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Tu X, Kahila MM, Zhou Q, Yu J, Kalari KR, Wang L, Harmsen WS, Yuan J, Boughey JC, Goetz MP, Sarkaria JN, Lou Z, Mutter RW. ATR Inhibition Is a Promising Radiosensitizing Strategy for Triple-Negative Breast Cancer. Mol Cancer Ther 2018; 17:2462-2472. [PMID: 30166399 DOI: 10.1158/1535-7163.mct-18-0470] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/22/2018] [Accepted: 08/23/2018] [Indexed: 01/28/2023]
Abstract
Triple-negative breast cancer (TNBC) is characterized by elevated locoregional recurrence risk despite aggressive local therapies. New tumor-specific radiosensitizers are needed. We hypothesized that the ATR inhibitor, VX-970 (now known as M6620), would preferentially radiosensitize TNBC. Noncancerous breast epithelial and TNBC cell lines were investigated in clonogenic survival, cell cycle, and DNA damage signaling and repair assays. In addition, patient-derived xenograft (PDX) models generated prospectively as part of a neoadjuvant chemotherapy study from either baseline tumor biopsies or surgical specimens with chemoresistant residual disease were assessed for sensitivity to fractionated radiotherapy, VX-970, or the combination. To explore potential response biomarkers, exome sequencing was assessed for germline and/or somatic alterations in homologous recombination (HR) genes and other alterations associated with ATR inhibitor sensitivity. VX-970 preferentially inhibited ATR-Chk1-CDC25a signaling, abrogated the radiotherapy-induced G2-M checkpoint, delayed resolution of DNA double-strand breaks, and reduced colony formation after radiotherapy in TNBC cells relative to normal-like breast epithelial cells. In vivo, VX-970 did not exhibit significant single-agent activity at the dose administered even in the context of genomic alterations predictive of ATR inhibitor responsiveness, but significantly sensitized TNBC PDXs to radiotherapy. Exome sequencing and functional testing demonstrated that combination therapy was effective in both HR-proficient and -deficient models. PDXs established from patients with chemoresistant TNBC were also highly radiosensitized. In conclusion, VX-970 is a tumor-specific radiosensitizer for TNBC. Patients with residual TNBC after neoadjuvant chemotherapy, a subset at particularly high risk of relapse, may be ideally suited for this treatment intensification strategy. Mol Cancer Ther; 17(11); 2462-72. ©2018 AACR.
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Affiliation(s)
- Xinyi Tu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Mohamed M Kahila
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Qin Zhou
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - William S Harmsen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jian Yuan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota.
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Fujiki Y, Yamamoto Y, Sueta A, Yamamoto-Ibusuki M, Goto-Yamaguchi L, Tomiguchi M, Takeshita T, Iwase H. APOBEC3B gene expression as a novel predictive factor for pathological complete response to neoadjuvant chemotherapy in breast cancer. Oncotarget 2018; 9:30513-30526. [PMID: 30093965 PMCID: PMC6078135 DOI: 10.18632/oncotarget.25495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 05/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3B (APOBEC3B) is a gene editing enzyme with cytidine deaminase activity and high expression of its mRNA in breast tumors have been shown to be associated with progressive cases and poor prognosis. In this study, we aimed to examine the relationship between the expression of APOBEC3B and the effect of neoadjuvant chemotherapy (NAC) using pretreatment biopsy tissue, and examined whether the expression of APOBEC3B influenced chemotherapy efficacy. Methods We retrospectively selected a total of 274 patients with primary breast cancer who received NAC in more than 4 courses and underwent surgery at our institute. We assessed the expression of APOBEC3B mRNA using pretreatment biopsy specimens of NAC by quantitative real-time PCR (qRT-PCR) and examined the relationship between APOBEC3B mRNA expression and sensitivity to chemotherapy using pathological complete response (pCR) as an indicator. Further, we assessed the prognostic value of APOBEC3B in the patients receiving NAC. Results APOBEC3B mRNA expression levels were successfully assessed in 173 (63.1%) of the 274 specimens. The total pCR rate was 36.4% (n = 63). An association between APOBEC3B expression levels and pCR was observed (Wilcoxon test, P ≤ 0.0001). The patients were divided into two groups, low (n = 66) and high (n = 107), according to the APOBEC3B expression levels, using the cut-off value calculated by the receiver operating characteristics (ROC) curve for pCR. The rate of pCR was significantly higher among the patients in the high group than among those in the low group (47.7% vs 18.2%, P ≤ 0.0001). High APOBEC3B expression was significantly associated with high nuclear grade (P = 0.0078), high Ki-67 labeling index (P = 0.0087), estrogen receptor (ER) negativity (P ≤ 0.0001) and human epidermal growth factor receptor 2 (HER2) negativity (P = 0.032). Tumor size (P = 0.011), ER (P ≤ 0.0001), HER2 (P = 0.0013) and APOBEC3B expression (P = 0.037) were independent predictive factors for pCR in multivariate analysis. However, there was no association between APOBEC3B expression and prognosis. Conclusions Our study showed that APOBEC3B mRNA expression correlated with sensitivity to NAC in breast cancer patients. In contrast to previous studies, APOBEC3B mRNA expression was not associated with breast cancer prognosis in patients receiving NAC.
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Affiliation(s)
- Yoshitaka Fujiki
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Yutaka Yamamoto
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Aiko Sueta
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Mutsuko Yamamoto-Ibusuki
- Department of Molecular-Targeting Therapy for Breast Cancer, Kumamoto University Hospital, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Lisa Goto-Yamaguchi
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Mai Tomiguchi
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Takashi Takeshita
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Kumamoto University Graduate School of Medical Sciences, Chuo-Ku, Kumamoto 860-8556, Japan
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Du Y, Tao X, Wu J, Yu H, Yu Y, Zhao H. APOBEC3B up-regulation independently predicts ovarian cancer prognosis: a cohort study. Cancer Cell Int 2018; 18:78. [PMID: 29853799 PMCID: PMC5975489 DOI: 10.1186/s12935-018-0572-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/23/2018] [Indexed: 01/22/2023] Open
Abstract
Background Ovarian cancer is a heterogeneous disease with a high degree of genomic instability, pro-/antitumor immunity and inflammation, and remains the most lethal gynecologic cancer worldwide. APOBEC3B, a member of the AID/APOBEC family, is part of the innate immune system which plays a key role in combating exogenous infection especially viral infection. Studies have shown that APOBEC3B expression is elevated in a variety of cancer tissues and cell lines, and plays a prominent role in the genesis and evolution of various cancers. However, the clinical relevance of APOBEC3B in ovarian cancer needs to be further investigated. The current study aimed to evaluate the predictive value of APOBEC3B in ovarian cancer clinical outcome, and to explore possible molecular mechanisms contributing to ovarian cancer progression. Methods The expression of APOBEC3B in biopsy tissue specimens from 88 ovarian cancer patients was examined using immunohistochemistry. In addition, ovarian cancer cell lines were transfected with APOBEC3B siRNA or pLenti-APOBEC3B construct. Western blotting and SRB assay were performed to explore the role of APOBEC3B in ovarian cancer. Results Patients were followed for a median of 74.77 months following the time of surgery. Forty-two patients had died, 5 had relapsed but were still alive at the end of study, and 41 patients remained alive and had no recurrence. Over-expression of APOBEC3B was associated with advanced FIGO stage and elevated CA125 (both p< 0.05). Univariate analysis result showed that histological subtype, FIGO stage, intravascular tumor thrombus, CA125 and APOBEC3B expression were associated with overall survival and disease-free survival of ovarian cancer patients. Multivariate analysis result showed that higher APOBEC3B expression were an independent prognostic factor to predict both worse overall survival (hazard ratio: 5.18, 95% confidence interval: 1.40–11.95, p= 0.003) and disease-free survival (hazard ratio: 4.23, 95% confidence interval: 1.60–11.17, p= 0.004) of ovarian cancer patients. Furthermore, knockdown of APOBEC3B expression in ovarian cancer cells caused an decrease in cell line viability. Conclusions APOBEC3B expression is an independent prognostic factor in ovarian cancer patients. Knockdown of APOBEC3B expression affects ovarian cancer viability.
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Affiliation(s)
- Yan Du
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,2The Academy of Integrative Medicine of Fudan University, 200011 Shanghai, People's Republic of China
| | - Xiang Tao
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Jing Wu
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Huandi Yu
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Yinhua Yu
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
| | - Hongbo Zhao
- 1Obstetrics and Gynecology Hospital, Fudan University, 419 Fangxie Rd, 200011 Shanghai, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, 200011 Shanghai, People's Republic of China
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Salamango DJ, McCann JL, Demir Ö, Brown WL, Amaro RE, Harris RS. APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces. J Mol Biol 2018; 430:2695-2708. [PMID: 29787764 DOI: 10.1016/j.jmb.2018.04.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 01/02/2023]
Abstract
The APOBEC3 family of cytosine deaminases catalyzes the conversion of cytosines-to-uracils in single-stranded DNA. Traditionally, these enzymes are associated with antiviral immunity and restriction of DNA-based pathogens. However, a role for these enzymes in tumor evolution and metastatic disease has also become evident. The primary APOBEC3 candidate in cancer mutagenesis is APOBEC3B (A3B) for three reasons: (1) A3B mRNA is upregulated in several different cancers, (2) A3B expression and mutational loads correlate with poor clinical outcomes, and (3) A3B is the only family member known to be constitutively nuclear. Previous studies have mapped non-canonical A3B nuclear localization determinants to a single surface-exposed patch within the N-terminal domain (NTD). Here, we show that A3B has an additional, distinct, surface-exposed NTD region that contributes to nuclear localization. Disruption of residues within the first 30 amino acids of A3B (import surface 1) or loop 5/α-helix 3 (import surface 2) completely abolish nuclear localization. These import determinants also graft into NTDs of related family members and mediate re-localization from cell-wide-to-nucleus or cytoplasm-to-nucleus. These findings demonstrate that both sets of residues are required for non-canonical A3B nuclear localization and describe unique surfaces that may serve as novel therapeutic targets.
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Affiliation(s)
- Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of San Diego, La Jolla 92093, CA, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of San Diego, La Jolla 92093, CA, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA.
