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Lima T, Ferreira R, Freitas M, Henrique R, Vitorino R, Fardilha M. Integration of Automatic Text Mining and Genomic and Proteomic Analysis to Unravel Prostate Cancer Biomarkers. J Proteome Res 2022; 21:447-458. [DOI: 10.1021/acs.jproteome.1c00763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tânia Lima
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
| | - Rita Ferreira
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marina Freitas
- Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP) & Porto Comprehensive Cancer Center (P.CCC), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4050-513 Porto, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
- Cardiovascular Research Centre (UnIC), Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine─iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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Meng F, Han X, Min Z, He X, Zhu S. Prognostic signatures associated with high infiltration of Tregs in bone metastatic prostate cancer. Aging (Albany NY) 2021; 13:17442-17461. [PMID: 34229299 PMCID: PMC8312432 DOI: 10.18632/aging.203234] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023]
Abstract
Metastatic cancer especially bone metastasis (BM) is the lethal end-stage of castration-resistant prostate cancer (CRPC). To understand the possible molecular mechanisms underlying the development of the distant metastasis is of potential clinical value. We sought to identify differentially expressed genes between patient-matched primary and bone metastatic CRPC tumors. Functional enrichment, protein-protein interaction networks, and survival analysis of DEGs were performed. DEGs with a prognostic value considered as candidate genes were evaluated, followed by genetic analysis of tumor infiltrating immune cells based on Wilcoxon test and immunofluorescence identification. Expression profiles analysis showed that 381 overlapping genes were screened as differentially expressed genes (DEGs), of which 16 DEGs were randomly selected to be validated and revealed that most of these genes showed a transcriptional profile similar to that seen in the datasets (Pearson’s r = 0.76). Six core genes were found to be involved in regulation of extracellular matrix receptor interaction and chemotactic activity, and four of them were significantly correlated with the survival of PCa patients with bone metastases. Immune infiltration analysis showed that the expressions levels of COL3A1, RAC1, FN1, and SDC2 in CD4+T cells were significantly higher than those in tumor cells, especially regulatory T cell infiltration was significantly increased in BM tumors. We analyzed gene expression signatures specifically associated with the development of bone metastases of CRPC patients. Characterization of genes associated with BM of mCRPC is critical for identification of predictive biomarkers and potential therapeutic targets.
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Affiliation(s)
- Fanjing Meng
- Key Laboratory of Tumor Immunity, Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xu Han
- Key Laboratory of Tumor Immunity, Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhixue Min
- Department of Pathology, The Third People's Hospital of Zhengzhou, Zhengzhou, China
| | - Xuehui He
- Key Laboratory of Tumor Immunity, Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Sha Zhu
- Key Laboratory of Tumor Immunity, Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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3
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Al-Mugotir M, Lovelace JJ, George J, Bessho M, Pal D, Struble L, Kolar C, Rana S, Natarajan A, Bessho T, Borgstahl GEO. Selective killing of homologous recombination-deficient cancer cell lines by inhibitors of the RPA:RAD52 protein-protein interaction. PLoS One 2021; 16:e0248941. [PMID: 33784323 DOI: 10.1371/journal.pone.0248941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/09/2021] [Indexed: 12/29/2022] Open
Abstract
Synthetic lethality is a successful strategy employed to develop selective chemotherapeutics against cancer cells. Inactivation of RAD52 is synthetically lethal to homologous recombination (HR) deficient cancer cell lines. Replication protein A (RPA) recruits RAD52 to repair sites, and the formation of this protein-protein complex is critical for RAD52 activity. To discover small molecules that inhibit the RPA:RAD52 protein-protein interaction (PPI), we screened chemical libraries with our newly developed Fluorescence-based protein-protein Interaction Assay (FluorIA). Eleven compounds were identified, including FDA-approved drugs (quinacrine, mitoxantrone, and doxorubicin). The FluorIA was used to rank the compounds by their ability to inhibit the RPA:RAD52 PPI and showed mitoxantrone and doxorubicin to be the most effective. Initial studies using the three FDA-approved drugs showed selective killing of BRCA1-mutated breast cancer cells (HCC1937), BRCA2-mutated ovarian cancer cells (PE01), and BRCA1-mutated ovarian cancer cells (UWB1.289). It was noteworthy that selective killing was seen in cells known to be resistant to PARP inhibitors (HCC1937 and UWB1 SYr13). A cell-based double-strand break (DSB) repair assay indicated that mitoxantrone significantly suppressed RAD52-dependent single-strand annealing (SSA) and mitoxantrone treatment disrupted the RPA:RAD52 PPI in cells. Furthermore, mitoxantrone reduced radiation-induced foci-formation of RAD52 with no significant activity against RAD51 foci formation. The results indicate that the RPA:RAD52 PPI could be a therapeutic target for HR-deficient cancers. These data also suggest that RAD52 is one of the targets of mitoxantrone and related compounds.
