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Li R, Tian Y, Yang Z, Ji Y, Ding J, Yan A. Classification models and SAR analysis on HDAC1 inhibitors using machine learning methods. Mol Divers 2022:10.1007/s11030-022-10466-w. [PMID: 35737257 DOI: 10.1007/s11030-022-10466-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/19/2022] [Indexed: 10/17/2022]
Abstract
Histone deacetylase (HDAC) 1, a member of the histone deacetylases family, plays a pivotal role in various tumors. In this study, we collected 7313 human HDAC1 inhibitors with bioactivities to form a dataset. Then, the dataset was divided into a training set and a test set using two splitting methods: (1) Kohonen's self-organizing map and (2) random splitting. The molecular structures were represented by MACCS fingerprints, RDKit fingerprints, topological torsions fingerprints and ECFP4 fingerprints. A total of 80 classification models were built by using five machine learning methods, including decision tree (DT), random forest, support vector machine, eXtreme Gradient Boosting and deep neural network. Model 15A_2 built by the XGBoost algorithm based on ECFP4 fingerprints showed the best performance, with an accuracy of 88.08% and an MCC value of 0.76 on the test set. Finally, we clustered the 7313 HDAC1 inhibitors into 31 subsets, and the substructural features in each subset were investigated. Moreover, using DT algorithm we analyzed the structure-activity relationship of HDAC1 inhibitors. It may conclude that some substructures have a significant effect on high activity, such as N-(2-amino-phenyl)-benzamide, benzimidazole, AR-42 analogues, hydroxamic acid with a middle chain alkyl and 4-aryl imidazole with a midchain of alkyl whose α carbon is chiral.
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Affiliation(s)
- Rourou Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Yujia Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Zhenwu Yang
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Yueshan Ji
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Jiaqi Ding
- School of International Education, Beijing University of Chemical Technology, Beijing, China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, China.
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Liao L, Yao Z, Fang W, He Q, Xu WW, Li B. Epigenetics in Esophageal Cancer: From Mechanisms to Therapeutics. SMALL METHODS 2020; 4:2000391. [DOI: 10.1002/smtd.202000391] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Indexed: 02/05/2023]
Affiliation(s)
- Long Liao
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes Institute of Life and Health Engineering College of Life Science and Technology Jinan University Guangzhou 510632 China
| | - Zi‐Ting Yao
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes Institute of Life and Health Engineering College of Life Science and Technology Jinan University Guangzhou 510632 China
| | - Wang‐Kai Fang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area Department of Biochemistry and Molecular Biology Shantou University Medical College Shantou 515041 China
| | - Qing‐Yu He
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes Institute of Life and Health Engineering College of Life Science and Technology Jinan University Guangzhou 510632 China
| | - Wen Wen Xu
- MOE Key Laboratory of Tumor Molecular Biology and Guangdong Provincial Key Laboratory of Bioengineering Medicine National Engineering Research Center of Genetic Medicine Institute of Biomedicine College of Life Science and Technology Jinan University Guangzhou 510632 China
| | - Bin Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes Institute of Life and Health Engineering College of Life Science and Technology Jinan University Guangzhou 510632 China
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Epigenetic Alterations in Oesophageal Cancer: Expression and Role of the Involved Enzymes. Int J Mol Sci 2020; 21:ijms21103522. [PMID: 32429269 PMCID: PMC7278932 DOI: 10.3390/ijms21103522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/25/2022] Open
Abstract
Oesophageal cancer is a life-threatening disease, accounting for high mortality rates. The poor prognosis of this malignancy is mostly due to late diagnosis and lack of effective therapies for advanced disease. Epigenetic alterations may constitute novel and attractive therapeutic targets, owing to their ubiquity in cancer and their reversible nature. Herein, we offer an overview of the most important studies which compared differences in expression of enzymes that mediate epigenetic alterations between oesophageal cancer and normal mucosa, as well as in vitro data addressing the role of these genes/proteins in oesophageal cancer. Furthermore, The Cancer Genome Atlas database was interrogated for the correlation between expression of these epigenetic markers and standard clinicopathological features. We concluded that most epigenetic players studied thus far are overexpressed in tumours compared to normal tissue. Furthermore, functional assays suggest an oncogenic role for most of those enzymes, supporting their potential as therapeutic targets in oesophageal cancer.