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Borzooee F, Asgharpour M, Quinlan E, Grant MD, Larijani M. Viral subversion of APOBEC3s: Lessons for anti-tumor immunity and tumor immunotherapy. Int Rev Immunol 2018; 37:151-164. [PMID: 29211501 DOI: 10.1080/08830185.2017.1403596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
APOBEC3s (A3) are endogenous DNA-editing enzymes that are expressed in immune cells including T lymphocytes. A3s target and mutate the genomes of retroviruses that infect immune tissues such as the human immunodeficiency virus (HIV). Therefore, A3s were classically defined as host anti-viral innate immune factors. In contrast, we and others showed that A3s can also benefit the virus by mediating escape from adaptive immune recognition and drugs. Crucially, whether A3-mediated mutations help or hinder HIV, is not up to chance. Rather, the virus has evolved multiple mechanisms to actively and maximally subvert A3 activity. More recently, extensive A3 mutational footprints in tumor genomes have been observed in many different cancers. This suggests a role for A3s in cancer initiation and progression. On the other hand, multiple anti-tumor activities of A3s have also come to light, including impact on immune checkpoint molecules and possible generation of tumor neo-antigens. Here, we review the studies that reshaped the view of A3s from anti-viral innate immune agents to host factors exploited by HIV to escape from immune recognition. Viruses and tumors share many attributes, including rapid evolution and adeptness at exploiting mutations. Given this parallel, we then discuss the pro- and anti-tumor roles of A3s, and suggest that lessons learned from studying A3s in the context of anti-viral immunity can be applied to tumor immunotherapy.
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Affiliation(s)
- Faezeh Borzooee
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mahdi Asgharpour
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Emma Quinlan
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Michael D Grant
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mani Larijani
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
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Shapiro M, Meier S, MacCarthy T. The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure. BMC Bioinformatics 2018; 19:163. [PMID: 29716522 PMCID: PMC5930495 DOI: 10.1186/s12859-018-2161-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 04/20/2018] [Indexed: 01/23/2023] Open
Abstract
Background Activation induced deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) are deaminases that mutate C to U on single-stranded DNA (ssDNA). AID is expressed primarily in germinal center B-cells, where it facilitates affinity maturation and class-switch recombination. APOBEC3 are a family of anti-viral proteins that act as part of the intrinsic immune response. In both cases, there are particular sequence motifs, also known as “mutation motifs”, to which these deaminases prefer to bind and mutate. Results We present a program, the cytidine deaminase under-representation reporter (CDUR) designed to statistically determine whether a given sequence has an under/over-representation of these mutation motifs. CDUR shows consitency with other studies of mutation motifs, as we show by analyzing sequences from the adeno-associated virus 2 (AAV2) and human papillomavirus (HPV). Conclusion Using various shuffling mechanisms to generate different null model distributions, we can tailor CDUR to correct for metrics such as GC-content, dinucleotide frequency, and codon bias.
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Affiliation(s)
- Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA
| | - Stephen Meier
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA. .,Laufer Center for Physical and Quantitative Biology, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, USA.
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Mishra N, Reddy KS, Timilsina U, Gaur D, Gaur R. Human APOBEC3B interacts with the heterogenous nuclear ribonucleoprotein A3 in cancer cells. J Cell Biochem 2018; 119:6695-6703. [PMID: 29693745 DOI: 10.1002/jcb.26855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/09/2018] [Indexed: 11/07/2022]
Abstract
Human APOBEC3B (A3B), like other APOBEC3 members, is a cytosine deaminase which causes hypermutation of single stranded genome. Recent studies have shown that A3B is predominantly elevated in multiple cancer tissues and cell lines such as the bladder, cervix, lung, head and neck, and breast. Upregulation and activation of A3B in developing tumors can cause an unexpected cluster of mutations which promote cancer development and progression. The cellular proteins which facilitate A3B function through direct or indirect interactions remain largely unknown. In this study, we performed LC-MS-based proteomics to identify cellular proteins which coimmunoprecipitated with A3B. Our results indicated a specific interaction of A3B with hnRNP A3 (heterogeneous nuclear ribonucleoprotein). This interaction was verified by co-immunoprecipitation and was found to be RNA-dependent. Furthermore, A3B and hnRNP A3 colocalized as evident from immunofluorescence analysis.
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Affiliation(s)
- Nawneet Mishra
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - K Sony Reddy
- School of Biotechnology, KIIT University, Odisha, India
| | - Uddhav Timilsina
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Deepak Gaur
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ritu Gaur
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
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Vural S, Simon R, Krushkal J. Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment. Hum Genomics 2018; 12:20. [PMID: 29642934 PMCID: PMC5896091 DOI: 10.1186/s40246-018-0150-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/23/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The APOBEC gene family of cytidine deaminases plays important roles in DNA repair and mRNA editing. In many cancers, APOBEC3B increases the mutation load, generating clusters of closely spaced, single-strand-specific DNA substitutions with a characteristic hypermutation signature. Some studies also suggested a possible involvement of APOBEC3A, REV1, UNG, and FHIT in molecular processes affecting APOBEC mutagenesis. It is important to understand how mutagenic processes linked to the activity of these genes may affect sensitivity of cancer cells to treatment. RESULTS We used information from the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer resources to examine associations of the prevalence of APOBEC-like motifs and mutational loads with expression of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT and with cell line chemosensitivity to 255 antitumor drugs. Among the five genes, APOBEC3B expression levels were bimodally distributed, whereas expression of APOBEC3A, REV1, UNG, and FHIT was unimodally distributed. The majority of the cell lines had low levels of APOBEC3A expression. The strongest correlations of gene expression levels with mutational loads or with measures of prevalence of APOBEC-like motif counts and kataegis clusters were observed for REV1, UNG, and APOBEC3A. Sensitivity or resistance of cell lines to JQ1, palbociclib, bicalutamide, 17-AAG, TAE684, MEK inhibitors refametinib, PD-0325901, and trametinib and a number of other agents was correlated with candidate gene expression levels or with abundance of APOBEC-like motif clusters in specific cancers or across cancer types. CONCLUSIONS We observed correlations of expression levels of the five candidate genes in cell line models with sensitivity to cancer drug treatment. We also noted suggestive correlations between measures of abundance of APOBEC-like sequence motifs with drug sensitivity in small samples of cell lines from individual cancer categories, which require further validation in larger datasets. Molecular mechanisms underlying the links between the activities of the products of each of the five genes, the resulting mutagenic processes, and sensitivity to each category of antitumor agents require further investigation.
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Affiliation(s)
- Suleyman Vural
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD 20850 USA
| | - Richard Simon
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD 20850 USA
| | - Julia Krushkal
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD 20850 USA
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Wang Y, Wang C, Zhang J, Zhu M, Zhang X, Li Z, Dai J, Ma H, Hu Z, Jin G, Shen H. Interaction analysis between germline susceptibility loci and somatic alterations in lung cancer. Int J Cancer 2018; 143:878-885. [PMID: 29492964 DOI: 10.1002/ijc.31351] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 12/16/2022]
Abstract
Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the germline-somatic interaction in lung cancer remains largely unknown. We investigated whether lung cancer driver genes (CDGs) were more likely to locate within cancer susceptibility regions. Pathway analysis was performed to identify common pathways underlying CDGs and cancer susceptibility genes (CSGs). Next, we analyzed the associations between lung cancer risk SNPs and somatic alterations, including mutations and copy number alterations, in the level of genes, pathways, and overall burden of alterations. Enrichment analysis showed that lung CDGs are more likely to locate within cancer susceptibility regions (p = 8.40 × 10-3 ). Both of lung CSGs and CDGs showed significant enrichment in pathways such as cell cycle and p53 signaling pathway. Gene-based analysis showed that rs36600 (22q12.2) was associated with somatic mutations within ARID1A (OR = 2.45, 95%CI: 1.47-4.08, p = 5.78 × 10-4 ). Pathway-based analysis of somatic truncation mutations identified rs2395185 and rs3817963 at 6p22.1 was associated with cell cycle pathway (OR = 1.56, p = 3.61 × 10-4 for rs2395185; OR = 1.58, p = 4.15 × 10-4 for rs3817963), and rs3817963 was also associated with MAPK signaling pathway (OR = 1.54, p = 8.58 × 10-4 ). Further analysis associated rs2395185 at 6p22.1 (HLA class II genes) with increased APOBEC3A expression (p = 9.50 × 10-3 ) and elevated APOBEC mutagenesis (p = 3.58 × 10-3 ). These results indicate germline-somatic interactions in lung tumorigenesis, and help to uncover the molecular mechanisms underlying lung cancer risk SNPs.
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Affiliation(s)
- Yuzhuo Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Jiahui Zhang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Xu Zhang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhihua Li
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
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Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H. Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep 2017; 7:17415. [PMID: 29234087 PMCID: PMC5727031 DOI: 10.1038/s41598-017-17694-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/29/2017] [Indexed: 02/07/2023] Open
Abstract
The APOBEC3B (A3B) single-stranded DNA (ssDNA) cytosine deaminase has important roles in innate immunity but is also a major endogenous source of mutations in cancer. Previous structural studies showed that the C-terminal catalytic domain of human A3B has a tightly closed active site, and rearrangement of the surrounding loops is required for binding to substrate ssDNA. Here we report structures of the A3B catalytic domain in a new crystal form that show alternative, yet still closed, conformations of active site loops. All-atom molecular dynamics simulations support the dynamic behavior of active site loops and recapitulate the distinct modes of interactions that maintain a closed active site. Replacing segments of A3B loop 1 to mimic the more potent cytoplasmic deaminase APOBEC3A leads to elevated ssDNA deaminase activity, likely by facilitating opening of the active site. These data collectively suggest that conformational equilibrium of the A3B active site loops, skewed toward being closed, controls enzymatic activity by regulating binding to ssDNA substrates.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Jeff Wagner
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kayo Kurahashi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, 55455, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, 55455, USA. .,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, 55455, USA.
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62
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Kim YA, Madan S, Przytycka TM. WeSME: uncovering mutual exclusivity of cancer drivers and beyond. Bioinformatics 2017; 33:814-821. [PMID: 27153670 DOI: 10.1093/bioinformatics/btw242] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/22/2016] [Indexed: 12/18/2022] Open
Abstract
Motivation Mutual exclusivity is a widely recognized property of many cancer drivers. Knowledge about these relationships can provide important insights into cancer drivers, cancer-driving pathways and cancer subtypes. It can also be used to predict new functional interactions between cancer driving genes and uncover novel cancer drivers. Currently, most of mutual exclusivity analyses are preformed focusing on a limited set of genes in part due to the computational cost required to rigorously compute P -values. Results To reduce the computing cost and perform less restricted mutual exclusivity analysis, we developed an efficient method to estimate P -values while controlling the mutation rates of individual patients and genes similar to the permutation test. A comprehensive mutual exclusivity analysis allowed us to uncover mutually exclusive pairs, some of which may have relatively low mutation rates. These pairs often included likely cancer drivers that have been missed in previous analyses. More importantly, our results demonstrated that mutual exclusivity can also provide information that goes beyond the interactions between cancer drivers and can, for example, elucidate different mutagenic processes in different cancer groups. In particular, including frequently mutated, long genes such as TTN in our analysis allowed us to observe interesting patterns of APOBEC activity in breast cancer and identify a set of related driver genes that are highly predictive of patient survival. In addition, we utilized our mutual exclusivity analysis in support of a previously proposed model where APOBEC activity is the underlying process that causes TP53 mutations in a subset of breast cancer cases. Availability and Implementation http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#wesme. Contact przytyck@ncbi.nlm.nih.gov. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoo-Ah Kim
- NCBI, NLM, NIH, Bethesda, MD, 20894, USA
| | - Sanna Madan
- Poolesville High School, Poolesville, 20837 MD, USA
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63
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APOBEC Enzymes as Targets for Virus and Cancer Therapy. Cell Chem Biol 2017; 25:36-49. [PMID: 29153851 DOI: 10.1016/j.chembiol.2017.10.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/11/2017] [Accepted: 10/18/2017] [Indexed: 01/08/2023]
Abstract
Human DNA cytosine-to-uracil deaminases catalyze mutations in both pathogen and cellular genomes. APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H restrict human immunodeficiency virus 1 (HIV-1) infection in cells deficient in the viral infectivity factor (Vif), and have the potential to catalyze sublethal levels of mutation in viral genomes in Vif-proficient cells. At least two APOBEC3 enzymes, and in particular APOBEC3B, are sources of somatic mutagenesis in cancer cells that drive tumor evolution and may manifest clinically as recurrence, metastasis, and/or therapy resistance. Consequently, APOBEC3 enzymes are tantalizing targets for developing chemical probes and therapeutic molecules to harness mutational processes in human disease. This review highlights recent efforts to chemically manipulate APOBEC3 activities.
