism and HPV infection and the development of cervical intraepithelial lesions and cervical cancer in Brazilian women. The study enrolled 369 women, who were categorized according to the presence of infection and subdivided according to the degree of intraepithelial lesion and cervical cancer. APOBEC3A/B was genotyped by allele-specific polymerase chain reaction (PCR). As for the A3A/B polymorphism, the distribution of genotypes was similar between groups and among the analyzed subgroups. There were no significant differences in the presence of infection or development of lesions, even after exclusion of confounding factors. This is the first study to show that the A3A/B polymorphism is not associated with HPV infection and the development of intraepithelial lesions and cervical cancer in Brazilian women.
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Affiliation(s)
- Eliza Pizarro Castilha
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | - Rafaela Roberta de Jaime Curti
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | - Janaina Nicolau de Oliveira
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | | | - Roberta Losi Guembarovski
- Department of Biological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
| | | | - Karen Brajão de Oliveira
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Londrina 86057-970, PR, Brazil
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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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Sofiyeva N, Krakstad C, Halle MK, O'Mara TA, Romundstad P, Hveem K, Vatten L, Lønning PE, Gansmo LB, Knappskog S.
APOBEC3A
/B
deletion polymorphism and endometrial cancer risk. Cancer Med 2022; 12:6659-6667. [PMID: 36394079 PMCID: PMC10067079 DOI: 10.1002/cam4.5448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A common 30 kb deletion affecting the APOBEC3A and APOBEC3B genes has been linked to increased APOBEC activity and APOBEC-related mutational signatures in human cancers. The role of this deletion as a cancer risk factor remains controversial. MATERIALS AND METHODS We genotyped the APOBEC3A/B deletion in a sample of 1,470 Norwegian endometrial cancer cases and compared to 1,918 healthy controls. For assessment across Caucasian populations, we mined genotypes of the SNP rs12628403, which is in strong linkage disequilibrium with the deletion, in a GWAS dataset of 4,274 cases and 18,125 healthy controls, through the ECAC consortium. RESULTS We found the APOBEC3A/B deletion variant to be significantly associated with reduced risk of endometrial cancer among Norwegian women (OR = 0.75; 95% CI = 0.62-0.91; p = 0.003; dominant model). Similar results were found in the subgroup of endometrioid endometrial cancer (OR = 0.64; 95% CI = 0.51-0.79; p = 3.6 × 10-5 ; dominant model). The observed risk reduction was particularly strong among individuals in the range of 50-60 years of age (OR = 0.51; 95% CI = 0.33-0.78; p = 0.002; dominant model). In the different populations included in the ECAC dataset, the ORs varied from 0.85 to 1.05. Although five out of six populations revealed ORs <1.0, the overall estimate was nonsignificant and, as such, did not formally validate the findings in the Norwegian cohort. CONCLUSION The APOBEC3A/B deletion polymorphism is associated with a decreased risk of endometrial cancer in the Norwegian population.
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Affiliation(s)
- Nigar Sofiyeva
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
| | - Camilla Krakstad
- Department of Clinical Science, Centre for Cancer Biomarkers University of Bergen Bergen Norway
- Department of Obstetrics and Gynaecology Haukeland University Hospital Bergen Norway
| | - Mari K. Halle
- Department of Clinical Science, Centre for Cancer Biomarkers University of Bergen Bergen Norway
- Department of Obstetrics and Gynaecology Haukeland University Hospital Bergen Norway
| | - Tracy A. O'Mara
- Cancer Program QIMR Berghofer Medical Research Institute Brisbane Australia
| | - Pål Romundstad
- Department of Public Health, Faculty of Medicine Norwegian University of Science and Technology Trondheim Norway
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, Faculty of Medicine Norwegian University of Science and Technology Trondheim Norway
| | - Lars Vatten
- Department of Public Health, Faculty of Medicine Norwegian University of Science and Technology Trondheim Norway
| | - Per E. Lønning
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
| | - Liv B. Gansmo
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
| | - Stian Knappskog
- K.G. Jebsen Center for Genome‐Directed Cancer Therapy, Department of Clinical Science University of Bergen Bergen Norway
- Department of Oncology Haukeland University Hospital Bergen Norway
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Petljak M, Green AM, Maciejowski J, Weitzman MD. Addressing the benefits of inhibiting APOBEC3-dependent mutagenesis in cancer. Nat Genet 2022; 54:1599-1608. [PMID: 36280735 PMCID: PMC9700387 DOI: 10.1038/s41588-022-01196-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 08/29/2022] [Indexed: 01/21/2023]
Abstract
Mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC)3 cytosine deaminase activity have been found in over half of cancer types, including some therapy-resistant and metastatic tumors. Driver mutations can occur in APOBEC3-favored sequence contexts, suggesting that mutagenesis by APOBEC3 enzymes may drive cancer evolution. The APOBEC3-mediated signatures are often detected in subclonal branches of tumor phylogenies and are acquired in cancer cell lines over long periods of time, indicating that APOBEC3 mutagenesis can be ongoing in cancer. Collectively, these and other observations have led to the proposal that APOBEC3 mutagenesis represents a disease-modifying process that could be inhibited to limit tumor heterogeneity, metastasis and drug resistance. However, critical aspects of APOBEC3 biology in cancer and in healthy tissues have not been clearly defined, limiting well-grounded predictions regarding the benefits of inhibiting APOBEC3 mutagenesis in different settings in cancer. We discuss the relevant mechanistic gaps and strategies to address them to investigate whether inhibiting APOBEC3 mutagenesis may confer clinical benefits in cancer.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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Abstract
Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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11
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Chen CH, Wei KC, Liao WC, Lin YY, Chen HC, Feng LY, Liu CH, Huang CY, Chen KT, Wu CS, Chang YS, Yu JS, Chang IYF. Prognostic value of an APOBEC3 deletion polymorphism for glioma patients in Taiwan. J Neurosurg 2022; 138:1325-1337. [PMID: 36152319 DOI: 10.3171/2022.7.jns2250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/20/2022] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The molecular pathogenesis of malignant gliomas, characterized by diverse tumor histology with differential prognosis, remains largely unelucidated. An APOBEC3 deletion polymorphism, with a deletion in APOBEC3B, has been correlated to risk and prognosis in several cancers, but its role in glioma is unclear. The authors aimed to examine the clinical relevance of the APOBEC3 deletion polymorphism to glioma risk and survival in a glioma patient cohort in Taiwan. METHODS The authors detected deletion genotypes in 403 glioma patients and 1365 healthy individuals in Taiwan and correlated the genotypes with glioma risk, clinicopathological factors, patient survival, and patient sex. APOBEC3 gene family expression was measured and correlated to the germline deletion. A nomogram model was constructed to predict patient survival in glioma. RESULTS The proportion of APOBEC3B-/- and APOBEC3B+/- genotypes was higher in glioblastoma (GBM) patients than healthy individuals and correlated with higher GBM risk in males. A higher percentage of cases with APOBEC3B- was observed in male than female glioma patients. The presence of APOBEC3B-/- was correlated with better overall survival (OS) in male astrocytic glioma patients. No significant correlation of the genotypes to glioma risk and survival was observed in the female patient cohort. Lower APOBEC3B expression was observed in astrocytic glioma patients with APOBEC3B-/- and was positively correlated with better OS. A 5-factor nomogram model was constructed based on male patients with astrocytic gliomas in the study cohort and worked efficiently for predicting patient OS. CONCLUSIONS The germline APOBEC3 deletion was associated with increased GBM risk and better OS in astrocytic glioma patients in the Taiwan male population. The APOBEC3B deletion homozygote was a potential independent prognostic factor predicting better survival in male astrocytic glioma patients.
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Affiliation(s)
| | - Kuo-Chen Wei
- 2School of Medicine, and.,5Department of Neurosurgery.,7Neuroscience Research Center, and.,11Department of Neurosurgery, New Taipei Municipal Tucheng Hospital, New Taipei City
| | - Wei-Chao Liao
- 1Molecular Medicine Research Center.,4Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Taoyuan
| | - You-Yu Lin
- 9Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei.,10Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei
| | | | - Li-Ying Feng
- 11Department of Neurosurgery, New Taipei Municipal Tucheng Hospital, New Taipei City
| | - Chiung-Hui Liu
- 12Department of Post-Baccalaureate Medicine and.,13PhD Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung City, Taiwan
| | - Chiung-Yin Huang
- 7Neuroscience Research Center, and.,11Department of Neurosurgery, New Taipei Municipal Tucheng Hospital, New Taipei City
| | - Ko-Ting Chen
- 2School of Medicine, and.,5Department of Neurosurgery.,7Neuroscience Research Center, and
| | - Chi-Sheng Wu
- 1Molecular Medicine Research Center.,6Department of Otolaryngology-Head & Neck Surgery
| | | | - Jau-Song Yu
- 1Molecular Medicine Research Center.,3Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan.,8Liver Research Center, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan
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Lawson JS, Glenn WK. Mouse Mammary Tumour Virus (MMTV) in Human Breast Cancer-The Value of Bradford Hill Criteria. Viruses 2022; 14:721. [PMID: 35458452 PMCID: PMC9028876 DOI: 10.3390/v14040721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/27/2023] Open
Abstract
For many decades, the betaretrovirus, mouse mammary tumour virus (MMTV), has been a causal suspect for human breast cancer. In recent years, substantial new evidence has been developed. Based on this evidence, we hypothesise that MMTV has a causal role. We have used an extended version of the classic A. Bradford Hill causal criteria to assess the evidence. 1. Identification of MMTV in human breast cancers: The MMTV 9.9 kb genome in breast cancer cells has been identified. The MMTV genome in human breast cancer is up to 98% identical to MMTV in mice. 2. EPIDEMIOLOGY The prevalence of MMTV positive human breast cancer is about 35 to 40% of breast cancers in Western countries and 15 to 20% in China and Japan. 3. Strength of the association between MMTV and human breast cancer: Consistency-MMTV env gene sequences are consistently five-fold higher in human breast cancer as compared to benign and normal breast controls. 4. Temporality (timing) of the association: MMTV has been identified in benign and normal breast tissues up to 10 years before the development of MMTV positive breast cancer in the same patient. 5. EXPOSURE Exposure of humans to MMTV leads to development of MMTV positive human breast cancer. 6. Experimental evidence: MMTVs can infect human breast cells in culture; MMTV proteins are capable of malignantly transforming normal human breast epithelial cells; MMTV is a likely cause of biliary cirrhosis, which suggests a link between MMTV and the disease in humans. 7. Coherence-analogy: The life cycle and biology of MMTV in humans is almost the same as in experimental and feral mice. 8. MMTV Transmission: MMTV has been identified in human sputum and human milk. Cereals contaminated with mouse fecal material may transmit MMTV. These are potential means of transmission. 9. Biological plausibility: Retroviruses are the established cause of human cancers. Human T cell leukaemia virus type I (HTLV-1) causes adult T cell leukaemia, and human immunodeficiency virus infection (HIV) is associated with lymphoma and Kaposi sarcoma. 10. Oncogenic mechanisms: MMTV oncogenesis in humans probably differs from mice and may involve the enzyme APOBEC3B. CONCLUSION In our view, the evidence is compelling that MMTV has a probable causal role in a subset of approximately 40% of human breast cancers.