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Ex vivo drug sensitivity testing as a means for drug repurposing in esophageal adenocarcinoma. PLoS One 2018; 13:e0203173. [PMID: 30212533 PMCID: PMC6136712 DOI: 10.1371/journal.pone.0203173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/15/2018] [Indexed: 12/13/2022] Open
Abstract
Background Esophageal cancer remains one of the hardest cancers to treat with rising incidence rates, low overall survival and high levels of treatment resistance. The lack of clinically available biomarkers hinder diagnosis and treatment stratification. While large scale sequencing approaches have uncovered a number of molecular makers, little has translated in the routine treatment of esophageal cancer patients. Material and methods We evaluate the treatment response towards a panel of 215 FDA-approved and 163 epigenetic compounds of 4 established and 2 patient-derived esophageal cancer cell lines. Cell viability was evaluated after 72h of treatment using cell titer glow. The drug sensitivity testing results for gemcitabine and cisplatin were validated using clonogenic assays. Results The tested cell lines display different drug sensitivity profiles, although we found compounds that display efficacy in all of the tested established or patient-derived cell lines. Clonogenic assays confirmed the validity of the drug sensitivity testing results. Using the epigenetic library, we observed high sensitivity towards a number of epigenetic modifiers. Discussion Ex vivo drug sensitivity testing may present a viable option for the treatment stratification of esophageal cancer patients and holds the potential to greatly improve patient outcome while reducing treatment toxicity.
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Screening candidate microRNA-mRNA regulatory pairs for predicting the response to chemoradiotherapy in rectal cancer by a bioinformatics approach. Sci Rep 2017; 7:11312. [PMID: 28900297 PMCID: PMC5595906 DOI: 10.1038/s41598-017-11840-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/30/2017] [Indexed: 01/06/2023] Open
Abstract
Extensive efforts have been undertaken in search of biomarkers for predicting the chemoradiotherapy response in rectal cancer. However, most attention on treatment efficiency prediction in carcinoma is addicted to single or limited molecules. Network biomarkers are considered to outperform single molecules in predictive power. In this study, candidate microRNAs (miRNAs) were identified from the PubMed citations and miRNA expression profiles. Targets of miRNAs were obtained from four experimentally confirmed interactions and three computationally predicted databases. Functional enrichment analysis of all the targets revealed their associations with chemoradiotherapy response, indicating they could be promising biomarkers. Two lists of key target mRNAs of the candidate miRNAs were retrieved from protein–protein interaction (PPI) network and mRNA expression profiles, respectively. Pathway analysis and literature validation revealed that the mRNA lists were highly related to the ionizing radiation. The above miRNAs along with the key miRNA targets provide potential miRNA-mRNA regulatory pairs as network biomarkers in which all the network components may be used for predicting the chemoradiotherapy response. These results demonstrated that the network biomarkers could provide a useful model for predicting the chemoradiotherapy response and help in further understanding the molecular basis of response differences, which should be prioritized for further study.