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64
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Hammerl D, Smid M, Timmermans AM, Sleijfer S, Martens JWM, Debets R. Breast cancer genomics and immuno-oncological markers to guide immune therapies. Semin Cancer Biol 2017; 52:178-188. [PMID: 29104025 DOI: 10.1016/j.semcancer.2017.11.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/28/2022]
Abstract
There is an increasing awareness of the importance of tumor - immune cell interactions to the evolution and therapy responses of breast cancer (BC). Not surprisingly, numerous studies are currently assessing the clinical value of immune modulation for BC patients. However, till now durable clinical responses are only rarely observed. It is important to realize that BC is a heterogeneous disease comprising several histological and molecular subtypes, which cannot be expected to be equally immunogenic and therefore not equally sensitive to single immune therapies. Here we review the characteristics of infiltrating leukocytes in healthy and malignant breast tissue, the prognostic and predictive values of immune cell subsets across different BC subtypes and the various existing immune evasive mechanisms. Furthermore, we describe the presence of certain groups of antigens as putative targets for treatment, evaluate the outcomes of current clinical immunotherapy trials, and finally, we propose a strategy to better implement immuno-oncological markers to guide future immune therapies in BC.
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Affiliation(s)
- D Hammerl
- Department of Medical Oncology, Erasmus MC - Cancer Institute, Rotterdam, the Netherlands
| | - M Smid
- Department of Medical Oncology, Erasmus MC - Cancer Institute, Rotterdam, the Netherlands
| | - A M Timmermans
- Department of Medical Oncology, Erasmus MC - Cancer Institute, Rotterdam, the Netherlands
| | - S Sleijfer
- Department of Medical Oncology, Erasmus MC - Cancer Institute, Rotterdam, the Netherlands
| | - J W M Martens
- Department of Medical Oncology, Erasmus MC - Cancer Institute, Rotterdam, the Netherlands
| | - R Debets
- Department of Medical Oncology, Erasmus MC - Cancer Institute, Rotterdam, the Netherlands.
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65
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Periyasamy M, Singh AK, Gemma C, Kranjec C, Farzan R, Leach DA, Navaratnam N, Pálinkás HL, Vértessy BG, Fenton TR, Doorbar J, Fuller-Pace F, Meek DW, Coombes RC, Buluwela L, Ali S. p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells. Nucleic Acids Res 2017; 45:11056-11069. [PMID: 28977491 PMCID: PMC5737468 DOI: 10.1093/nar/gkx721] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/30/2017] [Accepted: 08/08/2017] [Indexed: 12/28/2022] Open
Abstract
Cancer genome sequencing has implicated the cytosine deaminase activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) genes as an important source of mutations in diverse cancers, with APOBEC3B (A3B) expression especially correlated with such cancer mutations. To better understand the processes directing A3B over-expression in cancer, and possible therapeutic avenues for targeting A3B, we have investigated the regulation of A3B gene expression. Here, we show that A3B expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression. This occurs through the induction of p21 (CDKN1A) and the recruitment of the repressive DREAM complex to the A3B gene promoter, such that loss of p53 through mutation, or human papilloma virus-mediated inhibition, prevents recruitment of the complex, thereby causing elevated A3B expression and cytosine deaminase activity in cancer cells. As p53 is frequently mutated in cancer, our findings provide a mechanism by which p53 loss can promote cancer mutagenesis.
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Affiliation(s)
- Manikandan Periyasamy
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Anup K. Singh
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Carolina Gemma
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Christian Kranjec
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Raed Farzan
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Damien A. Leach
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Naveenan Navaratnam
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Hajnalka L. Pálinkás
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Beata G. Vértessy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Tim R. Fenton
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - John Doorbar
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Frances Fuller-Pace
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - David W. Meek
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - R. Charles Coombes
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Laki Buluwela
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
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66
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Xiao X, Yang H, Arutiunian V, Fang Y, Besse G, Morimoto C, Zirkle B, Chen XS. Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation. Nucleic Acids Res 2017; 45:7494-7506. [PMID: 28575276 PMCID: PMC5499559 DOI: 10.1093/nar/gkx362] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 05/27/2017] [Indexed: 12/26/2022] Open
Abstract
The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species after RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.
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Affiliation(s)
- Xiao Xiao
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- These authors contributed equally to this work as first authors
| | - Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- These authors contributed equally to this work as first authors
| | - Vagan Arutiunian
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yao Fang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Clinical Microbiology and Immunology of Southwest Hospital, Third Military Medical University, Chongqing 400038, China
- 161 Hospital, Wuhan 430012, China
| | - Guillaume Besse
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Polytech' Clermont-Ferrand, Université Blaise Pascal, Clermont-Ferrand, France
| | - Cherie Morimoto
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Brett Zirkle
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S. Chen
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
- To whom correspondence should be addressed. Tel: +1 213 740 5487; Fax: +1 213 740 4340;
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67
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Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IYF, Yeh YM, Chen CD, Li HP, Luo JD, Tan BCM, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS. APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nat Commun 2017; 8:465. [PMID: 28878238 PMCID: PMC5587710 DOI: 10.1038/s41467-017-00493-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 07/04/2017] [Indexed: 12/29/2022] Open
Abstract
Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses in 50 matched samples, we uncover in Taiwanese patients a predominant mutation signature associated with cytidine deaminase APOBEC, which correlates with the upregulation of APOBEC3A expression in the APOBEC3 gene cluster at 22q13. APOBEC3A expression is significantly higher in tumors carrying APOBEC3B-deletion allele(s). High-level APOBEC3A expression is associated with better overall survival, especially among patients carrying APOBEC3B-deletion alleles, as examined in a second cohort (n = 188; p = 0.004). The frequency of APOBEC3B-deletion alleles is ~50% in 143 genotyped oral squamous cell carcinoma -Taiwan samples (27A3B−/−:89A3B+/−:27A3B+/+), compared to the 5.8% found in 314 OSCC-TCGA samples. We thus report a frequent APOBEC mutational profile, which relates to a APOBEC3B-deletion germline polymorphism in Taiwanese oral squamous cell carcinoma that impacts expression of APOBEC3A, and is shown to be of clinical prognostic relevance. Our finding might be recapitulated by genomic studies in other cancer types. Oral squamous cell carcinoma is a prevalent malignancy in Taiwan. Here, the authors show that OSCC in Taiwanese show a frequent deletion polymorphism in the cytidine deaminases gene cluster APOBEC3 resulting in increased expression of A3A, which is shown to be of clinical prognostic relevance.
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Affiliation(s)
- Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chi-Ching Lee
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biochemistry, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Chi-Sheng Wu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Curtis R Pickering
- Departments of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Po-Jung Huang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Jing Wang
- Departments of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chih-De Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Hsin-Pai Li
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Ji-Dung Luo
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Bertrand Chin-Ming Tan
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Timothy En Haw Chan
- Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chuen Hsueh
- Pathology Core of the Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Pathology, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Bing Zhang
- Department of Molecular and Human Genetics Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Chia-Yu Yang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chih-Ching Wu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Lai-Chu See
- Department of Public Health, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Biostatistics Core Laboratory, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Petrus Tang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Molecular Regulation and Bioinformatics Laboratory, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Cell and Molecular Biology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Wei-Chao Liao
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, 736, Taiwan.,School of Dentistry, National Yang Ming University, Taipei, 112, Taiwan
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Jeffrey N Myers
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan. .,College of Medicine, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan. .,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan. .,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.
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68
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Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression. Viruses 2017; 9:v9080233. [PMID: 28825669 PMCID: PMC5580490 DOI: 10.3390/v9080233] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 02/06/2023] Open
Abstract
The apolipoprotein B messenger RNA-editing, enzyme-catalytic, polypeptide-like 3 (APOBEC3) family of cytidine deaminases plays an important role in the innate immune response to viral infections by editing viral genomes. However, the cytidine deaminase activity of APOBEC3 enzymes also induces somatic mutations in host genomes, which may drive cancer progression. Recent studies of human papillomavirus (HPV) infection and disease outcome highlight this duality. HPV infection is potently inhibited by one family member, APOBEC3A. Expression of APOBEC3A and APOBEC3B is highly elevated by the HPV oncoproteins E6 and E7 during persistent virus infection and disease progression. Furthermore, there is a high prevalence of APOBEC3A and APOBEC3B mutation signatures in HPV-associated cancers. These findings suggest that induction of an APOBEC3-mediated antiviral response during HPV infection may inadvertently contribute to cancer mutagenesis and virus evolution. Here, we discuss current understanding of APOBEC3A and APOBEC3B biology in HPV restriction, evolution, and associated cancer mutagenesis.
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69
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Yang B, Li X, Lei L, Chen J. APOBEC: From mutator to editor. J Genet Genomics 2017; 44:423-437. [PMID: 28964683 DOI: 10.1016/j.jgg.2017.04.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Abstract
APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) are a family of cytidine deaminases that prefer single-stranded nucleic acids as substrates. Besides their physiological functions, APOBEC family members have been found to cause hypermutations of cancer genomes, which could be correlated with cancer development and poor prognosis. Recently, APOBEC family members have been combined with the versatile CRISPR/Cas9 system to perform targeted base editing or induce hypermutagenesis. This combination improved the CRISPR/Cas9-mediated gene editing at single-base precision, greatly enhancing its usefulness. Here, we review the physiological functions and structural characteristics of APOBEC family members and their roles as endogenous mutators that contribute to hypermutations during carcinogenesis. We also review the various iterations of the APOBEC-CRISPR/Cas9 gene-editing tools, pointing out their features and limitations as well as the possibilities for future developments.