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Affiliation(s)
- James S. Lawson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia;
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Revisiting the MMTV Zoonotic Hypothesis to Account for Geographic Variation in Breast Cancer Incidence. Viruses 2022; 14:v14030559. [PMID: 35336966 PMCID: PMC8955943 DOI: 10.3390/v14030559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 12/27/2022] Open
Abstract
Human breast cancer incidence varies by geographic location. More than 20 years ago, we proposed that zoonotic transmission of the mouse mammary tumor virus (MMTV) from the western European house mouse, Mus musculus domesticus, might account for the regional differences in breast cancer incidence. In the intervening years, several developments provide additional support for this hypothesis, including the limited impact of genetic factors for breast cancer susceptibility revealed by genome-wide association studies and the strong effect of antiretroviral therapy to reduce breast cancer incidence. At the same time, economic globalization has further expanded the distribution of M. m. domesticus to Asia, leading to a significant increase in breast cancer incidence in this region. Here, we revisit this evidence and provide an update to the MMTV zoonotic hypothesis for human breast cancer at a time when the world is recovering from the global COVID-19 zoonotic pandemic. We present evidence that mouse population outbreaks are correlated with spikes in breast cancer incidence in Australia and New Zealand and that globalization has increased the range of M. m. domesticus and MMTV. Given the success of global vaccination campaigns for HPV to eradicate cervical cancer, a similar strategy for MMTV may be warranted. Until breast cancer incidence is reduced by such an approach, zoonotic transmission of MMTV from mice to humans as an etiologic factor for breast cancer will remain controversial.
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14
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APOBEC mediated mutagenesis drives genomic heterogeneity in endometriosis. J Hum Genet 2022; 67:323-329. [PMID: 35017684 DOI: 10.1038/s10038-021-01003-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/11/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022]
Abstract
Endometriosis is a benign gynecologic condition, acting as a precursor of certain histological subtypes of ovarian cancers. The epithelial cells of endometriotic tissues and normal uterine endometrium accumulated somatic mutations in cancer-associated genes such as phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and Kirsten rat sarcoma (KRAS) proto-oncogene. To determine the genomic characteristic of endometriotic epithelial cells and normal uterine endometrium and to identify the predominant mutational process acting on them, we studied the somatic mutation profiles obtained from whole exome sequencing of 14 endometriotic epithelium and 11 normal uterine endometrium tissues and classified them into mutational signatures. We observed that single base substitutions 2/13 (SBS), attributed to Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit (APOBEC) induced mutagenesis, were significant in endometriotic tissues, but not in the normal uterine endometrium. Additionally, the larger number and wider allele frequency distribution of APOBEC signature mutations, compared to cancer-associated driver mutations in endometriotic epithelium suggested APOBEC mutagenesis as an important source of mutational burden and heterogeneity in endometriosis. Further, the relative risk of enriched APOBEC signature mutations was higher in endometriosis patients who were carriers of APOBEC3A/3B germline deletion, a common polymorphism in East Asians which involves the complete loss of APOBEC3B coding region. Our results illustrate the significance of APOBEC induced mutagenesis in driving the genomic heterogeneity of endometriosis.
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15
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Morka N, Norris JM, Emberton M, Kelly D. Prostate cancer and the human papilloma virus: causative association, role of vaccines, and the impact of the COVID-19 pandemic. Prostate Cancer Prostatic Dis 2022; 25:55-57. [PMID: 34145427 PMCID: PMC8212277 DOI: 10.1038/s41391-021-00404-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/12/2021] [Accepted: 05/27/2021] [Indexed: 02/04/2023]
Abstract
Prostate cancer affects a significant proportion of men worldwide. Evidence from genetic and clinical studies suggests that there may be a causal association between prostate cancer and the human papilloma virus (HPV). As HPV is a vaccine-preventable pathogen, the possibility of a role in prostate cancer causation may reinforce the importance of effective HPV vaccination campaigns. This is of particular relevance in light of the COVID-19 pandemic, which may have considerable effects on HPV vaccine uptake and distribution.
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Affiliation(s)
- Naomi Morka
- grid.83440.3b0000000121901201University College London Medical School, London, UK
| | - Joseph M. Norris
- grid.83440.3b0000000121901201UCL Division of Surgery & Interventional Science, University College London, London, UK ,grid.52996.310000 0000 8937 2257Department of Urology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Mark Emberton
- grid.83440.3b0000000121901201UCL Division of Surgery & Interventional Science, University College London, London, UK ,grid.52996.310000 0000 8937 2257Department of Urology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Daniel Kelly
- grid.5600.30000 0001 0807 5670School of Healthcare Sciences, Cardiff University, Cardiff, Wales UK
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16
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Impact of the APOBEC3A/B deletion polymorphism on risk of ovarian cancer. Sci Rep 2021; 11:23463. [PMID: 34873230 PMCID: PMC8648731 DOI: 10.1038/s41598-021-02820-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
A germline 29.5-kb deletion variant removes the 3’ end of the APOBEC3A gene and a large part of APOBEC3B, creating a hybrid gene that has been linked to increased APOBEC3 activity and DNA damage in human cancers. We genotyped the APOBEC3A/B deletion in hospital-based samples of 1398 Norwegian epithelial ovarian cancer patients without detected BRCA1/2 germline mutations and compared to 1,918 healthy female controls, to assess the potential cancer risk associated with the deletion. We observed an association between APOBEC3A/B status and reduced risk for ovarian cancer (OR = 0.75; CI = 0.61–0.91; p = 0.003) applying the dominant model. Similar results were found in other models. The association was observed both in non-serous and serous cases (dominant model: OR = 0.69; CI = 0.50–0.95; p = 0.018 and OR = 0.77; CI = 0.62–0.96; p = 0.019, respectively) as well as within high-grade serous cases (dominant model: OR = 0.79; CI = 0.59–1.05). For validation purposes, we mined an available large multinational GWAS-based data set of > 18,000 cases and > 26,000 controls for SNP rs12628403, known to be in linkage disequilibrium with the APOBEC3A/B deletion. We found a non-significant trend for SNP rs12628403 being linked to reduced risk of ovarian cancer in general and similar trends for all subtypes. For clear cell cancers, the risk reduction reached significance (OR = 0.85; CI = 0.69–1.00).
