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Volovat SR, Augustin I, Zob D, Boboc D, Amurariti F, Volovat C, Stefanescu C, Stolniceanu CR, Ciocoiu M, Dumitras EA, Danciu M, Apostol DGC, Drug V, Shurbaji SA, Coca LG, Leon F, Iftene A, Herghelegiu PC. Use of Personalized Biomarkers in Metastatic Colorectal Cancer and the Impact of AI. Cancers (Basel) 2022; 14:cancers14194834. [PMID: 36230757 PMCID: PMC9562853 DOI: 10.3390/cancers14194834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 12/09/2022] Open
Abstract
Colorectal cancer is a major cause of cancer-related death worldwide and is correlated with genetic and epigenetic alterations in the colonic epithelium. Genetic changes play a major role in the pathophysiology of colorectal cancer through the development of gene mutations, but recent research has shown an important role for epigenetic alterations. In this review, we try to describe the current knowledge about epigenetic alterations, including DNA methylation and histone modifications, as well as the role of non-coding RNAs as epigenetic regulators and the prognostic and predictive biomarkers in metastatic colorectal disease that can allow increases in the effectiveness of treatments. Additionally, the intestinal microbiota’s composition can be an important biomarker for the response to strategies based on the immunotherapy of CRC. The identification of biomarkers in mCRC can be enhanced by developing artificial intelligence programs. We present the actual models that implement AI technology as a bridge connecting ncRNAs with tumors and conducted some experiments to improve the quality of the model used as well as the speed of the model that provides answers to users. In order to carry out this task, we implemented six algorithms: the naive Bayes classifier, the random forest classifier, the decision tree classifier, gradient boosted trees, logistic regression and SVM.
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Affiliation(s)
- Simona-Ruxandra Volovat
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Iolanda Augustin
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Daniela Zob
- Department of Medical Oncology, AI.Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Diana Boboc
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Florin Amurariti
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Constantin Volovat
- Department of Medical Oncology, “Euroclinic” Center of Oncology, 2 Vasile Conta Str., 700106 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cipriana Stefanescu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Correspondence: (C.V.); (C.S.)
| | - Cati Raluca Stolniceanu
- Department of Biophysics and Medical Physics-Nuclear Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
| | - Manuela Ciocoiu
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Eduard Alexandru Dumitras
- Department of Pathophysiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- Department of Anesthesiology and Intensive Care, Regional Institute of Oncology, 700115 Iasi, Romania
| | - Mihai Danciu
- Pathology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Vasile Drug
- Department of Gastroenterology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Str., 700115 Iasi, Romania
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Sinziana Al Shurbaji
- Gastroenterology Clinic, Institute of Gastroenterology and Hepatology, ‘St. Spiridon’ Clinical Hospital, 700115 Iasi, Romania
| | - Lucia-Georgiana Coca
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Florin Leon
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
| | - Adrian Iftene
- Faculty of Computer Science, Alexandru Ioan Cuza University, 700115 Iasi, Romania
| | - Paul-Corneliu Herghelegiu
- Faculty of Automatic Control and Computer Engineering, Gheorghe Asachi Technical University, 700115 Iasi, Romania
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Li S, Li L, Meng X, Sun P, Liu Y, Song Y, Zhang S, Jiang C, Cai J, Zhao Z. DREAM: a database of experimentally supported protein-coding RNAs and drug associations in human cancer. Mol Cancer 2021; 20:148. [PMID: 34774049 PMCID: PMC8590212 DOI: 10.1186/s12943-021-01436-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
Abstract
The Drug Response Gene Expression Associated Map, also referred as “DREAM” (http://bio-big-data.cn:8080/DREAM), is a manually curated database of experimentally supported protein-coding RNAs and drugs associations in human cancers. The current version of the DREAM documents 3048 entries about scientific literatures supported drug sensitivity or drug intervention related protein-coding RNAs from PubMed database and 195 high-throughput microarray data about drug sensitivity or drug intervention related protein-coding RNAs data from GEO database. Each entry in DREAM database contains detailed information on protein-coding RNA, drug, cancer, and other information including title, PubMed ID, journal, publish time. The DREAM database also provides some data visualization and online analysis services such as volcano plot, GO/KEGG enrichment function analysis, and novel drug discovery analysis. We hope the DREAM database should serve as a valuable resource for clinical practice and basic research, which could help researchers better understand the effects of protein-coding RNAs on drug response in human cancers.
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Affiliation(s)
- Shupeng Li
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China
| | - Lulu Li
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China
| | - Xiangqi Meng
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China
| | - Penggang Sun
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China
| | - Yi Liu
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China
| | - Yuntang Song
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China
| | - Sijia Zhang
- Department of Educational Administration, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Chuanlu Jiang
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China.
| | - Jinquan Cai
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin, 150086, China. .,Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, 171 65, Stockholm, Sweden.
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.