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Zhao H, Yu Z, Zhao L, He M, Ren J, Wu H, Chen Q, Yao W, Wei M. HDAC2 overexpression is a poor prognostic factor of breast cancer patients with increased multidrug resistance-associated protein expression who received anthracyclines therapy. Jpn J Clin Oncol 2016; 46:893-902. [DOI: 10.1093/jjco/hyw096] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 06/21/2016] [Indexed: 01/29/2023] Open
Affiliation(s)
- Haishan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Zhaojin Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Jie Ren
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Qiuchen Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Weifan Yao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China
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Song M, He G, Wang Y, Pang X, Zhang B. Lentivirus-mediated Knockdown of HDAC1 Uncovers Its Role in Esophageal Cancer Metastasis and Chemosensitivity. J Cancer 2016; 7:1694-1700. [PMID: 27698906 PMCID: PMC5039390 DOI: 10.7150/jca.15086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/07/2016] [Indexed: 01/28/2023] Open
Abstract
Histone deacetylationase 1 (HDAC1) is ubiquitously expressed in various cell lines and tissues and play an important role of regulation gene expression. Overexpression of HDAC1 has been observed in various types of cancers, which indicated that it might be a target for cancer therapy. To test HDAC1 inhibition for cancer treatment, the gene expression of HDAC1 was knockdown mediated by a lentivirus system. Our data showed the gene expression of HDAC1 could be efficiently knockdown by RNAi mediated by lentivirus in esophageal carcinoma EC109 cells. Knockdown of HDAC1 led to significant decrease of cell growth and altered cell cycle distribution. The result of transwell assay showed that the numbers of cells travelled through the micropore membrane was significantly decreased as HDAC1 expression was knockdown. Moreover, HDAC1 knockdown inhibited the migration of EC109 cells as determining by scratch test. Additionally, enhancement of cisplatin-stimulated apoptosis was detected by HDAC1 knockdown. Our data suggested inhibition of HDAC1 expression by lentivirus mediated shRNA might be further applied for esophageal cancer chemotherapy.
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Affiliation(s)
- Min Song
- Department of Medical Genetics, Third Military Medical University; Department of neurology, the second Affiliated Hospital of Chongqing Medical University
| | - Gang He
- Department of Medical Genetics, Third Military Medical University
| | - Yan Wang
- Department of Medical Genetics, Third Military Medical University
| | - Xueli Pang
- Department of oncology, Southwest Hospital, Third Military Medical University
| | - Bo Zhang
- Department of Medical Genetics, Third Military Medical University
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Zhao R, Chen K, Cao J, Yu H, Tian L, Liu M. A correlation analysis between HDAC1 over-expression and clinical features of laryngeal squamous cell carcinoma. Acta Otolaryngol 2015; 136:172-6. [PMID: 26588579 DOI: 10.3109/00016489.2015.1101781] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CONCLUSION HDAC1 may be a prognostic biomarker for LSCC malignant potency and a potent factor resulting in decreased sensitivity of LSCC in radiotherapy. OBJECTIVE The aim of this study was to evaluate the correlation between histone deacetylase 1 (HDAC1) over-expression and clinical features in laryngeal squamous cell carcinoma (LSCC). METHODS This study assessed the HDAC1 expressions in 90 formalin-fixed paraffin-embedded LSCC samples, 30 adjacent non-neoplastic tissues, and 30 laryngeal polyp tissues by immunohistochemistry (IHC). In addition, another 40 LSCC samples were collected that were divided into two groups after 3-month radiotherapy: the high radio-sensitive group (HRS) and low radio-sensitive group (LRS). Overall survival curves of all the LSCC patients were constructed by Kaplan-Meier method and long-rank test. RESULTS All ninety samples were positively immunostained for HDAC1. The expression of HDAC1 was up-regulated and significantly associated with T classification, lymph node metastases, tumor location and clinical stage. HDAC1 was mainly labeled in the epithelial cells of laryngeal polyp tissues and adjacent non-neoplastic tissues. In addition, the expression of HDAC1 was significantly higher in LRS than that in HRS. The positive rates for stage III-IV tumor were significantly higher than those for stage II. LSCC patients with HDAC1 over-expression and LRS presented a shorter 5-year overall survival rate.