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Affiliation(s)
- Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Xiaosa Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Liqun Lei
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jia Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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Klonowska K, Kluzniak W, Rusak B, Jakubowska A, Ratajska M, Krawczynska N, Vasilevska D, Czubak K, Wojciechowska M, Cybulski C, Lubinski J, Kozlowski P. The 30 kb deletion in the APOBEC3 cluster decreases APOBEC3A and APOBEC3B expression and creates a transcriptionally active hybrid gene but does not associate with breast cancer in the European population. Oncotarget 2017; 8:76357-76374. [PMID: 29100317 PMCID: PMC5652711 DOI: 10.18632/oncotarget.19400] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/10/2017] [Indexed: 02/06/2023] Open
Abstract
APOBEC3B, in addition to other members of the APOBEC3 gene family, has recently been intensively studied due to its identification as a gene whose activation in cancer is responsible for a specific pattern of massively occurring somatic mutations. It was recently shown that a common large deletion in the APOBEC3 cluster (the APOBEC3B deletion) may increase the risk of breast cancer. However, conflicting evidence regarding this association was also reported. In the first step of our study, using different approaches, including an in-house designed multiplex ligation-dependent probe amplification assay, we analyzed the structure of the deletion and showed that although the breakpoints are located in highly homologous regions, which may generate recurrent occurrence of similar but not identical deletions, there is no sign of deletion heterogeneity. This knowledge allowed us to distinguish transcripts of all affected genes, including the highly homologous canonical APOBEC3A and APOBEC3B, and the hybrid APOBEC3A/APOBEC3B gene. We unambiguously confirmed the presence of the hybrid transcript and showed that the APOBEC3B deletion negatively correlates with APOBEC3A and APOBEC3B expression and positively correlates with APOBEC3A/APOBEC3B expression, whose mRNA level is >10-fold and >1500-fold lower than the level of APOBEC3A and APOBEC3B, respectively. In the next step, we performed a large-scale association study in three different cohorts (2972 cases and 3682 controls) and showed no association of the deletion with breast cancer, familial breast cancer or ovarian cancer. Further, we conducted a meta-analysis that confirmed the lack of the association of the deletion with breast cancer in non-Asian populations.
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Affiliation(s)
- Katarzyna Klonowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wojciech Kluzniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Bogna Rusak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Natalia Krawczynska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Danuta Vasilevska
- Department of Gynecology, Centre of Obstetrics and Gynecology, Vilnius University Hospital Santariskiu Klinikos, Vilnius, Lithuania
| | - Karol Czubak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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71
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Chen Z, Eggerman TL, Bocharov AV, Baranova IN, Vishnyakova TG, Kurlander R, Patterson AP. Heat shock proteins stimulate APOBEC-3-mediated cytidine deamination in the hepatitis B virus. J Biol Chem 2017. [PMID: 28637869 DOI: 10.1074/jbc.m116.760637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic subunit 3 (APOBEC-3) enzymes are cytidine deaminases that are broadly and constitutively expressed. They are often up-regulated during carcinogenesis and candidate genes for causing the major single-base substitution in cancer-associated DNA mutations. Moreover, APOBEC-3s are involved in host innate immunity against many viruses. However, how APOBEC-3 mutational activity is regulated in normal and pathological conditions remains largely unknown. Heat shock protein levels are often elevated in both carcinogenesis and viral infection and are associated with DNA mutations. Here, using mutational analyses of hepatitis B virus (HBV), we found that Hsp90 stimulates deamination activity of APOBEC-3G (A3G), A3B, and A3C during co-expression in human liver HepG2 cells. Hsp90 directly stimulated A3G deamination activity when the purified proteins were used in in vitro reactions. Hsp40, -60, and -70 also had variable stimulatory effects in the cellular assay, but not in vitro Sequencing analyses further demonstrated that Hsp90 increased both A3G cytosine mutation efficiency on HBV DNA and total HBV mutation frequency. In addition, Hsp90 shifted A3G's cytosine region selection in HBV DNA and increased A3G's 5' nucleoside preference for deoxycytidine (5'-CC). Furthermore, the Hsp90 inhibitor 17-N-allylamino-17-demethoxygeldanamycin dose dependently inhibited A3G and A3B mutational activity on HBV viral DNA. Hsp90 knockdown by siRNA or by Hsp90 active-site mutation also decreased A3G activity. These results indicate that heat shock proteins, in particular Hsp90, stimulate APOBEC-3-mediated DNA deamination activity, suggesting a potential physiological role in carcinogenesis and viral innate immunity.
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Affiliation(s)
- Zhigang Chen
- From the Department of Laboratory Medicine, Clinical Center
| | - Thomas L Eggerman
- From the Department of Laboratory Medicine, Clinical Center.,the Division of Diabetes, Endocrinology, and Metabolic Diseases, NIDDK, and
| | | | | | | | | | - Amy P Patterson
- From the Department of Laboratory Medicine, Clinical Center, .,NHLBI, National Institutes of Health, Bethesda, Maryland 20892
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72
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Zou J, Wang C, Ma X, Wang E, Peng G. APOBEC3B, a molecular driver of mutagenesis in human cancers. Cell Biosci 2017; 7:29. [PMID: 28572915 PMCID: PMC5450379 DOI: 10.1186/s13578-017-0156-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023] Open
Abstract
Human cancers results in large part from the accumulation of multiple mutations. The progression of premalignant cells is an evolutionary process in which mutations provide the fundamental driving force for genetic diversity. The increased mutation rate in premalignant cells allows selection for increased proliferation and survival and ultimately leads to invasion, metastasis, recurrence, and therapeutic resistance. Therefore, it is important to understand the molecular determinants of the mutational processes. Recent genome-wide sequencing data showed that apolipoprotein B mRNA editing catalytic polypeptide-like 3B (APOBEC3B) is a key molecular driver inducing mutations in multiple human cancers. APOBEC3B, a DNA cytosine deaminase, is overexpressed in a wide spectrum of human cancers. Its overexpression and aberrant activation lead to unexpected clusters of mutations in the majority of cancers. This phenomenon of clustered mutations, termed kataegis (from the Greek word for showers), forms unique mutation signatures. In this review, we will discuss the biological function of APOBEC3B, its tumorigenic role in promoting mutational processes in cancer development and the clinical potential to develop novel therapeutics by targeting APOBEC3B.
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Affiliation(s)
- Jun Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Chen Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Edward Wang
- OncoMed Pharmaceuticals, 800 Chesapeake Dr., Redwood City, CA 94063 USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030 USA
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73
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Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res 2017; 77:1510-1541. [PMID: 28373404 PMCID: PMC6681830 DOI: 10.1158/0008-5472.can-16-2346] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.
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Affiliation(s)
- Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ludmil Alexandrov
- Theoretical Division, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Rafael Bejar
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Madhav Dhodapkar
- Department of Hematology and Immunology, Yale Cancer Center, New Haven, Connecticut
| | - Neil E Kay
- Department of Hematology, Mayo Clinic Hospital, Rochester, Minnesota
| | - Esteban Braggio
- Department of Hematology, Mayo Clinic Hospital, Phoenix, Arizona
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah A Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Timothy R Rebbeck
- Division of Hematology and Oncology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor E Velculescu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Mary L Disis
- Department of Medicine, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott M Lippman
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California.
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Shi K, Carpenter M, Banerjee S, Shaban N, Kurahashi K, Salamango D, McCann J, Starrett G, Duffy J, Demir Ö, Amaro R, Harki D, Harris R, Aihara H. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol 2017; 24:131-139. [PMID: 27991903 PMCID: PMC5296220 DOI: 10.1038/nsmb.3344] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022]
Abstract
APOBEC-catalyzed cytosine-to-uracil deamination of single-stranded DNA (ssDNA) has beneficial functions in immunity and detrimental effects in cancer. APOBEC enzymes have intrinsic dinucleotide specificities that impart hallmark mutation signatures. Although numerous structures have been solved, mechanisms for global ssDNA recognition and local target-sequence selection remain unclear. Here we report crystal structures of human APOBEC3A and a chimera of human APOBEC3B and APOBEC3A bound to ssDNA at 3.1-Å and 1.7-Å resolution, respectively. These structures reveal a U-shaped DNA conformation, with the specificity-conferring -1 thymine flipped out and the target cytosine inserted deep into the zinc-coordinating active site pocket. The -1 thymine base fits into a groove between flexible loops and makes direct hydrogen bonds with the protein, accounting for the strong 5'-TC preference. These findings explain both conserved and unique properties among APOBEC family members, and they provide a basis for the rational design of inhibitors to impede the evolvability of viruses and tumors.
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Affiliation(s)
- K. Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - M.A. Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - S. Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, USA, 60439
| | - N.M. Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - K. Kurahashi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - D.J. Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - J.L. McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - G.J. Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - J.V. Duffy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Ö. Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - R.E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - D.A. Harki
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - R.S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - H. Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
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75
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Sieuwerts AM, Schrijver WAME, Dalm SU, de Weerd V, Moelans CB, ter Hoeve N, van Diest PJ, Martens JWM, van Deurzen CHM. Progressive APOBEC3B mRNA expression in distant breast cancer metastases. PLoS One 2017; 12:e0171343. [PMID: 28141868 PMCID: PMC5283735 DOI: 10.1371/journal.pone.0171343] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/19/2017] [Indexed: 02/07/2023] Open
Abstract
Background APOBEC3B was recently identified as a gain-of-function enzymatic source of mutagenesis, which may offer novel therapeutic options with molecules that specifically target this enzyme. In primary breast cancer, APOBEC3B mRNA is deregulated in a substantial proportion of cases and its expression is associated with poor prognosis. However, its expression in breast cancer metastases, which are the main causes of breast cancer-related death, remained to be elucidated. Patients and methods RNA was isolated from 55 primary breast cancers and paired metastases, including regional lymph node (N = 20) and distant metastases (N = 35). APOBEC3B mRNA levels were measured by RT-qPCR. Expression levels of the primary tumors and corresponding metastases were compared, including subgroup analysis by estrogen receptor (ER/ESR1) status. Results Overall, APOBEC3B mRNA levels of distant metastases were significantly higher as compared to the corresponding primary breast tumor (P = 0.0015), an effect that was not seen for loco-regional lymph node metastases (P = 0.23). Subgroup analysis by ER-status showed that increased APOBEC3B levels in distant metastases were restricted to metastases arising from ER-positive primary breast cancers (P = 0.002). However, regarding ER-negative primary tumors, only loco-regional lymph node metastases showed increased APOBEC3B expression when compared to the corresponding primary tumor (P = 0.028). Conclusion APOBEC3B mRNA levels are significantly higher in breast cancer metastases as compared to the corresponding ER-positive primary tumors. This suggests a potential role for APOBEC3B in luminal breast cancer progression, and consequently, a promising role for anti-APOBEC3B therapies in advanced stages of this frequent form of breast cancer.