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Fernandes MT, Yassuda V, Bragança J, Link W, Ferreira BI, De Sousa-Coelho AL. Tribbles Gene Expression Profiles in Colorectal Cancer. GASTROINTESTINAL DISORDERS 2021; 3:218-236. [DOI: https:/doi.org/10.3390/gidisord3040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death due to cancer in the world. Therefore, the identification of novel druggable targets is urgently needed. Tribbles proteins belong to a pseudokinase family, previously recognized in CRC as oncogenes and potential therapeutic targets. Here, we analyzed the expression of TRIB1, TRIB2, and TRIB3 simultaneously in 33 data sets from CRC based on available GEO profiles. We show that all three Tribbles genes are overrepresented in CRC cell lines and primary tumors, though depending on specific features of the CRC samples. Higher expression of TRIB2 in the tumor microenvironment and TRIB3 overexpression in an early stage of CRC development, unveil a potential and unexplored role for these proteins in the context of CRC. Differential Tribbles expression was also explored in diverse cellular experimental conditions where either genetic or pharmacological approaches were used, providing novel hints for future research. This comprehensive bioinformatic analysis provides new insights into Tribbles gene expression and transcript regulation in CRC.
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Tribbles Gene Expression Profiles in Colorectal Cancer. GASTROINTESTINAL DISORDERS 2021. [DOI: 10.3390/gidisord3040021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of death due to cancer in the world. Therefore, the identification of novel druggable targets is urgently needed. Tribbles proteins belong to a pseudokinase family, previously recognized in CRC as oncogenes and potential therapeutic targets. Here, we analyzed the expression of TRIB1, TRIB2, and TRIB3 simultaneously in 33 data sets from CRC based on available GEO profiles. We show that all three Tribbles genes are overrepresented in CRC cell lines and primary tumors, though depending on specific features of the CRC samples. Higher expression of TRIB2 in the tumor microenvironment and TRIB3 overexpression in an early stage of CRC development, unveil a potential and unexplored role for these proteins in the context of CRC. Differential Tribbles expression was also explored in diverse cellular experimental conditions where either genetic or pharmacological approaches were used, providing novel hints for future research. This comprehensive bioinformatic analysis provides new insights into Tribbles gene expression and transcript regulation in CRC.
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5
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Wang Y, Zhang Y, Kong L, Song C, Chen X, Fang X, Zhang C. tRNA-derived RNA fragments in the exosomes of bovine milk and colostrum. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Qin C, Feng H, Zhang C, Zhang X, Liu Y, Yang DG, Du LJ, Sun YC, Yang ML, Gao F, Li JJ. Differential Expression Profiles and Functional Prediction of tRNA-Derived Small RNAs in Rats After Traumatic Spinal Cord Injury. Front Mol Neurosci 2020; 12:326. [PMID: 31998075 PMCID: PMC6968126 DOI: 10.3389/fnmol.2019.00326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Spinal cord injury (SCI) is mostly caused by trauma. As the primary mechanical injury is unavoidable, a focus on the underlying molecular mechanisms of the SCI-induced secondary injury is necessary to develop promising treatments for patients with SCI. Transfer RNA-derived small RNA (tsRNA) is a novel class of short, non-coding RNA, possessing potential regulatory functions in various diseases. However, the functional roles of tsRNAs in traumatic SCI have not been determined yet. We used a combination of sequencing, quantitative reverse transcription-polymerase chain reaction (qRT-PCR), bioinformatics, and luciferase reporter assay to screen the expression profiles and identify the functional roles of tsRNAs after SCI. As a result, 297 differentially expressed tsRNAs were identified in rats' spinal cord 1 day after contusion. Of those, 155 tsRNAs were significantly differentially expressed: 91 were significantly up-regulated, whereas 64 were significantly down-regulated after SCI (fold change > 1.5; P < 0.05). Bioinformatics analyses revealed candidate tsRNAs (tiRNA-Gly-GCC-001, tRF-Gly-GCC-012, tRF-Gly-GCC-013, and tRF-Gly-GCC-016) that might play regulatory roles through the mitogen-activated protein kinase (MAPK) and neurotrophin signaling pathways by targeting brain-derived neurotrophic factor (BDNF). We validated the candidate tsRNAs and found opposite trends in the expression levels of the tsRNAs and BDNF after SCI. Finally, tiRNA-Gly-GCC-001 was identified to target BDNF using the luciferase reporter assay. In summary, we found an altered tsRNA expression pattern and predicted tiRNA-Gly-GCC-001 might be involved in the MAPK and neurotrophin pathways by targeting the BDNF, thus regulating the post-SCI pathophysiologic processes. This study provides novel insights for future investigations to explore the mechanisms and therapeutic targets for SCI.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Hao Feng
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Yi Liu
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ying-Chun Sun
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,TCM Treatment Center, China Rehabilitation Research Center, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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7