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17
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Liu W, Deng Y, Li Z, Chen Y, Zhu X, Tan X, Cao G. Cancer Evo-Dev: A Theory of Inflammation-Induced Oncogenesis. Front Immunol 2021; 12:768098. [PMID: 34880864 PMCID: PMC8645856 DOI: 10.3389/fimmu.2021.768098] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic inflammation is a prerequisite for the development of cancers. Here, we present the framework of a novel theory termed as Cancer Evolution-Development (Cancer Evo-Dev) based on the current understanding of inflammation-related carcinogenesis, especially hepatocarcinogenesis induced by chronic infection with hepatitis B virus. The interaction between genetic predispositions and environmental exposures, such as viral infection, maintains chronic non-resolving inflammation. Pollution, metabolic syndrome, physical inactivity, ageing, and adverse psychosocial exposure also increase the risk of cancer via inducing chronic low-grade smoldering inflammation. Under the microenvironment of non-resolving inflammation, pro-inflammatory factors facilitate the generation of somatic mutations and viral mutations by inducing the imbalance between the mutagenic forces such as cytidine deaminases and mutation-correcting forces including uracil-DNA glycosylase. Most cells with somatic mutations and mutated viruses are eliminated in survival competition. Only a small percentage of mutated cells survive, adapt to the hostile environment, retro-differentiate, and function as cancer-initiating cells via altering signaling pathways. These cancer-initiating cells acquire stem-ness, reprogram metabolic patterns, and affect the microenvironment. The carcinogenic process follows the law of "mutation-selection-adaptation". Chronic physical activity reduces the levels of inflammation via upregulating the activity and numbers of NK cells and lymphocytes and lengthening leukocyte telomere; downregulating proinflammatory cytokines including interleukin-6 and senescent lymphocytes especially in aged population. Anti-inflammation medication reduces the occurrence and recurrence of cancers. Targeting cancer stemness signaling pathways might lead to cancer eradication. Cancer Evo-Dev not only helps understand the mechanisms by which inflammation promotes the development of cancers, but also lays the foundation for effective prophylaxis and targeted therapy of various cancers.
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Affiliation(s)
- Wenbin Liu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yang Deng
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai’an, China
| | - Zishuai Li
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yifan Chen
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Xiaoqiong Zhu
- Department of Nutrition, School of Public Health, Anhui Medical University, Hefei, China
| | - Xiaojie Tan
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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18
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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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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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20
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Revathidevi S, Murugan AK, Nakaoka H, Inoue I, Munirajan AK. APOBEC: A molecular driver in cervical cancer pathogenesis. Cancer Lett 2020; 496:104-116. [PMID: 33038491 PMCID: PMC7539941 DOI: 10.1016/j.canlet.2020.10.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/16/2020] [Accepted: 10/04/2020] [Indexed: 02/09/2023]
Abstract
Cervical cancer is one of the foremost common cancers in women. Human papillomavirus (HPV) infection remains a major risk factor of cervical cancer. In addition, numerous other genetic and epigenetic factors also are involved in the underlying pathogenesis of cervical cancer. Recently, it has been reported that apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC), DNA-editing protein plays an important role in the molecular pathogenesis of cancer. Particularly, the APOBEC3 family was shown to induce tumor mutations by aberrant DNA editing mechanism. In general, APOBEC3 enzymes play a pivotal role in the deamination of cytidine to uridine in DNA and RNA to control diverse biological processes such as regulation of protein expression, innate immunity, and embryonic development. Innate antiviral activity of the APOBEC3 family members restrict retroviruses, endogenous retro-element, and DNA viruses including the HPV that is the leading risk factor for cervical cancer. This review briefly describes the pathogenesis of cervical cancer and discusses in detail the recent findings on the role of APOBEC in the molecular pathogenesis of cervical cancer. APOBEC enzymes deaminate cytidine to uridine and control diverse biological processes including viral restriction. APOBEC3, DNA/RNA-editing enzyme plays an important role in the molecular pathogenesis of cervical cancer. APOBEC3-mediated DNA editing leads to the accumulation of somatic mutations in tumors and HPV genome. Deregulation of APOBEC3 family genes cause genomic instability and result in drug resistance, and immune-evasion in tumors.
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Affiliation(s)
- Sundaramoorthy Revathidevi
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India; Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan; Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Chiyoda-ku, 101-0062, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, 600113, India.
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De Souza ALPB. Finding the hot spot: identifying immune sensitive gastrointestinal tumors. Transl Gastroenterol Hepatol 2020; 5:48. [PMID: 33073043 DOI: 10.21037/tgh.2019.12.11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022] Open
Abstract
Although researchers have been trying to harness the immune system for over 100 years, the advent of immune checkpoint blockers (ICB) marks an era of significant clinical outcomes in various metastatic solid tumors, characterized by complete and durable responses. ICBs are monoclonal antibodies that target either of a pair of transmembrane molecules in tumors or T-cells involved in immune evasion. Currently 2 ICBs targeting the checkpoint program death 1 (PD-1), nivolumab and pembrolizumab, and one cytotoxic lymphocyte antigen-4 (CTLA-4) inhibitor (ipilimumab) are approved in gastrointestinal malignancies. We review herein the current evidence on predictive biomarkers for ICB response in gastrointestinal tumors. A review of literature based on the National Cancer Institute list of FDA-approved drugs for neoplasms and FDA-approved therapies at the FDA website was performed. An initial literature review was based on the American Association for Clinical Research meeting 2019, the American Society of Clinical Oncology meeting 2019 and the European Society of Medical Oncology 2019 proceedings. A systematic search of PubMed was performed involving MeSH browser terms such as biomarkers, immunotherapy, gastrointestinal diseases and neoplasms. When appropriate, American and British terms were used in the search. The most relevant predictor of response to ICBs is microsatellite instability (MSI) and the data is strongest for colorectal cancer. At least 3 prospective trials show evidence of PD-L1 as a predictive biomarker for ICB response in gastroesophageal malignancies. At least one prospective trial has described tumor mutational burden high (TMB-H), independent of MSI, as predictive of response in anal and biliary tract carcinomas. DNA Polymerase Epsilon (POLE) or delta (POL-D) mutations have been implicated in a subset of MSS colorectal cancer with TMB-H but this biomarker requires prospective validation. There is evolving data based on retrospective observations that gene alterations predicting acquired resistance and hyper-progression. Ongoing clinical research is assessing the role of the human microbiome and RNA-editing complex mutations as predictive biomarkers of response to ICBs. MSI has the strongest predictive power among current biomarkers for ICB response in gastrointestinal cancers. Data continue to accumulate from ongoing clinical trials and new biomarkers are emerging from pre-clinical studies, suggesting that drug combinations targeting pathways complimentary to the PD-1/PD-L1 axis inhibition will define a robust field of clinical research.