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Affiliation(s)
- Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
- Cancer Genomics Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
- * E-mail:
| | | | - Simone U. Dalm
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
| | - Cathy B. Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Natalie ter Hoeve
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul J. van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
- Cancer Genomics Center, Erasmus MC Cancer Institute, Erasmus MC, Rotterdam, The Netherlands
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76
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Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity. Genes (Basel) 2017; 8:genes8010046. [PMID: 28117753 PMCID: PMC5295039 DOI: 10.3390/genes8010046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.
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77
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Greil R, Hutterer E, Hartmann TN, Pleyer L. Reactivation of dormant anti-tumor immunity - a clinical perspective of therapeutic immune checkpoint modulation. Cell Commun Signal 2017; 15:5. [PMID: 28100240 PMCID: PMC5244547 DOI: 10.1186/s12964-016-0155-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/06/2016] [Indexed: 12/17/2022] Open
Abstract
In favor of their outgrowth, cancer cells must resist immune surveillance and edit the immune response. Cancer immunoediting is characterized by fundamental changes in the cellular composition and the inflammatory cytokine profiles in the microenvironment of the primary tumor and metastatic niches, with an ever increasing complexity of interactions between tumor cells and the immune system. Recent data suggest that genetic instability and immunoediting are not necessarily disparate processes. Increasing mutational load may be associated with multiple neoepitopes expressed by the tumor cells and thus increased chances for the immune system to recognize and combat these cells. At the same time the immune system is more and more suppressed and exhausted by this process. Consequently, immune checkpoint modulation may have the potential to be most successful in genetically highly altered and usually extremely unfavorable types of cancer. Moreover, the fact that epitopes recognized by the immune system are preferentially encoded by passenger gene mutations opens windows of synergy in targeting cancer-specific signaling pathways by small molecules simultaneously with antibodies modifying T-cell activation or exhaustion. This review covers some aspects of the current understanding of the immunological basis necessary to understand the rapidly developing therapeutic endeavours in cancer treatment, the clinical achievements made, and raises some burning questions for translational research in this field.
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Affiliation(s)
- Richard Greil
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria. .,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria. .,Arbeitsgemeinschaft Medikamentöse Tumortherapie (AGMT) Study Group, Salzburg, Austria. .,Cancer Cluster Salzburg (CCS), Salzburg, Austria.
| | - Evelyn Hutterer
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria.,Cancer Cluster Salzburg (CCS), Salzburg, Austria
| | - Tanja Nicole Hartmann
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria.,Cancer Cluster Salzburg (CCS), Salzburg, Austria
| | - Lisa Pleyer
- Third Medical Department with Hematology, Medical Oncology, Hemostaseology, Infectious Disease and Rheumatology, Oncologic Center, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.,Salzburg Cancer Research Institute (SCRI) - Laboratory for Immunological and Molecular Cancer Research (LIMCR), Salzburg, Austria.,Arbeitsgemeinschaft Medikamentöse Tumortherapie (AGMT) Study Group, Salzburg, Austria.,Cancer Cluster Salzburg (CCS), Salzburg, Austria
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78
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Radmanesh H, Spethmann T, Enßen J, Schürmann P, Bhuju S, Geffers R, Antonenkova N, Khusnutdinova E, Sadr-Nabavi A, Shandiz FH, Park-Simon TW, Hillemanns P, Christiansen H, Bogdanova N, Dörk T. Assessment of an APOBEC3B truncating mutation, c.783delG, in patients with breast cancer. Breast Cancer Res Treat 2017; 162:31-37. [PMID: 28062980 DOI: 10.1007/s10549-016-4100-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/30/2016] [Indexed: 12/30/2022]
Abstract
PURPOSE APOBEC3B belongs to the family of DNA-editing enzymes. A copy number variant targeting the genomic APOBEC3A-APOBEC3B locus has a significant impact on breast cancer risk, but the relative contribution of APOBEC3B is uncertain. In this study, we investigate a loss-of-function mutation that selectively targets APOBEC3B, for its association with breast cancer risk. METHODS We performed exome sequencing on genomic DNA samples of 6 Byelorussian patients with familial breast cancer. We then studied through mutation-specific genotyping four hospital-based breast cancer case-control series from Belarus, Russia, Germany, and Iran, respectively, comprising a total of 3070 breast cancer patients and 2878 healthy females. Results were evaluated using fixed-effects meta-analyses. RESULTS Exome sequencing uncovered a frameshift mutation, APOBEC3B*c.783delG, that was recurrent in the study populations. Subsequent genotyping identified this mutation in 23 additional breast cancer cases and 9 healthy female controls, with an adjusted Odds Ratio 2.29 (95% CI 1.04; 5.03, P = 0.04) in the combined analysis. There was an enrichment of the c.783delG mutation in patients with breast cancer diagnosed below 50 years of age (OR 3.22, 95% CI 1.37; 7.56, P = 0.007). CONCLUSIONS APOBEC3B*c.783delG showed evidence of modest association with breast cancer and seemed to contribute to earlier onset of the disease. These results may need to be reconciled with proposals to consider APOBEC3B as a possible therapeutic target in breast cancer.
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Affiliation(s)
- Hoda Radmanesh
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Tessa Spethmann
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Julia Enßen
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Sabin Bhuju
- Genome Analytics Unit, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Robert Geffers
- Genome Analytics Unit, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Natalia Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Science Center, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Ariane Sadr-Nabavi
- Medical Genetic Research Center (MGRC), School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Molecular Medicine Research Group, Academic Centers for EducationCulture and Research (ACECR), Khorasan Basavi Branch, Mashhad, Iran.,Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Homaei Shandiz
- Radiation Oncology Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tjoung-Won Park-Simon
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Hans Christiansen
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Natalia Bogdanova
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany.
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79
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Zacksenhaus E, Liu J, Jiang Z, Yao Y, Xia L, Shrestha M, Ben-David Y. Transcription Factors in Breast Cancer—Lessons From Recent Genomic Analyses and Therapeutic Implications. CHROMATIN PROTEINS AND TRANSCRIPTION FACTORS AS THERAPEUTIC TARGETS 2017; 107:223-273. [DOI: 10.1016/bs.apcsb.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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80
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Tokunaga E, Yamashita N, Tanaka K, Inoue Y, Akiyoshi S, Saeki H, Oki E, Kitao H, Maehara Y. Expression of APOBEC3B mRNA in Primary Breast Cancer of Japanese Women. PLoS One 2016; 11:e0168090. [PMID: 27977754 PMCID: PMC5158016 DOI: 10.1371/journal.pone.0168090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/25/2016] [Indexed: 12/19/2022] Open
Abstract
Recent studies have identified the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3B (APOBEC3B) as a source of mutations in various malignancies. APOBEC3B is overexpressed in several human cancer types, including breast cancer. In this study, we analyzed APOBEC3B mRNA expression in 305 primary breast cancers of Japanese women using quantitative reverse transcription-PCR, and investigated the relationships between the APOBEC3B mRNA expression and clinicopathological characteristics, prognosis, and TP53 mutations. The expression of APOBEC3B mRNA was detected in 277 tumors and not detected in 28 tumors. High APOBEC3B mRNA expression was significantly correlated with ER- and PR-negativity, high grade and high Ki67 index. The APOBEC3B mRNA expression was highest in the triple-negative and lowest in the hormone receptor-positive/HER2-negative subtypes. The TP53 gene was more frequently mutated in the tumors with high APOBEC3B mRNA expression. High APOBEC3B mRNA expression was significantly associated with poor recurrence-free survival in all cases and the ER-positive cases. These findings were almost consistent with the previous reports from the Western countries. In conclusion, high APOBEC3B mRNA expression was related to the aggressive phenotypes of breast cancer, high frequency of TP53 mutation and poor prognosis, especially in ER-positive tumors.
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Affiliation(s)
- Eriko Tokunaga
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
- * E-mail: ,
| | - Nami Yamashita
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Kimihiro Tanaka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Yuka Inoue
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Sayuri Akiyoshi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hiroshi Saeki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hiroyuki Kitao
- Department of Molecular Oncology, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
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81
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Middlebrooks CD, Banday AR, Matsuda K, Udquim KI, Onabajo OO, Paquin A, Figueroa JD, Zhu B, Koutros S, Kubo M, Shuin T, Freedman ND, Kogevinas M, Malats N, Chanock SJ, Garcia-Closas M, Silverman DT, Rothman N, Prokunina-Olsson L. Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. Nat Genet 2016; 48:1330-1338. [PMID: 27643540 PMCID: PMC6583788 DOI: 10.1038/ng.3670] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/18/2016] [Indexed: 12/14/2022]
Abstract
High rates of APOBEC-signature mutations are found in many tumors, but factors affecting this mutation pattern are not well understood. Here we explored the contribution of two common germline variants in the APOBEC3 region. SNP rs1014971 was associated with bladder cancer risk, increased APOBEC3B expression, and enrichment with APOBEC-signature mutations in bladder tumors. In contrast, a 30-kb deletion that eliminates APOBEC3B and creates an APOBEC3A-APOBEC3B chimera was not important in bladder cancer, whereas it was associated with breast cancer risk and enrichment with APOBEC-signature mutations in breast tumors. In vitro, APOBEC3B expression was predominantly induced by treatment with a DNA-damaging drug in bladder cancer cell lines, and APOBEC3A expression was induced as part of the antiviral interferon-stimulated response in breast cancer cell lines. These findings suggest a tissue-specific role of environmental oncogenic triggers, particularly in individuals with germline APOBEC3 risk variants.
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Affiliation(s)
- Candace D. Middlebrooks
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - A. Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Krizia-Ivana Udquim
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Olusegun O. Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Ashley Paquin
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Jonine D. Figueroa
- Usher Institute of Population Health Sciences and Informatics, Medical School, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Michiaki Kubo
- Center for Integrative Medical Science, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Taro Shuin
- Department of Urology, School of Medicine, Kochi University, Koichi, Japan
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Manolis Kogevinas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Epidemiologia y Salud Pública (CIBERESP), Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - Nuria Malats
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | | | - Debra T. Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
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82
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Law EK, Sieuwerts AM, LaPara K, Leonard B, Starrett GJ, Molan AM, Temiz NA, Vogel RI, Meijer-van Gelder ME, Sweep FCGJ, Span PN, Foekens JA, Martens JWM, Yee D, Harris RS. The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer. SCIENCE ADVANCES 2016; 2:e1601737. [PMID: 27730215 PMCID: PMC5055383 DOI: 10.1126/sciadv.1601737] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/31/2016] [Indexed: 05/27/2023]
Abstract
Breast tumors often display extreme genetic heterogeneity characterized by hundreds of gross chromosomal aberrations and tens of thousands of somatic mutations. Tumor evolution is thought to be ongoing and driven by multiple mutagenic processes. A major outstanding question is whether primary tumors have preexisting mutations for therapy resistance or whether additional DNA damage and mutagenesis are necessary. Drug resistance is a key measure of tumor evolvability. If a resistance mutation preexists at the time of primary tumor presentation, then the intended therapy is likely to fail. However, if resistance does not preexist, then ongoing mutational processes still have the potential to undermine therapeutic efficacy. The antiviral enzyme APOBEC3B (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3B) preferentially deaminates DNA C-to-U, which results in signature C-to-T and C-to-G mutations commonly observed in breast tumors. We use clinical data and xenograft experiments to ask whether APOBEC3B contributes to ongoing breast tumor evolution and resistance to the selective estrogen receptor modulator, tamoxifen. First, APOBEC3B levels in primary estrogen receptor-positive (ER+) breast tumors inversely correlate with the clinical benefit of tamoxifen in the treatment of metastatic ER+ disease. Second, APOBEC3B depletion in an ER+ breast cancer cell line results in prolonged tamoxifen responses in murine xenograft experiments. Third, APOBEC3B overexpression accelerates the development of tamoxifen resistance in murine xenograft experiments by a mechanism that requires the enzyme's catalytic activity. These studies combine to indicate that APOBEC3B promotes drug resistance in breast cancer and that inhibiting APOBEC3B-dependent tumor evolvability may be an effective strategy to improve efficacies of targeted cancer therapies.