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Affiliation(s)
- Rui Zhao
- a Department of Otorhinolaryngology, Head and Neck Surgery , The Second Affiliated Hospital of Harbin Medical University , Harbin , PR China
| | - Kexin Chen
- a Department of Otorhinolaryngology, Head and Neck Surgery , The Second Affiliated Hospital of Harbin Medical University , Harbin , PR China
| | - Jing Cao
- a Department of Otorhinolaryngology, Head and Neck Surgery , The Second Affiliated Hospital of Harbin Medical University , Harbin , PR China
| | - Hao Yu
- a Department of Otorhinolaryngology, Head and Neck Surgery , The Second Affiliated Hospital of Harbin Medical University , Harbin , PR China
| | - Linli Tian
- a Department of Otorhinolaryngology, Head and Neck Surgery , The Second Affiliated Hospital of Harbin Medical University , Harbin , PR China
| | - Ming Liu
- a Department of Otorhinolaryngology, Head and Neck Surgery , The Second Affiliated Hospital of Harbin Medical University , Harbin , PR China
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Knockdown of Rad9A enhanced DNA damage induced by trichostatin A in esophageal cancer cells. Tumour Biol 2015; 37:963-70. [DOI: 10.1007/s13277-015-3879-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/30/2015] [Indexed: 12/24/2022] Open
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Makita N, Ninomiya I, Tsukada T, Okamoto K, Harada S, Nakanuma S, Sakai S, Makino I, Kinoshita J, Hayashi H, Oyama K, Nakagawara H, Miyashita T, Tajima H, Takamura H, Fushida S, Ohta T. Inhibitory effects of valproic acid in DNA double-strand break repair after irradiation in esophageal squamous carcinoma cells. Oncol Rep 2015; 34:1185-92. [PMID: 26135807 DOI: 10.3892/or.2015.4089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/15/2015] [Indexed: 12/24/2022] Open
Abstract
Radiation therapy is one of the most promising therapeutic strategies in unresectable esophageal squamous cell carcinoma (ESCC). The histone deacetylase (HDAC) inhibitor has been shown to enhance radiosensitivity. Valproic acid (VPA) is a well-known drug used to treat seizure disorders and epilepsy, and has been shown to inhibit HDACs. We recently reported that a clinically safe dose of VPA enhances radiation‑induced cytotoxicity in human ESCC cells. However, the mechanism of radiosensitizing effect of VPA has not yet been confirmed. The present study examined the effect of VPA on DNA double-strand break (DSB) repair after radiation in the human ESCC cell lines KES, TE9 and TE11 by examining H2AX phosphorylation (γH2AX) levels as a marker of radiation‑induced DSBs. The present study also examined whether VPA inhibited radiation-induced DNA DSB repair by suppressing non-homologous end joining (NHEJ), focusing particularly on the acetylation of Ku70. VPA was shown to prolong γH2AX levels after irradiation in all three ESCC cell lines. Moreover, prolonged γH2AX foci formation after irradiation was also observed by immunocytochemistry following VPA pretreatment in KES and TE9 cells. VPA was shown to induce Ku70 acetylation after irradiation in all three ESCC cell lines. Our results suggest that VPA prolonged radiation‑induced DSBs by inhibiting NHEJ in DSB repair pathways in ESCC. VPA could therefore be used as an effective radiosensitizer in ESCC radiotherapy.
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Affiliation(s)
- Naoki Makita
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Itasu Ninomiya
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Tomoya Tsukada
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Koichi Okamoto
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Shinichi Harada
- Center for Biomedical Research and Education, School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Shinichi Nakanuma
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Seisho Sakai
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Isamu Makino
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Jun Kinoshita
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Hironori Hayashi
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Katsunobu Oyama
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Hisatoshi Nakagawara
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Tomoharu Miyashita
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Hidehiro Tajima
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Hiroyuki Takamura
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Sachio Fushida
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Tetsuo Ohta
- Department of Gastroenterological Surgery, Division of Cancer Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
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Digklia A, Voutsadakis IA. Targeted treatments for metastatic esophageal squamous cell cancer. World J Gastrointest Oncol 2013; 5:88-96. [PMID: 23799158 PMCID: PMC3682173 DOI: 10.4251/wjgo.v5.i5.88] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/27/2013] [Accepted: 05/18/2013] [Indexed: 02/05/2023] Open
Abstract
Squamous cell carcinoma, one of the two major sub-types of esophageal carcinomas, constitutes the great majority of tumors in the upper and middle third of the organ. Declining in incidence in western countries, it continues to be a significant public health problem in the far east. Targeted treatments are novel therapies introduced in the clinical therapeutic armamentarium of oncology in the last 10-15 years. They represent a rational way of treating various cancers based on their molecular lesions. Although no such agent has been approved so far for the treatment of esophageal squamous cell carcinomas (ESCC), several are in clinical trials and several others have displayed pre-clinical activity that would justify the efforts and risks of pursuing their clinical development in this disease. This paper discusses some of these targeted agents in more advanced development in metastatic ESCC, as well as some promising drugs with pre-clinical or initial clinical data in the disease.