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22
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Petljak M, Maciejowski J. Molecular origins of APOBEC-associated mutations in cancer. DNA Repair (Amst) 2020; 94:102905. [PMID: 32818816 PMCID: PMC7494591 DOI: 10.1016/j.dnarep.2020.102905] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 01/03/2023]
Abstract
The APOBEC family of cytidine deaminases has been proposed to represent a major enzymatic source of mutations in cancer. Here, we summarize available evidence that links APOBEC deaminases to cancer mutagenesis. We also highlight newly identified human cell models of APOBEC mutagenesis, including cancer cell lines with suspected endogenous APOBEC activity and a cell system of telomere crisis-associated mutations. Finally, we draw on recent data to propose potential causes of APOBEC misregulation in cancer, including the instigating factors, the relevant mutator(s), and the mechanisms underlying generation of the genome-dispersed and clustered APOBEC-induced mutations.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 , USA.
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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Lawson JS, Glenn WK. Evidence for a causal role by human papillomaviruses in prostate cancer - a systematic review. Infect Agent Cancer 2020; 15:41. [PMID: 32684946 PMCID: PMC7359253 DOI: 10.1186/s13027-020-00305-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
It is hypothesised that high risk for cancer human papillomaviruses (HPVs) have a causal role in prostate cancer. In 26 case control studies, high risk HPVs have been identified in benign and prostate cancers. High risk HPVs were identified in 325 (22.6%) of 1284 prostate cancers and in 113 (8.6%) of 1313 normal or benign prostate controls (p = 0.001). High risk HPVs of the same type have been identified in both normal and benign prostate tissues prior to the development of HPV positive prostate cancer. High risk HPVs can be associated with inflammatory prostatitis leading to benign prostate hyperplasia and later prostate cancer. Normal human prostate epithelial cells can be immortalised by experimental exposure to HPVs. HPVs are probably sexually transmitted. The role of HPVs in prostate cancer is complex and differs from HPVs associated cervical cancer. HPV infections may initiate prostate oncogenesis directly and influence oncogenesis indirectly via APOBEC enzymes. HPVs may collaborate with other pathogens in prostate oncogenesis. Although HPVs are only one of many pathogens that have been identified in prostate cancer, they are the only infectious pathogen which can be prevented by vaccination. A causal role for HPVs in prostate cancer is highly likely.
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Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Wendy K Glenn
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
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24
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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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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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26
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Hashemi M, Moazeni-Roodi A, Taheri M. Association of APOBEC3 deletion with cancer risk: A meta-analysis of 26 225 cases and 37 201 controls. Asia Pac J Clin Oncol 2019; 15:275-287. [PMID: 30693645 DOI: 10.1111/ajco.13107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/27/2018] [Indexed: 12/11/2022]
Abstract
Previous studies have found inconsistent results regarding gene deletion in APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) and risk of cancer. We conducted a meta-analysis of all eligible case-control studies to find out the associations between APOBEC3 deletion and cancer risk by pooling the odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Overall, the findings from 20 studies (13 articles) involving of a total of 26 225 cases and 37 201 controls revealed that DD genotype was associated significantly with increased cancer risk compared to II genotype (OR = 1.25, 95% CI = 1.01-1.56, P = 0.04). Stratified analysis from 10 studies including 14 757 cases and 17 930 controls revealed that I/D variant significantly increased the risk of breast cancer in heterozygous codominant (OR = 1.15, 95% CI = 1.03-1.28, P = 0.02, ID vs II), dominant (OR = 1.15, 95% CI = 1.01-1.31, P = 0.03, ID + DD vs II), overdominant (OR = 1.11, 95% CI = 1.05-1.25, P < 0.0001, ID vs DD + II) and allele (OR = 1.15, 95% CI = 1.13-1.25, P = 0.03, D vs I) inheritance models. In conclusion, the data propose that APOBEC3 deletion is significantly associated with increased susceptibility to cancer in overall and breast cancer. Our findings require well-designed replication in a larger independent genetic association study with larger sample sizes in diverse ethnicities.