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Affiliation(s)
- Mona Al-Mugotir
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Joseph George
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mika Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Dhananjaya Pal
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Lucas Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Carol Kolar
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sandeep Rana
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Amarnath Natarajan
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Tadayoshi Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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Feng Z, Wang H, Liu M, Chen T, Liu Y, Xu W, Wang H, Liu J. In situ grafting of PEG Acrylate on drugs with aliphatic hydroxyl functionalities via RAFT polymerization to synthesize drug/polymer conjugates with improved water solubility. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2020.110123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Dashti S, Taherian-Esfahani Z, Kholghi-Oskooei V, Noroozi R, Arsang-Jang S, Ghafouri-Fard S, Taheri M. In silico identification of MAPK14-related lncRNAs and assessment of their expression in breast cancer samples. Sci Rep 2020; 10:8316. [PMID: 32433496 PMCID: PMC7239855 DOI: 10.1038/s41598-020-65421-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/05/2020] [Indexed: 01/21/2023] Open
Abstract
Mitogen-activated protein kinase (MAP kinase) pathways participate in regulation of several cellular processes involved in breast carcinogenesis. A number of non-coding RNAs including both microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) regulate or being regulated by MAPKs. We performed an in-silico method for identification of MAPKs with high number of interactions with miRNAs and lncRNAs. Bioinformatics approaches revealed that MAPK14 ranked first among MAPKs. Subsequently, we identified miRNAs and lncRNAs that were predicted to be associated with MAPK14. Finally, we selected four lncRNAs with higher predicted scores (NORAD, HCG11, ZNRD1ASP and TTN-AS1) and assessed their expression in 80 breast cancer tissues and their adjacent non-cancerous tissues (ANCTs). Expressions of HCG11 and ZNRD1ASP were lower in tumoral tissues compared with ANCTs (P values < 0.0001). However, expression levels of MAPK14 and NORAD were not significantly different between breast cancer tissues and ANCTs. A significant association was detected between expression of HCG11 and estrogen receptor (ER) status in a way that tumors with up-regulation of this lncRNA were mostly ER negative (P value = 0.04). Expressions of ZNRD1ASP and HCG11 were associated with menopause age and breast feeding duration respectively (P values = 0.02 and 0.04 respectively). There was a trend towards association between ZNRD1ASP expression and patients' age of cancer diagnosis. Finally, we detected a trend toward association between expression of NORAD and history of hormone replacement therapy (P value = 0.06). Expression of MAPK14 was significantly higher in grade 1 tumors compared with grade 2 tumors (P value = 0.02). Consequently, the current study provides evidences for association between lncRNA expressions and reproductive factors or tumor features.
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Affiliation(s)
- Sepideh Dashti
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Taherian-Esfahani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi-Oskooei
- Department of Laboratory Sciences, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Sharam Arsang-Jang
- Department of Biostatistics and Epidemiology, Cancer Gene Therapy Research Center, Faculty of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Zhu S, Min Z, Qiao X, Chen S, Yang J, Zhang X, Liu X, Ran W, Lv R, Lin Y, Wang J. Expression profile-based screening for critical genes reveals S100A4, ACKR3 and CDH1 in docetaxel-resistant prostate cancer cells. Aging (Albany NY) 2019; 11:12754-12772. [PMID: 31895690 PMCID: PMC6949054 DOI: 10.18632/aging.102600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
Docetaxel is a first-line anticancer drug widely used in the treatment of advanced prostate cancer. However, its therapeutic efficacy is limited by its side effects and the development of chemoresistance by the tumor. Using a gene differential expression microarray, we identified 449 genes differentially expressed in docetaxel-resistant DU145 and PC3 cell lines as compared to docetaxel-sensitive controls. Moreover, western blotting and immunohistochemistry revealed altered expression of S100A4, ACKR3 and CDH1in clinical tumor samples. Cytoscape software was used to investigate the relationship between critical proteins and their signaling transduction networks. Functional and pathway enrichment analyses revealed that these signaling pathways were closely related to cellular proliferation, cell adhesion, cell migration and metastasis. In addition, ACKR3 knockout using the crispr/cas9 method andS100A4knockdownusing targeted shRNA exerted additive effects suppressing cancer cell proliferation and migration. This exploratory analysis provides information about potential candidate genes. It also provides new insight into the molecular mechanism underlying docetaxel-resistance in androgen-independent prostate cancer and highlights potential targets to improve therapeutic outcomes.