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Affiliation(s)
- Emily K. Law
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anieta M. Sieuwerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - Kelly LaPara
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brandon Leonard
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabriel J. Starrett
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amy M. Molan
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rachel Isaksson Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Marion E. Meijer-van Gelder
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - Fred C. G. J. Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Paul N. Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - John A. Foekens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - John W. M. Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S. Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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83
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Cescon DW, Haibe-Kains B. DNA replication stress: a source of APOBEC3B expression in breast cancer. Genome Biol 2016; 17:202. [PMID: 27716362 PMCID: PMC5045630 DOI: 10.1186/s13059-016-1069-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
APOBEC cytidine deaminases have been implicated as major contributors to the mutation burden in many cancers on the basis of their mutational signature. A new experimental study sheds light on the inciting factors, linking APOBEC3B expression to oncogene- and drug-induced replication stress.
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Affiliation(s)
- David W Cescon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. .,Campbell Family Institute for Breast Cancer Research, Toronto, Canada. .,Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Canada.
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,Department of Computer Science, University of Toronto, Toronto, ON, Canada. .,Ontario Institute of Cancer Research, Toronto, ON, Canada.
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84
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Starrett GJ, Luengas EM, McCann JL, Ebrahimi D, Temiz NA, Love RP, Feng Y, Adolph MB, Chelico L, Law EK, Carpenter MA, Harris RS. The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis. Nat Commun 2016; 7:12918. [PMID: 27650891 PMCID: PMC5036005 DOI: 10.1038/ncomms12918] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/16/2016] [Indexed: 12/17/2022] Open
Abstract
Cytosine mutations within TCA/T motifs are common in cancer. A likely cause is the DNA cytosine deaminase APOBEC3B (A3B). However, A3B-null breast tumours still have this mutational bias. Here we show that APOBEC3H haplotype I (A3H-I) provides a likely solution to this paradox. A3B-null tumours with this mutational bias have at least one copy of A3H-I despite little genetic linkage between these genes. Although deemed inactive previously, A3H-I has robust activity in biochemical and cellular assays, similar to A3H-II after compensation for lower protein expression levels. Gly105 in A3H-I (versus Arg105 in A3H-II) results in lower protein expression levels and increased nuclear localization, providing a mechanism for accessing genomic DNA. A3H-I also associates with clonal TCA/T-biased mutations in lung adenocarcinoma suggesting this enzyme makes broader contributions to cancer mutagenesis. These studies combine to suggest that A3B and A3H-I, together, explain the bulk of ‘APOBEC signature' mutations in cancer. The APOBEC family of enzymes are cytidine deaminases with APOBEC3A and APOBEC3B thought to contribute to DNA damage signatures detected in cancer genomes. Here, the authors demonstrate an unappreciated role for APOBEC3H haplotype I in the generation of DNA damage in breast cancer.
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Affiliation(s)
- Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Elizabeth M Luengas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Diako Ebrahimi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nuri A Temiz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Robin P Love
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Yuqing Feng
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Madison B Adolph
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Linda Chelico
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
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85
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Land AM, Wang J, Law EK, Aberle R, Kirmaier A, Krupp A, Johnson WE, Harris RS. Degradation of the cancer genomic DNA deaminase APOBEC3B by SIV Vif. Oncotarget 2016; 6:39969-79. [PMID: 26544511 PMCID: PMC4741873 DOI: 10.18632/oncotarget.5483] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 10/19/2015] [Indexed: 12/17/2022] Open
Abstract
APOBEC3B is a newly identified source of mutation in many cancers, including breast, head/neck, lung, bladder, cervical, and ovarian. APOBEC3B is a member of the APOBEC3 family of enzymes that deaminate DNA cytosine to produce the pro-mutagenic lesion, uracil. Several APOBEC3 family members function to restrict virus replication. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H combine to restrict HIV-1 in human lymphocytes. HIV-1 counteracts these APOBEC3s with the viral protein Vif, which targets the relevant APOBEC3s for proteasomal degradation. While APOBEC3B does not restrict HIV-1 and is not targeted by HIV-1 Vif in CD4-positive T cells, we asked whether related lentiviral Vif proteins could degrade APOBEC3B. Interestingly, several SIV Vif proteins are capable of promoting APOBEC3B degradation, with SIVmac239 Vif proving the most potent. This likely occurs through the canonical polyubiquitination mechanism as APOBEC3B protein levels are restored by MG132 treatment and by altering a conserved E3 ligase-binding motif. We further show that SIVmac239 Vif can prevent APOBEC3B mediated geno/cytotoxicity and degrade endogenous APOBEC3B in several cancer cell lines. Our data indicate that the APOBEC3B degradation potential of SIV Vif is an effective tool for neutralizing the cancer genomic DNA deaminase APOBEC3B. Further optimization of this natural APOBEC3 antagonist may benefit cancer therapy.
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Affiliation(s)
- Allison M Land
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.,Present address: Department of Biological Sciences, Minnesota State University Mankato, Mankato, Minnesota, USA
| | - Jiayi Wang
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ryan Aberle
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrea Kirmaier
- Department of Biology, Boston College, Boston, Massachusetts, USA
| | - Annabel Krupp
- Department of Biology, Boston College, Boston, Massachusetts, USA.,Present address: Biogen Idec, Cambridge, Massachusetts, USA
| | - Welkin E Johnson
- Department of Biology, Boston College, Boston, Massachusetts, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA
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86
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Abstract
Prevention is an essential component of cancer eradication. Next-generation sequencing of cancer genomes and epigenomes has defined large numbers of driver mutations and molecular subgroups, leading to therapeutic advances. By comparison, there is a relative paucity of such knowledge in premalignant neoplasia, which inherently limits the potential to develop precision prevention strategies. Studies on the interplay between germ-line and somatic events have elucidated genetic processes underlying premalignant progression and preventive targets. Emerging data hint at the immune system's ability to intercept premalignancy and prevent cancer. Genetically engineered mouse models have identified mechanisms by which genetic drivers and other somatic alterations recruit inflammatory cells and induce changes in normal cells to create and interact with the premalignant tumor microenvironment to promote oncogenesis and immune evasion. These studies are currently limited to only a few lesion types and patients. In this Perspective, we advocate a large-scale collaborative effort to systematically map the biology of premalignancy and the surrounding cellular response. By bringing together scientists from diverse disciplines (e.g., biochemistry, omics, and computational biology; microbiology, immunology, and medical genetics; engineering, imaging, and synthetic chemistry; and implementation science), we can drive a concerted effort focused on cancer vaccines to reprogram the immune response to prevent, detect, and reject premalignancy. Lynch syndrome, clonal hematopoiesis, and cervical intraepithelial neoplasia which also serve as models for inherited syndromes, blood, and viral premalignancies, are ideal scenarios in which to launch this initiative.
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87
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Maruyama W, Shirakawa K, Matsui H, Matsumoto T, Yamazaki H, Sarca AD, Kazuma Y, Kobayashi M, Shindo K, Takaori-Kondo A. Classical NF-κB pathway is responsible for APOBEC3B expression in cancer cells. Biochem Biophys Res Commun 2016; 478:1466-71. [PMID: 27577680 DOI: 10.1016/j.bbrc.2016.08.148] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/26/2016] [Indexed: 01/05/2023]
Abstract
APOBEC3B (A3B) is a DNA cytosine deaminase and catalyzes cytosine deamination, resulting in mutations in genomic DNA. A3B is aberrantly expressed in a variety of cancers and considered to be a source of genomic mutations that contribute to cancer progression and metastasis. However, the mechanisms through which A3B expression is dysregulated in cancer cells are not fully elucidated. Here we report that the classical NF-κB pathway plays a crucial role in the transcriptional regulation of A3B in various cancer cells, including lymphoid malignancies. PMA, a strong activator of PKC, induces A3B at both mRNA and protein levels in cancer cell lines, and specific inhibitors of both PKC and IKK downregulate A3B expression. Using luciferase reporter and EMSA assays, we identify 3 NF-κΒ binding sites in the A3B promoter and reveal that NF-κB p65/p50 and p65/c-Rel heterodimers are important for A3B transcription. These results suggest that the classical NF-κB pathway is responsible for activation of A3B mRNA expression and further imply that inhibition of PKC and IKK might augment cancer treatment by reducing cancer progression and metastasis through downregulation of A3B expression.
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Affiliation(s)
- Wataru Maruyama
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Matsui
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadahiko Matsumoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Yamazaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Anamaria D Sarca
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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88
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Liu J, Sieuwerts AM, Look MP, van der Vlugt-Daane M, Meijer-van Gelder ME, Foekens JA, Hollestelle A, Martens JWM. The 29.5 kb APOBEC3B Deletion Polymorphism Is Not Associated with Clinical Outcome of Breast Cancer. PLoS One 2016; 11:e0161731. [PMID: 27552096 PMCID: PMC4995039 DOI: 10.1371/journal.pone.0161731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/10/2016] [Indexed: 12/25/2022] Open
Abstract
Increased APOBEC3B mRNA levels are associated with a hypermutator phenotype and poor prognosis in ER-positive breast cancer patients. In addition, a 29.5 kb deletion polymorphism of APOBEC3B, resulting in an APOBEC3A-B hybrid transcript, has been associated with an increased breast cancer risk and the hypermutator phenotype. Here we evaluated whether the APOBEC3B deletion polymorphism also associates with clinical outcome of breast cancer. Copy number analysis was performed by quantitative PCR (qPCR) in primary tumors of 1,756 Dutch breast cancer patients. The APOBEC3B deletion was found in 187 patients of whom 16 carried a two-copy deletion and 171 carried a one-copy deletion. The prognostic value of the APOBEC3B deletion for the natural course of the disease was evaluated among 1,076 lymph-node negative (LNN) patients who did not receive adjuvant systemic treatment. No association was found between APOBEC3B copy number values and the length of metastasis-free survival (MFS; hazard ratio (HR) = 1.00, 95% confidence interval (CI) = 0.90–1.11, P = 0.96). Subgroup analysis by ER status also did not reveal an association between APOBEC3B copy number values and the length of MFS. The predictive value of the APOBEC3B deletion was assessed among 329 ER-positive breast cancer patients who received tamoxifen as the first-line therapy for recurrent disease and 226 breast cancer patients who received first-line chemotherapy for recurrent disease. No association between APOBEC3B copy number values and the overall response rate (ORR) to either tamoxifen (odds ratio (OR) = 0.88, 95% CI = 0.69–1.13, P = 0.31) or chemotherapy (OR = 0.97, 95% CI = 0.71–1.33, P = 0.87) was found. Thus, in contrast to APOBEC3B mRNA levels, the APOBEC3B deletion polymorphism has neither a prognostic nor a predictive value for breast cancer patients. Although a correlation exists between APOBEC3B copy number and mRNA expression, it is relatively weak. This suggests that other mechanisms exist that may affect and therefore determine the prognostic value of APOBEC3B mRNA levels.