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Liu YJ, Lin YF, Chen YF, Luo EC, Sher YP, Tsai MH, Chuang EY, Lai LC. MicroRNA-449a enhances radiosensitivity in CL1-0 lung adenocarcinoma cells. PLoS One 2013; 8:e62383. [PMID: 23614048 PMCID: PMC3629161 DOI: 10.1371/journal.pone.0062383] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 03/21/2013] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Radiotherapy is often applied for treating lung cancer, but it often fails because of the relative non-susceptibility of lung cancer cells to radiation. MicroRNAs (miRNAs) have been reported to modulate the radiosensitivity of lung cancer cells and have the potential to improve the efficacy of radiotherapy. The purpose of this study was to identify a miRNA that can adjust radiosensitivity in lung adenocarcinoma cells. Two lung adenocarcinoma cell lines (CL1-0 and CL1-5) with different metastatic ability and radiosensitivity were used. In order to understand the regulatory mechanisms of differential radiosensitivity in these isogenic tumor cells, both CL1-0 and CL1-5 were treated with 10 Gy radiation, and were harvested respectively at 0, 1, 4, and 24 h after radiation exposure. The changes in expression of miRNA upon irradiation were examined using Illumina Human microRNA BeadChips. Twenty-six miRNAs were identified as having differential expression post-irradiation in CL1-0 or CL1-5 cells. Among these miRNAs, miR-449a, which was down-regulated in CL1-0 cells at 24 h after irradiation, was chosen for further investigation. Overexpression of miR-449a in CL1-0 cells effectively increased irradiation-induced DNA damage and apoptosis, altered the cell cycle distribution and eventually led to sensitization of CL1-0 to irradiation.
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Affiliation(s)
- Yi-Jyun Liu
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Yu-Fen Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yi-Fan Chen
- YongLin Biomedical Engineering Center, National Taiwan University, Taipei, Taiwan
| | - En-Ching Luo
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
| | - Yuh-Ping Sher
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
| | - Eric Y. Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- YongLin Biomedical Engineering Center, National Taiwan University, Taipei, Taiwan
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, National Taiwan University, Taipei, Taiwan
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail:
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13
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Pang XL, He G, Liu YB, Wang Y, Zhang B. Endoplasmic reticulum stress sensitizes human esophageal cancer cell to radiation. World J Gastroenterol 2013; 19:1736-1748. [PMID: 23555162 PMCID: PMC3607750 DOI: 10.3748/wjg.v19.i11.1736] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 12/03/2012] [Accepted: 01/07/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the role of endoplasmic reticulum (ER) stress in cancer radiotherapy and its molecular mechanism.
METHODS: Tunicamycin (TM) was applied to induce ER stress in human esophageal cancer cell line EC109, and the radiosensitization effects were detected by acute cell death and clonogenic survival assay. Cell cycle arrest induced by TM was determined by flow cytometric analysis after the cellular DNA content was labeled with propidium iodide. Apoptosis of EC109 cells induced by TM was detected by annexin V staining and Western blotting of caspase-3 and its substrate poly ADP-ribose polymerase. Autophagic response was determined by acridine orange (AO) staining and Western blotting of microtubule-associated protein-1 light chain-3 (LC3) and autophagy related gene 5 (ATG5). In order to test the biological function of autophagy, specific inhibitor or Beclin-1 knockdown was used to inhibit autophagy, and its effect on cell apoptosis was thus detected. Additionally, involvement of the phosphatidylinositol-3 kinase (PI3K)/Akt/mammalian target of the rapamycin (mTOR) pathway was also detected by Western blotting. Finally, male nude mice inoculated subcutaneously with EC109 cells were used to confirm cell model observations.