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Affiliation(s)
- Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Abdolkarim Moazeni-Roodi
- Department of Clinical Biochemistry, School of Medicine, Iranshahr University of Medical Sciences, Iranshahr, Iran
| | - Mohsen Taheri
- Department of Genetics, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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Caval V, Jiao W, Berry N, Khalfi P, Pitré E, Thiers V, Vartanian JP, Wain-Hobson S, Suspène R. Mouse APOBEC1 cytidine deaminase can induce somatic mutations in chromosomal DNA. BMC Genomics 2019; 20:858. [PMID: 31726973 PMCID: PMC6854741 DOI: 10.1186/s12864-019-6216-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Background APOBEC1 (A1) enzymes are cytidine deaminases involved in RNA editing. In addition to this activity, a few A1 enzymes have been shown to be active on single stranded DNA. As two human ssDNA cytidine deaminases APOBEC3A (A3A), APOBEC3B (A3B) and related enzymes across the spectrum of placental mammals have been shown to introduce somatic mutations into nuclear DNA of cancer genomes, we explored the mutagenic threat of A1 cytidine deaminases to chromosomal DNA. Results Molecular cloning and expression of various A1 enzymes reveal that the cow, pig, dog, rabbit and mouse A1 have an intracellular ssDNA substrate specificity. However, among all the enzymes studied, mouse A1 appears to be singular, being able to introduce somatic mutations into nuclear DNA with a clear 5’TpC editing context, and to deaminate 5-methylcytidine substituted DNA which are characteristic features of the cancer related mammalian A3A and A3B enzymes. However, mouse A1 activity fails to elicit formation of double stranded DNA breaks, suggesting that mouse A1 possess an attenuated nuclear DNA mutator phenotype reminiscent of human A3B. Conclusions At an experimental level mouse APOBEC1 is remarkable among 12 mammalian A1 enzymes in that it represents a source of somatic mutations in mouse genome, potentially fueling oncogenesis. While the order Rodentia is bereft of A3A and A3B like enzymes it seems that APOBEC1 may well substitute for it, albeit remaining much less active. This modifies the paradigm that APOBEC3 and AID enzymes are the sole endogenous mutator enzymes giving rise to off-target editing of mammalian genomes.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.
| | - Wenjuan Jiao
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Emmanuelle Pitré
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Valérie Thiers
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
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28
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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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29
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Png G, Suveges D, Park YC, Walter K, Kundu K, Ntalla I, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E, Gilly A. Population-wide copy number variation calling using variant call format files from 6,898 individuals. Genet Epidemiol 2019; 44:79-89. [PMID: 31520489 PMCID: PMC8653900 DOI: 10.1002/gepi.22260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/31/2019] [Accepted: 08/28/2019] [Indexed: 11/10/2022]
Abstract
Copy number variants (CNVs) play an important role in a number of human diseases, but the accurate calling of CNVs remains challenging. Most current approaches to CNV detection use raw read alignments, which are computationally intensive to process. We use a regression tree-based approach to call germline CNVs from whole-genome sequencing (WGS, >18x) variant call sets in 6,898 samples across four European cohorts, and describe a rich large variation landscape comprising 1,320 CNVs. Eighty-one percent of detected events have been previously reported in the Database of Genomic Variants. Twenty-three percent of high-quality deletions affect entire genes, and we recapitulate known events such as the GSTM1 and RHD gene deletions. We test for association between the detected deletions and 275 protein levels in 1,457 individuals to assess the potential clinical impact of the detected CNVs. We describe complex CNV patterns underlying an association with levels of the CCL3 protein (MAF = 0.15, p = 3.6x10-12 ) at the CCL3L3 locus, and a novel cis-association between a low-frequency NOMO1 deletion and NOMO1 protein levels (MAF = 0.02, p = 2.2x10-7 ). This study demonstrates that existing population-wide WGS call sets can be mined for germline CNVs with minimal computational overhead, delivering insight into a less well-studied, yet potentially impactful class of genetic variant.
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Affiliation(s)
- Grace Png
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniel Suveges
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Young-Chan Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | | | | | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, Athens, Greece
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Arthur Gilly
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.,Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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30
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He X, Xu H, Wang X, Wu J, Niu J, Gao P. Associations between the single nucleotide polymorphisms of APOBEC3A, APOBEC3B and APOBEC3H, and chronic hepatitis B progression and hepatocellular carcinoma in a Chinese population. Mol Med Rep 2019; 20:2177-2188. [PMID: 31322199 PMCID: PMC6691201 DOI: 10.3892/mmr.2019.10455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
The present study examined the relationships between the single nucleotide polymorphisms (SNPs) of three members of the apolipoprotein B mRNA‑editing catalytic polypeptide‑like 3 (A3) gene family, A3A, A3B and A3H, and hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) in a Han Chinese population. A total of 654 patients were enrolled in the study between January 2012 and July 2016, including 104 patients with chronic HBV infection (CHB), 265 patients with HBV‑related liver cirrhosis and 285 patients with HBV‑related HCC. A total of two A3A SNPs (rs7286317 and rs7290153), three A3B SNPs (rs2267398, rs2267401 and rs2076109), and five A3H SNPs (rs56695217, rs139302, rs139297, rs139316 and rs139292) were genotyped using a MassArray system. Statistical analysis and haplotype estimation were conducted using Haploview and Unphased software. No significant associations were observed between the A3A, A3B and A3H SNPs and the development of CHB and HCC. Haplotype analysis revealed that the mutant haplotypes C‑T‑A, C‑T‑G, T‑G‑G and T‑T‑G from the A3B SNPs rs2267398‑rs2267401‑rs2076109 carried a lower risk of HCC than the reference haplotype. These findings suggested that there was no relationship between A3A, A3B and A3H SNPs and CHB progression or HCC development in the Han Chinese population.
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Affiliation(s)
- Xiuting He
- Department of Geriatrics, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hongqin Xu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xiaomei Wang
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Jing Wu
- Department of Geriatrics, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Junqi Niu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Pujun Gao
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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31
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Buisson R, Langenbucher A, Bowen D, Kwan EE, Benes CH, Zou L, Lawrence MS. Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. Science 2019; 364:eaaw2872. [PMID: 31249028 PMCID: PMC6731024 DOI: 10.1126/science.aaw2872] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Cancer drivers require statistical modeling to distinguish them from passenger events, which accumulate during tumorigenesis but provide no fitness advantage to cancer cells. The discovery of driver genes and mutations relies on the assumption that exact positional recurrence is unlikely by chance; thus, the precise sharing of mutations across patients identifies drivers. Examining the mutation landscape in cancer genomes, we found that many recurrent cancer mutations previously designated as drivers are likely passengers. Our integrated bioinformatic and biochemical analyses revealed that these passenger hotspot mutations arise from the preference of APOBEC3A, a cytidine deaminase, for DNA stem-loops. Conversely, recurrent APOBEC-signature mutations not in stem-loops are enriched in well-characterized driver genes and may predict new drivers. This demonstrates that mesoscale genomic features need to be integrated into computational models aimed at identifying mutations linked to diseases.