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Affiliation(s)
- Jingjing Liu
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
- Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Maxime P. Look
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Michelle van der Vlugt-Daane
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion E. Meijer-van Gelder
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John A. Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
- * E-mail:
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
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89
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Austin R, Smyth MJ, Lane SW. Harnessing the immune system in acute myeloid leukaemia. Crit Rev Oncol Hematol 2016; 103:62-77. [DOI: 10.1016/j.critrevonc.2016.04.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 02/13/2016] [Accepted: 04/28/2016] [Indexed: 12/13/2022] Open
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90
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Wen WX, Soo JSS, Kwan PY, Hong E, Khang TF, Mariapun S, Lee CSM, Hasan SN, Rajadurai P, Yip CH, Mohd Taib NA, Teo SH. Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation. Breast Cancer Res 2016; 18:56. [PMID: 27233495 PMCID: PMC4884363 DOI: 10.1186/s13058-016-0717-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/08/2016] [Indexed: 01/05/2023] Open
Abstract
Background APOBEC3B is a cytosine deaminase implicated in immune response to viral infection, cancer predisposition and carcinogenesis. Germline APOBEC3B deletion is more common in East Asian women and confers a modest risk to breast cancer in both East Asian and Caucasian women. Analysis of tumour samples from women of European descent has shown that germline APOBEC3B deletion is associated with an increased propensity to develop somatic mutations and with an enrichment for immune response-related gene sets. However, this has not been examined in Asian tumour samples, where population differences in genetic and dietary factors may have an impact on the immune system. Methods In this study, we determined the prevalence of germline APOBEC3B deletion and its association with breast cancer risk in a cross-sectional hospital-based Asian multi-ethnic cohort of 1451 cases and 1442 controls from Malaysia. We compared gene expression profiles of breast cancers arising from APOBEC3B deletion carriers and non-carriers using microarray analyses. Finally, we characterised the overall abundance of tumour-infiltrating immune cells in breast cancers from TCGA and METABRIC using ESTIMATE and relative frequency of 22 immune cell subsets in breast cancers from METABRIC using CIBERSORT. Results The minor allelic frequency of APOBEC3B deletion was estimated to be 0.35, 0.42 and 0.16 in female populations of Chinese, Malay and Indian descent, respectively, and that germline APOBEC3B deletion was associated with breast cancer risk with odds ratios of 1.23 (95 % CI: [1.05, 1.44]) for one-copy deletion and 1.38 (95 % CI: [1.10, 1.74]) for two-copy deletion compared to women with no deletion. Germline APOBEC3B deletion was not associated with any clinicopathologic features or the expression of any APOBEC family members but was associated with immune response-related gene sets (FDR q values < 0.05). Analysis of breast cancers from METABRIC revealed breast cancers from APOBEC3B deletion carriers to have significantly higher abundance of tumour-infiltrating immune cells (P < 0.001). Conclusions Taken together, our data suggests that tumour-infiltrating immune cells may be an important feature of breast cancers arising in women with APOBEC3B germline deletion, and that this may be of particular interest in Asian women where the germline deletion is more common. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0717-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Xiong Wen
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Jaslyn Sian-Siu Soo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Pui Yoke Kwan
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Elaine Hong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Tsung Fei Khang
- Institute of Mathematical Sciences, Faculty of Science, University Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | | - Cheng Har Yip
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Sime Darby Medical Centre, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia. .,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia. .,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, Kuala Lumpur, Malaysia.
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91
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Byeon IJL, Byeon CH, Wu T, Mitra M, Singer D, Levin JG, Gronenborn AM. Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity. Biochemistry 2016; 55:2944-59. [PMID: 27163633 DOI: 10.1021/acs.biochem.6b00382] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Human APOBEC3B (A3B) is a member of the APOBEC3 (A3) family of cytidine deaminases, which function as DNA mutators and restrict viral pathogens and endogenous retrotransposons. Recently, A3B was identified as a major source of genetic heterogeneity in several human cancers. Here, we determined the solution nuclear magnetic resonance structure of the catalytically active C-terminal domain (CTD) of A3B and performed detailed analyses of its deaminase activity. The core of the structure comprises a central five-stranded β-sheet with six surrounding helices, common to all A3 proteins. The structural fold is most similar to that of A3A and A3G-CTD, with the most prominent difference being found in loop 1. The catalytic activity of A3B-CTD is ∼15-fold lower than that of A3A, although both exhibit a similar pH dependence. Interestingly, A3B-CTD with an A3A loop 1 substitution had significantly increased deaminase activity, while a single-residue change (H29R) in A3A loop 1 reduced A3A activity to the level seen with A3B-CTD. This establishes that loop 1 plays an important role in A3-catalyzed deamination by precisely positioning the deamination-targeted C into the active site. Overall, our data provide important insights into the determinants of the activities of individual A3 proteins and facilitate understanding of their biological function.
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Affiliation(s)
| | | | - Tiyun Wu
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Mithun Mitra
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Dustin Singer
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Judith G Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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92
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Akre MK, Starrett GJ, Quist JS, Temiz NA, Carpenter MA, Tutt ANJ, Grigoriadis A, Harris RS. Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B. PLoS One 2016; 11:e0155391. [PMID: 27163364 PMCID: PMC4862684 DOI: 10.1371/journal.pone.0155391] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022] Open
Abstract
Molecular, cellular, and clinical studies have combined to demonstrate a contribution from the DNA cytosine deaminase APOBEC3B (A3B) to the overall mutation load in breast, head/neck, lung, bladder, cervical, ovarian, and other cancer types. However, the complete landscape of mutations attributable to this enzyme has yet to be determined in a controlled human cell system. We report a conditional and isogenic system for A3B induction, genomic DNA deamination, and mutagenesis. Human 293-derived cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs. Cells were subjected to 10 rounds of A3B-eGFP exposure that each caused 80–90% cell death. Control pools were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. Targeted sequencing of portions of TP53 and MYC demonstrated greater mutation accumulation in the A3B-eGFP exposed pools. Clones were generated and microarray analyses were used to identify those with the greatest number of SNP alterations for whole genome sequencing. A3B-eGFP exposed clones showed global increases in C-to-T transition mutations, enrichments for cytosine mutations within A3B-preferred trinucleotide motifs, and more copy number aberrations. Surprisingly, both control and A3B-eGFP clones also elicited strong mutator phenotypes characteristic of defective mismatch repair. Despite this additional mutational process, the 293-based system characterized here still yielded a genome-wide view of A3B-catalyzed mutagenesis in human cells and a system for additional studies on the compounded effects of simultaneous mutation mechanisms in cancer cells.
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Affiliation(s)
- Monica K. Akre
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Gabriel J. Starrett
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Jelmar S. Quist
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Nuri A. Temiz
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Michael A. Carpenter
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Andrew N. J. Tutt
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, United States of America
- * E-mail:
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93
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Leonard B, Starrett GJ, Maurer MJ, Oberg AL, Van Bockstal M, Van Dorpe J, De Wever O, Helleman J, Sieuwerts AM, Berns EMJJ, Martens JWM, Anderson BD, Brown WL, Kalli KR, Kaufmann SH, Harris RS. APOBEC3G Expression Correlates with T-Cell Infiltration and Improved Clinical Outcomes in High-grade Serous Ovarian Carcinoma. Clin Cancer Res 2016; 22:4746-55. [PMID: 27016308 PMCID: PMC5026552 DOI: 10.1158/1078-0432.ccr-15-2910] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/09/2016] [Indexed: 01/05/2023]
Abstract
PURPOSE APOBEC3 DNA cytosine deaminase family members normally defend against viruses and transposons. However, deregulated APOBEC3 activity causes mutations in cancer. Because of broad expression profiles and varying mixtures of normal and cancer cells in tumors, including immune cell infiltration, it is difficult to determine where different APOBEC3s are expressed. Here, we ask whether correlations exist between APOBEC3 expression and T-cell infiltration in high-grade serous ovarian cancer (HGSOC), and assess whether these correlations have prognostic value. EXPERIMENTAL DESIGN Transcripts for APOBEC3G, APOBEC3B, and the T-cell markers, CD3D, CD4, CD8A, GZMB, PRF1, and RNF128 were quantified by RT-qPCR for a cohort of 354 HGSOC patients. Expression values were correlated with each other and clinical parameters. Two additional cohorts were used to extend HGSOC clinical results. Immunoimaging was used to colocalize APOBEC3G and the T-cell marker CD3. TCGA data extended expression analyses to additional cancer types. RESULTS A surprising positive correlation was found for expression of APOBEC3G and several T cell genes in HGSOC. Immunohistochemistry and immunofluorescent imaging showed protein colocalization in tumor-infiltrating T lymphocytes. High APOBEC3G expression correlated with improved outcomes in multiple HGSOC cohorts. TCGA data analyses revealed that expression of APOBEC3D and APOBEC3H also correlates with CD3D across multiple cancer types. CONCLUSIONS Our results identify APOBEC3G as a new candidate biomarker for tumor-infiltrating T lymphocytes and favorable prognoses for HGSOC. Our data also highlight the complexity of the tumor environment with respect to differential APOBEC family gene expression in both tumor and surrounding normal cell types. Clin Cancer Res; 22(18); 4746-55. ©2016 AACR.
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Affiliation(s)
- Brandon Leonard
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Matthew J Maurer
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Ann L Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | | | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jozien Helleman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Els M J J Berns
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Brett D Anderson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - William L Brown
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Kimberly R Kalli
- Women's Cancer Program, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Scott H Kaufmann
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, Minnesota. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota.