RESULTS: Our results showed that TM treatment enhanced cell death and reduced the colony survival fraction induced by ionizing radiation (IR), which suggested an obvious radiosensitization effect of TM. Moreover, TM and IR combination treatment led to a significant increase of G2/M phase and apoptotic cells, compared with IR alone. We also observed an increase of AO positive cells, and the protein level of LC3-II and ATG5 was induced by TM treatment, which suggested an autophagic response in EC109 cells. However, inhibition of autophagy by using a chemical inhibitor or Beclin-1 silencing led to increased cell apoptosis and decreased cell viability, which suggested a cytoprotective role of autophagy in stressed EC109 cells. Furthermore, TM treatment also activated mTORC1, and in turn reduced Akt phosphorylation, which suggested the PI3K/Akt/mTOR signal pathway was involved in the TM-induced autophagic response in EC109 cells. Tumor xenograft results also showed synergistic retarded tumor growth by TM treatment and IR, as well as the involvement of the PI3K/Akt/mTOR pathway.
CONCLUSION: Our data showed that TM treatment sensitized human esophageal cancer cells to radiation via apoptosis and autophagy both in vitro and in vivo.
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Dai ZJ, Gao J, Kang HF, Ma YG, Ma XB, Lu WF, Lin S, Ma HB, Wang XJ, Wu WY. Targeted inhibition of mammalian target of rapamycin (mTOR) enhances radiosensitivity in pancreatic carcinoma cells. DRUG DESIGN DEVELOPMENT AND THERAPY 2013; 7:149-59. [PMID: 23662044 PMCID: PMC3610438 DOI: 10.2147/dddt.s42390] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The mammalian target of rapamycin (mTOR) is a protein kinase that regulates protein translation, cell growth, and apoptosis. Rapamycin (RPM), a specific inhibitor of mTOR, exhibits potent and broad in vitro and in vivo antitumor activity against leukemia, breast cancer, and melanoma. Recent studies showing that RPM sensitizes cancers to chemotherapy and radiation therapy have attracted considerable attention. This study aimed to examine the radiosensitizing effect of RPM in vitro, as well as its mechanism of action. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and colony formation assay showed that 10 nmol/L to 15 nmol/L of RPM had a radiosensitizing effects on pancreatic carcinoma cells in vitro. Furthermore, a low dose of RPM induced autophagy and reduced the number of S-phase cells. When radiation treatment was combined with RPM, the PC-2 cell cycle arrested in the G2/M phase of the cell cycle. Complementary DNA (cDNA) microarray and reverse transcription polymerase chain reaction (RT-PCR) revealed that the expression of DDB1, RAD51, and XRCC5 were downregulated, whereas the expression of PCNA and ABCC4 were upregulated in PC-2 cells. The results demonstrated that RPM effectively enhanced the radiosensitivity of pancreatic carcinoma cells.
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Affiliation(s)
- Zhi-Jun Dai
- Department of Oncology, Second Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, People's Republic of China.
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Oh JH, Wong HP, Wang X, Deasy JO. A bioinformatics filtering strategy for identifying radiation response biomarker candidates. PLoS One 2012; 7:e38870. [PMID: 22768051 PMCID: PMC3387230 DOI: 10.1371/journal.pone.0038870] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/15/2012] [Indexed: 02/06/2023] Open
Abstract
The number of biomarker candidates is often much larger than the number of clinical patient data points available, which motivates the use of a rational candidate variable filtering methodology. The goal of this paper is to apply such a bioinformatics filtering process to isolate a modest number (<10) of key interacting genes and their associated single nucleotide polymorphisms involved in radiation response, and to ultimately serve as a basis for using clinical datasets to identify new biomarkers. In step 1, we surveyed the literature on genetic and protein correlates to radiation response, in vivo or in vitro, across cellular, animal, and human studies. In step 2, we analyzed two publicly available microarray datasets and identified genes in which mRNA expression changed in response to radiation. Combining results from Step 1 and Step 2, we identified 20 genes that were common to all three sources. As a final step, a curated database of protein interactions was used to generate the most statistically reliable protein interaction network among any subset of the 20 genes resulting from Steps 1 and 2, resulting in identification of a small, tightly interacting network with 7 out of 20 input genes. We further ranked the genes in terms of likely importance, based on their location within the network using a graph-based scoring function. The resulting core interacting network provides an attractive set of genes likely to be important to radiation response.
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Affiliation(s)
- Jung Hun Oh
- Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Harry P. Wong
- Department of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Joseph O. Deasy
- Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
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