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Affiliation(s)
- Rémi Buisson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | - Adam Langenbucher
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Danae Bowen
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | - Eugene E Kwan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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32
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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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33
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Hernandez-Pacheco N, Farzan N, Francis B, Karimi L, Repnik K, Vijverberg SJ, Soares P, Schieck M, Gorenjak M, Forno E, Eng C, Oh SS, Pérez-Méndez L, Berce V, Tavendale R, Samedy LA, Hunstman S, Hu D, Meade K, Farber HJ, Avila PC, Serebrisky D, Thyne SM, Brigino-Buenaventura E, Rodriguez-Cintron W, Sen S, Kumar R, Lenoir M, Rodriguez-Santana JR, Celedón JC, Mukhopadhyay S, Potočnik U, Pirmohamed M, Verhamme KM, Kabesch M, Palmer CNA, Hawcutt DB, Flores C, Maitland-van der Zee AH, Burchard EG, Pino-Yanes M. Genome-wide association study of inhaled corticosteroid response in admixed children with asthma. Clin Exp Allergy 2019; 49:789-798. [PMID: 30697902 DOI: 10.1111/cea.13354] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/30/2018] [Accepted: 12/29/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Inhaled corticosteroids (ICS) are the most widely prescribed and effective medication to control asthma symptoms and exacerbations. However, many children still have asthma exacerbations despite treatment, particularly in admixed populations, such as Puerto Ricans and African Americans. A few genome-wide association studies (GWAS) have been performed in European and Asian populations, and they have demonstrated the importance of the genetic component in ICS response. OBJECTIVE We aimed to identify genetic variants associated with asthma exacerbations in admixed children treated with ICS and to validate previous GWAS findings. METHODS A meta-analysis of two GWAS of asthma exacerbations was performed in 1347 admixed children treated with ICS (Hispanics/Latinos and African Americans), analysing 8.7 million genetic variants. Those with P ≤ 5 × 10-6 were followed up for replication in 1697 asthmatic patients from six European studies. Associations of ICS response described in published GWAS were followed up for replication in the admixed populations. RESULTS A total of 15 independent variants were suggestively associated with asthma exacerbations in admixed populations (P ≤ 5 × 10-6 ). One of them, located in the intergenic region of APOBEC3B and APOBEC3C, showed evidence of replication in Europeans (rs5995653, P = 7.52 × 10-3 ) and was also associated with change in lung function after treatment with ICS (P = 4.91 × 10-3 ). Additionally, the reported association of the L3MBTL4-ARHGAP28 genomic region was confirmed in admixed populations, although a different variant was identified. CONCLUSIONS AND CLINICAL RELEVANCE This study revealed the novel association of APOBEC3B and APOBEC3C with asthma exacerbations in children treated with ICS and replicated previously identified genomic regions. This contributes to the current knowledge about the multiple genetic markers determining responsiveness to ICS which could lead in the future the clinical identification of those asthma patients who are not able to respond to such treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Ben Francis
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Leila Karimi
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Patricia Soares
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Maximilian Schieck
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of the University of Pittsburgh, Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, California
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, California
| | - Lina Pérez-Méndez
- Department of Clinic Epidemiology and Biostatistics, Research Unit, Hospital Universitario N.S. de Candelaria, Gerencia de Atención Primaria, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Lesly-Anne Samedy
- Department of Medicine, University of California, San Francisco, California.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Scott Hunstman
- Department of Medicine, University of California, San Francisco, California
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, California
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, California
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, Illinois.,Allergy & ENT Associates, The Woodland, Texas
| | | | - Shannon M Thyne
- Department of Pediatrics, University of California, San Francisco, California
| | | | | | - Saunak Sen
- University of Tennessee Health Science Center, Memphis, Tennessee
| | - Rajesh Kumar
- Feinberg School of Medicine's Division of Allergy and Immunology, Northwestern University, Chicago, Illinois.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | | | | | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of the University of Pittsburgh, Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK.,Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Colin N A Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK.,Alder Hey Children's Hospital, Liverpool, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Department of Pediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, California.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Lerner T, Papavasiliou FN, Pecori R. RNA Editors, Cofactors, and mRNA Targets: An Overview of the C-to-U RNA Editing Machinery and Its Implication in Human Disease. Genes (Basel) 2018; 10:E13. [PMID: 30591678 PMCID: PMC6356216 DOI: 10.3390/genes10010013] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022] Open
Abstract
One of the most prevalent epitranscriptomic modifications is RNA editing. In higher eukaryotes, RNA editing is catalyzed by one of two classes of deaminases: ADAR family enzymes that catalyze A-to-I (read as G) editing, and AID/APOBEC family enzymes that catalyze C-to-U. ADAR-catalyzed deamination has been studied extensively. Here we focus on AID/APOBEC-catalyzed editing, and review the emergent knowledge regarding C-to-U editing consequences in the context of human disease.
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Affiliation(s)
- Taga Lerner
- Division of Immune Diversity, Program in Cancer Immunology, German Cancer Research Centre, 69120 Heidelberg, Germany.
- Division of Biosciences, Uni Heidelberg, 69120 Heidelberg, Germany.
| | - F Nina Papavasiliou
- Division of Immune Diversity, Program in Cancer Immunology, German Cancer Research Centre, 69120 Heidelberg, Germany.
| | - Riccardo Pecori
- Division of Immune Diversity, Program in Cancer Immunology, German Cancer Research Centre, 69120 Heidelberg, Germany.