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Affiliation(s)
- Sha Zhu
- Key laboratory of Tumor Immunology, Center of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China.,Collaborative Innovation Center of Cancer Chemoprevention, School of Physics and Engineering, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Zhixue Min
- The Third People's Hospital of Zhengzhou, Zhengzhou 450000, P.R. China
| | - Xianli Qiao
- Collaborative Innovation Center of Cancer Chemoprevention, School of Physics and Engineering, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Shengxian Chen
- Collaborative Innovation Center of Cancer Chemoprevention, School of Physics and Engineering, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jian Yang
- School of Medicine, Shanghai Jiao Tong University, Shanghai 20040, P.R. China
| | - Xiao Zhang
- Key laboratory of Tumor Immunology, Center of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Xigang Liu
- Key laboratory of Tumor Immunology, Center of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Weijie Ran
- Key laboratory of Tumor Immunology, Center of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Renguang Lv
- Key laboratory of Tumor Immunology, Center of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Ying Lin
- Key laboratory of Tumor Immunology, Center of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jin Wang
- Key laboratory of Tumor Immunology, Center of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, P. R. China
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ZeOncoTest: Refining and Automating the Zebrafish Xenograft Model for Drug Discovery in Cancer. Pharmaceuticals (Basel) 2019; 13:ph13010001. [PMID: 31878274 PMCID: PMC7169390 DOI: 10.3390/ph13010001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/12/2019] [Accepted: 12/23/2019] [Indexed: 12/24/2022] Open
Abstract
The xenograft of human cancer cells in model animals is a powerful tool for understanding tumor progression and metastatic potential. Mice represent a validated host, but their use is limited by the elevated experimental costs and low throughput. To overcome these restrictions, zebrafish larvae might represent a valuable alternative. Their small size and transparency allow the tracking of transplanted cells. Therefore, tumor growth and early steps of metastasis, which are difficult to evaluate in mice, can be addressed. In spite of its advantages, the use of this model has been hindered by lack of experimental homogeneity and validation. Considering these facts, the aim of our work was to standardize, automate, and validate a zebrafish larvae xenograft assay with increased translatability and higher drug screening throughput. The ZeOncoTest reliability is based on the optimization of different experimental parameters, such as cell labeling, injection site, automated individual sample image acquisition, and analysis. This workflow implementation finally allows a higher precision and experimental throughput increase, when compared to previous reports. The approach was validated with the breast cancer cell line MDA-MB-231, the colorectal cancer cells HCT116, and the prostate cancer cells PC3; and known drugs, respectively RKI-1447, Docetaxel, and Mitoxantrone. The results recapitulate growth and invasion for all tested tumor cells, along with expected efficacy of the compounds. Finally, the methodology has proven useful for understanding specific drugs mode of action. The insights gained bring a step further for zebrafish larvae xenografts to enter the regulated preclinical drug discovery path.
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8
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Li S, Li R, Ma Y, Zhang C, Huang T, Zhu S. Transcriptome analysis of differentially expressed genes and pathways associated with mitoxantrone treatment prostate cancer. J Cell Mol Med 2018; 23:1987-2000. [PMID: 30592148 PMCID: PMC6378179 DOI: 10.1111/jcmm.14100] [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: 10/20/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
The global physiological function of specifically expressed genes of mitoxantrone (MTX)‐resistant prostate cancer (PCa) is unclear. In this study, gene expression pattern from microarray data was investigated for identifying differentially expressed genes (DEGs) in MTX‐resistant PCa xenografts. Human PCa cell lines DU145 and PC3 were cultured in vitro and xenografted into severe combined immunodeficiency (SCID) mice, treated with MTX intragastrically, three times a week until all mice relapsed. Gene expression profiles of the xenografts from castrated mice were performed with Affymetrix human whole genomic oligonucleotide microarray. The Cytoscape software was used to investigate the relationship between proteins and the signalling transduction network. A total of 355 overlapping genes were differentially expressed in MTX‐resistant DU145R and PC3R xenografts. Of these, 16 genes were selected to be validated by quantitative real‐time PCR (qRT‐PCR) in these xenografts, and further tested in a set of formalin‐fixed, paraffin‐embedded and optimal cutting temperature (OCT) clinical tumour samples. Functional and pathway enrichment analyses revealed that these DEGs were closely related to cellular activity, androgen synthesis, DNA damage and repair, also involved in the ERK/MAPK, PI3K/serine‐threonine protein kinase, also known as protein kinase B, PKB (AKT) and apoptosis signalling pathways. This exploratory analysis provides information about potential candidate genes and may bring new insights into the molecular cascade involvement in MTX‐resistant PCa.
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Affiliation(s)
- Sanqiang Li
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Medical College, Henan University of Science and Technology, Luoyang, Henan, China
| | - Ruifang Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan, China
| | - Yu Ma
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Cong Zhang
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Tao Huang
- Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Sha Zhu
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Collaborative Innovation Center of Cancer Chemoprevention, Zhengzhou, Henan, China
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