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94
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Yan S, He F, Gao B, Wu H, Li M, Huang L, Liang J, Wu Q, Li Y. Increased APOBEC3B Predicts Worse Outcomes in Lung Cancer: A Comprehensive Retrospective Study. J Cancer 2016; 7:618-25. [PMID: 27076842 PMCID: PMC4829547 DOI: 10.7150/jca.14030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/26/2016] [Indexed: 12/28/2022] Open
Abstract
Lung cancer ranks as the most common and lethal malignancy in America and worldwide. APOBEC3B is a newly identified DNA cytosine deaminase, which is supposed to function as a major source of DNA mutation in many different tumors. In this study, we combine the data of online databases and two hundred and twenty-one primary non-small-cell lung carcinoma (NSCLC) specimens from Sun Yat-sen University Cancer Center to investigate, for the first time, the clinical role of APOBEC3B in lung cancer. We found that the APOBEC3 expression was commonly elevated in NSCLC tissues and overexpression of APOBEC3B was correlated with unfavorable prognosis of the patients with NSCLC. Furthermore, APOBEC3B expression was associated with nodal status, TNM staging and adjuvant chemotherapy of the patients with NSCLC. Further research is warranted.
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Affiliation(s)
- Shumei Yan
- 1. State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou City, Guangdong Province, P.R. China;; 2. Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Fan He
- 3. Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bei Gao
- 4. State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou City, Guangdong Province, P.R. China
| | - Huini Wu
- 5. Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Mei Li
- 1. State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou City, Guangdong Province, P.R. China;; 2. Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Liyun Huang
- 1. State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou City, Guangdong Province, P.R. China;; 2. Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Jianzhong Liang
- 1. State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou City, Guangdong Province, P.R. China;; 2. Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Qiuliang Wu
- 1. State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou City, Guangdong Province, P.R. China;; 2. Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Yong Li
- 1. State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou City, Guangdong Province, P.R. China;; 2. Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
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95
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APOBEC3B is an enzymatic source of molecular alterations in esophageal squamous cell carcinoma. Med Oncol 2016; 33:26. [PMID: 26880326 DOI: 10.1007/s12032-016-0739-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 01/31/2016] [Indexed: 02/07/2023]
Abstract
APOBEC3B belongs to the cytidine deaminase apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC3) family of enzymes and induces C to T transitions of target DNA by cytidine deamination. Recently, several mutations in various cancers have been linked to APOBEC3B, suggesting a crucial role for this protein in carcinogenesis and cancer development. However, the significance of APOBEC3B in esophageal squamous cell carcinoma (ESCC) remains uncertain. In addition, the APOBEC3B immunoreactivity in cancer tissues is uncertain. Recently, we have demonstrated that PIK3CA mutation and the methylation level of long interspersed nucleotide element 1 (LINE-1) (a surrogate marker of global DNA methylation level) are prognostic markers and have crucial role on malignancy in ESCC patients. This study aims to clarify the impact of APOBEC3B on the clinical, pathological, and molecular features of ESCC. We evaluated APOBEC3B expression in ESCC and investigated the relationships among the immunoreactivity of APOBEC3B, clinical and pathological features, and the molecular features of ESCC (PIK3CA mutation, p53 expression, and LINE-1 methylation level). The immunoreactivity and mRNA level of APOBEC3B were significantly higher in cancer tissues than in noncancerous esophageal mucosae (P = 0.050). APOBEC3B expression was significantly correlated with PIK3CA mutation (P = 0.013), particularly with C to T transitions of PIK3CA (P = 0.041). Moreover, a high expression of APOBEC3B was significantly associated with LINE-1 hypomethylation (P = 0.027). Given the crucial roles of PIK3CA mutation and LINE-1 methylation levels, our findings might provide new insights into the biological mechanisms of ESCC tumorigenesis and progression.
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Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res 2016; 26:174-82. [PMID: 26755635 PMCID: PMC4728370 DOI: 10.1101/gr.197046.115] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022]
Abstract
APOBEC3A and APOBEC3B, cytidine deaminases of the APOBEC family, are among the main factors causing mutations in human cancers. APOBEC deaminates cytosines in single-stranded DNA (ssDNA). A fraction of the APOBEC-induced mutations occur as clusters ("kataegis") in single-stranded DNA produced during repair of double-stranded breaks (DSBs). However, the properties of the remaining 87% of nonclustered APOBEC-induced mutations, the source and the genomic distribution of the ssDNA where they occur, are largely unknown. By analyzing genomic and exomic cancer databases, we show that >33% of dispersed APOBEC-induced mutations occur on the lagging strand during DNA replication, thus unraveling the major source of ssDNA targeted by APOBEC in cancer. Although methylated cytosine is generally more mutation-prone than nonmethylated cytosine, we report that methylation reduces the rate of APOBEC-induced mutations by a factor of roughly two. Finally, we show that in cancers with extensive APOBEC-induced mutagenesis, there is almost no increase in mutation rates in late replicating regions (contrary to other cancers). Because late-replicating regions are depleted in exons, this results in a 1.3-fold higher fraction of mutations residing within exons in such cancers. This study provides novel insight into the APOBEC-induced mutagenesis and describes the peculiarity of the mutational processes in cancers with the signature of APOBEC-induced mutations.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Konstantin Y Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Georgii A Bazykin
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva, Switzerland
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97
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Wu A, Lim M. Issues to Consider in Designing Immunotherapy Clinical Trials for Glioblastoma Management. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/jct.2016.78060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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98
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Zhang Y, Delahanty R, Guo X, Zheng W, Long J. Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer. Hum Genomics 2015; 9:34. [PMID: 26682542 PMCID: PMC4684623 DOI: 10.1186/s40246-015-0056-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 12/09/2015] [Indexed: 11/23/2022] Open
Abstract
Background The human APOBEC protein family plays critical but distinct roles in host defense. Recent studies revealed that APOBECs mediate C-to-T mutagenesis in multiple cancers, including breast cancer. It is still unclear whether APOBEC gene family shows functional diversification involved in cancer mutagenesis. Results We performed an integrated analysis to characterize the functional diversification of APOBEC gene family associated with breast cancer mutagenesis relative to estrogen receptor (ER) status. Among the APOBEC family, we found that both APOBEC3B and APOBEC3C mRNA levels were significantly higher in estrogen receptor negative (ER−) subtype compared with estrogen receptor positive (ER+) subtype (P < 2.2 × 10−16 and P < 3.1 × 10−5, respectively). Epigenomic data further reflected the distinct chromatin states of APOBEC3B and APOBEC3C relative to ER status. Notably, we observed the significantly positive correlation between the APOBEC3B-mediated mutagenesis and APOBEC3B expression levels in ER+ cancers but not in ER− cancers. In contrast, we discovered the negative correlation of APOBEC3C mRNA levels with base-substitution mutations in ER− tumors. Meanwhile, we observed that breast cancers in carriers of germline deletion of APOBEC3B gene harbor similar mutation patterns, but higher mutation rates in the TCW motif (W corresponds to A or T) than cancers in non-carriers, indicating additional factors may also induce carcinogenic mutagenesis. Conclusions These results suggest that functional potential of APOBEC3B and APOBEC3C involved in cancer mutagenesis is associated with ER status. Electronic supplementary material The online version of this article (doi:10.1186/s40246-015-0056-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanfeng Zhang
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, 37203, USA. .,Present address: HudsonAlpha Institute for Biotechnology, Huntsville, 35806, USA.
| | - Ryan Delahanty
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, 37203, USA.
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, 37203, USA.
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, 37203, USA.
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, 37203, USA.
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99
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Leonard B, McCann JL, Starrett GJ, Kosyakovsky L, Luengas EM, Molan AM, Burns MB, McDougle RM, Parker PJ, Brown WL, Harris RS. The PKC/NF-κB signaling pathway induces APOBEC3B expression in multiple human cancers. Cancer Res 2015; 75:4538-47. [PMID: 26420215 PMCID: PMC4631676 DOI: 10.1158/0008-5472.can-15-2171-t] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/12/2015] [Indexed: 01/05/2023]
Abstract
Overexpression of the antiviral DNA cytosine deaminase APOBEC3B has been linked to somatic mutagenesis in many cancers. Human papillomavirus infection accounts for APOBEC3B upregulation in cervical and head/neck cancers, but the mechanisms underlying nonviral malignancies are unclear. In this study, we investigated the signal transduction pathways responsible for APOBEC3B upregulation. Activation of protein kinase C (PKC) by the diacylglycerol mimic phorbol-myristic acid resulted in specific and dose-responsive increases in APOBEC3B expression and activity, which could then be strongly suppressed by PKC or NF-κB inhibition. PKC activation caused the recruitment of RELB, but not RELA, to the APOBEC3B promoter, implicating noncanonical NF-κB signaling. Notably, PKC was required for APOBEC3B upregulation in cancer cell lines derived from multiple tumor types. By revealing how APOBEC3B is upregulated in many cancers, our findings suggest that PKC and NF-κB inhibitors may be repositioned to suppress cancer mutagenesis, dampen tumor evolution, and decrease the probability of adverse outcomes, such as drug resistance and metastasis.
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Affiliation(s)
- Brandon Leonard
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Leah Kosyakovsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Elizabeth M Luengas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Amy M Molan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Michael B Burns
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Rebecca M McDougle
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Medical School, University of Minnesota, Minneapolis, Minnesota
| | - Peter J Parker
- Protein Phosphorylation Laboratory, Francis Crick Institute, London, United Kingdom. Division of Cancer Studies, King's College London, London, United Kingdom
| | - William L Brown
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota.
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100
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The eQTL-missense polymorphisms of APOBEC3H are associated with lung cancer risk in a Han Chinese population. Sci Rep 2015; 5:14969. [PMID: 26459911 PMCID: PMC4602211 DOI: 10.1038/srep14969] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/14/2015] [Indexed: 12/15/2022] Open
Abstract
APOBEC (Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) enzymes may involve in mutagenic processes in multiple cancer types, including lung cancer. APOBEC family of cytidine deaminases induces base substitutions with a stringent TCW motif, which is widespread in multiple human cancers. We hypothesized that common missense variants in coding regions of APOBEC genes might damage the structure of proteins and modify lung cancer risk. To test this hypothesis, we systematically screened predicted deleterious polymorphisms in the exon regions of 10 APOBEC core genes (APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, APOBEC3H, and APOBEC4) and evaluated them with a case-control study including 1200 cases and 1253 controls. We found that the T allele of rs139293 in exon 2 of APOBEC3H was significantly associated with decreased risk of lung cancer (odds ratio = 0.76, 95% confidence interval: 0.63–0.91). Similar inverse association of this variant was observed in subgroups. Further study showed that the T allele of rs139293 was associated with the altered expression of APOBEC3H and APOBEC3C and that the two genes were co-expressed in both tumor and adjacent normal tissues. These results indicate that genetic variants in APOBEC3H may contribute to lung cancer susceptibility in Chinese population.
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