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35
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Zhang B, Zhang X, Jin M, Hu L, Zang M, Qiu W, Wang S, Liu B, Liu S, Guo D. CagA increases DNA methylation and decreases PTEN expression in human gastric cancer. Mol Med Rep 2018; 19:309-319. [PMID: 30431097 PMCID: PMC6297774 DOI: 10.3892/mmr.2018.9654] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/28/2018] [Indexed: 01/15/2023] Open
Abstract
Gastric cancer is one of the leading causes of cancer-associated mortality worldwide. Cytotoxin-associated gene A (CagA) has been reported to be associated with gastric diseases. Phosphatase and tensin homolog (PTEN) and tet methylcytosine dioxygenase 1 (Tet1) are important tumor-suppressor genes. The present study aimed to investigate the underlying functions of CagA in human gastric cancer, and to explore the associations between CagA, PTEN and Tet1 in gastric cancer. For that purpose, CagA overexpression and Tet1 interference recombinant lentiviral plasmids were constructed. Quantitative polymerase chain reaction (qPCR) was utilized to screen gene expression in HGC-27 human gastric cancer cells overexpressing CagA. qPCR and western blotting were used to detect gene and protein expression, respectively. In addition, the methylation status of PTEN was detected by methylation-specific PCR. The expression levels of PTEN, Tet1, apolipoprotein B mRNA editing enzyme catalytic subunit (APOBEC)3A, APOBEC3C and APOBEC3F were significantly decreased in the CagA overexpression group compared with in the negative control group in HGC-27 cells. Compared with in the negative control group, the mRNA and protein expression levels of PTEN were markedly decreased in cells with Tet1 interference. The decreased expression of PTEN was associated with increased methylation levels in the cells. In addition, the protein expression levels of PTEN were significantly decreased in HGC-27 cells when CagA was overexpressed. The expression levels of PTEN and Tet1 were also markedly decreased in CagA+ gastric cancer tissues compared with in non-cancerous tissues. The decreased expression of PTEN in CagA+ gastric cancer tissues was associated with increased methylation levels. In conclusion, overexpression of CagA significantly decreased the expression of PTEN, Tet1, APOBEC3A, APOBEC3C and APOBEC3F in human gastric cancer. In addition, CagA increased DNA methylation and decreased PTEN expression, which was reversed by Tet1 overexpression. The present study may facilitate future therapeutic approaches targeting human gastric cancer.
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Affiliation(s)
- Baogui Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Xiaobei Zhang
- Department of Central Laboratory, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Meng Jin
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Lei Hu
- Department of General Surgery Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui 230001, P.R. China
| | - Mingde Zang
- Department of Gastric Cancer Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Weilong Qiu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Shouqi Wang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Bingya Liu
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Shiqi Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
| | - Dongli Guo
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining, Shandong 272000, P.R. China
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36
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Saini N, Gordenin DA. Somatic mutation load and spectra: A record of DNA damage and repair in healthy human cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:672-686. [PMID: 30152078 PMCID: PMC6188803 DOI: 10.1002/em.22215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/07/2018] [Accepted: 06/11/2018] [Indexed: 05/31/2023]
Abstract
Somatic genome instability is a hallmark of cancer genomes and has been linked to aging and a variety of other pathologies. Large-scale cancer genome and exome sequencing have revealed that mutation load and spectra in cancers can be influenced by environmental exposures, the anatomical site of exposures, and tissue type. There is now an abundance of data favoring the hypothesis that a substantial portion of the mutations in cancers originate prior to carcinogenesis in stem cells of the healthy individual. Rapid advances in sequencing of noncancer cells from healthy humans have shown that their mutation loads and spectra resemble cancer data. Similar to cancer genomes, mutation profiles of healthy cells show marked intra-individual variation, thus providing a metric of the various factors-environmental and endogenous-involved in mutagenesis in these individuals. This review focuses on the current methodologies to measure mutation loads and to determine mutation signatures for evaluating the environmental and endogenous sources of DNA damage in human somatic cells. We anticipate that in future, such large-scale studies aimed at exploring the landscapes of somatic mutations across different cell types in healthy people would provide a valuable resource for designing personalized preventative strategies against diseases associated with somatic genome instability. Environ. Mol. Mutagen. 59:672-686, 2018. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
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37
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Yang Z, Tao Y, Xu X, Cai F, Yu Y, Ma L. Bufalin inhibits cell proliferation and migration of hepatocellular carcinoma cells via APOBEC3F induced intestinal immune network for IgA production signaling pathway. Biochem Biophys Res Commun 2018; 503:2124-2131. [PMID: 30100060 DOI: 10.1016/j.bbrc.2018.07.169] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
OBJECTIVE This study aimed to evaluate functions of APOBEC3F gene in biological process of hepatocellular carcinoma (HCC) and anti-tumor mechanisms of bufalin. METHODS Effect of APOBEC3F and bufalin on cell proliferation and migration abilities were evaluated by CCK-8, wounding healing tests and transwell assays in SK-Hep1 and Bel-7404 cells. Bioinformatic analysis were also used to compare APOBEC3F expression levels, detect coexpressed genes and enrichment of pathways. RESULTS APOBEC3F was overexpressed in tumor tissues compared to adjacent tissues in HCC patients. And, APOBEC3F promotes cell proliferation and migration in SK-Hep1 and Bel-7404 cells. Bufalin inhibits cell proliferation and migration and reduces APOBEC3F expression. GO and KEGG enrichment of APOBEC3F-coexpressed genes revealed that APOBEC3F might active intestinal immune network for IgA production signaling pathway, leading to malignant biological behaviors of HCC cells. Additionally, siAPOBEC3F could decrease pIgR, CCR9, CCR10 and CXCR4 protein levels. And, bufalin inhibits the pIgR, CCR9, CCR10 and CXCR4 protein expressions. CONCLUSIONS Bufalin inhibits cell proliferation and migration of HCC cells via APOBEC3F induced intestinal immune network for IgA production signaling pathway.
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Affiliation(s)
- Zongguo Yang
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China; Department of Integrative Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, PR China
| | - Yuquan Tao
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China
| | - Xin Xu
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China
| | - Feng Cai
- Department of Clinical Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China
| | - Yongchun Yu
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China; Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, PR China.
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China.
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