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Rafieenia F, Abbaszadegan MR, Poursheikhani A, Razavi SMS, Jebelli A, Molaei F, Aghaee‐Bakhtiari SH. In silico evidence of high frequency of miRNA‐related SNPs in Esophageal Squamous Cell Carcinoma. J Cell Physiol 2019; 235:966-978. [DOI: 10.1002/jcp.29012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/31/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Fatemeh Rafieenia
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
- Student Research Committee Mashhad University of Medical Sciences Mashhad Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
- Immunology Research Center Mashhad University of Medical Sciences Mashhad Iran
| | - Arash Poursheikhani
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
| | | | - Amir Jebelli
- Stem Cell and Regenerative Medicine Research Department Iranian Academic Center for Education, Culture and Research (ACECR), Mashhad Branch Mashhad Iran
| | - Fatemeh Molaei
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
| | - Seyed Hamid Aghaee‐Bakhtiari
- Bioinformatics Research Group Mashhad University of Medical Sciences Mashhad Iran
- Department of Medical Biotechnology, Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran
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Qi L, Gao C, Feng F, Zhang T, Yao Y, Wang X, Liu C, Li J, Li J, Sun C. MicroRNAs associated with lung squamous cell carcinoma: New prognostic biomarkers and therapeutic targets. J Cell Biochem 2019; 120:18956-18966. [PMID: 31241205 DOI: 10.1002/jcb.29216] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/31/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Lingyu Qi
- College of First Clinical MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Chundi Gao
- College of First Clinical MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Fubin Feng
- Department of OncologyWeifang Traditional Chinese Hospital Weifang Shandong PR China
| | - Tingting Zhang
- College of Traditional Chinese MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Yan Yao
- Clinical Medical CollegesWeifang Medical University Weifang Shandong PR China
| | - Xue Wang
- College of Basic MedicineQingdao University Qingdao Shandong PR China
| | - Cun Liu
- College of Traditional Chinese MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Jia Li
- Clinical Medical CollegesWeifang Medical University Weifang Shandong PR China
| | - Jie Li
- College of First Clinical MedicineShandong University of Traditional Chinese Medicine Jinan Shandong PR China
| | - Changgang Sun
- Department of OncologyAffiliated Hospital of Weifang Medical University Weifang Shandong PR China
- Department of OncologyAffiliated Hospital of Shandong University of Traditional Chinese Medicine Jinan Shandong PR China
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Huang YF, Niu WB, Hu R, Wang LJ, Huang ZY, Ni SH, Wang MQ, Yang Y, Huang YS, Feng WJ, Xiao W, Zhu DJ, Xian SX, Lu L. FIBP knockdown attenuates growth and enhances chemotherapy in colorectal cancer via regulating GSK3β-related pathways. Oncogenesis 2018; 7:77. [PMID: 30275459 PMCID: PMC6167373 DOI: 10.1038/s41389-018-0088-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/15/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer stem cells (CSCs), characterized by self-renewal ability and high expression of proliferative genes, contribute to the chemoresistance of colorectal cancer (CRC). We aimed to identify the molecular mechanisms underlying CRC chemoresistance through comprehensive bioinformatics screenings and experimental confirmation of gene functions. We found that high expression of FGF1 intracellular binding protein (FIBP) was correlated with chemoresistance and poor prognosis in CRC patients. Therefore, the chemoresistant CRC cell line HCT116-CSC with high expression of the stem cell markers CD44 and CD133 was established for further phenotypic tests. FIBP knockdown inhibited proliferation, enhanced chemotherapy effects, and attenuated the stemness markers of CRC cells in vivo and in vitro. Through RNA-seq and gene set enrichment analysis, we identified cyclin D1 as a key downstream target in FIBP-regulated cell cycle progression and proliferation. Moreover, FIBP bound to GSK3β, inhibited its phosphorylation at Tyr216, and activated β-catenin/TCF/cyclin D1 signaling in HCT116-CSCs. Additional GSK3β knockdown reversed the FIBP silencing-induced inhibition of proliferation and decreased stemness marker expression in HCT116-CSCs. Furthermore, DNA methylation profiling suggested that FIBP regulated the stemness of CRC cells via methylation activity that was dependent on GSK3β but independent of β-catenin signaling. Our data illuminate the potential of FIBP as a novel therapeutic target for treating chemoresistant CRC through inhibition of GSK3β-related signaling.
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Affiliation(s)
- Yan-Feng Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.,Shunde Hospital (The first People's Hospital of Shunde Foshan), Southern Medical University, 528300, Foshan, China
| | - Wen-Bo Niu
- Cancer Research Institute, Southern Medical University, 510515, Guangzhou, China
| | - Rong Hu
- Cancer Research Institute, Southern Medical University, 510515, Guangzhou, China.,School of Traditional Chinese Medicine, Southern Medical University, 510515, Guangzhou, China
| | - Ling-Jun Wang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.,Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China
| | - Zeng-Yan Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.,Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China
| | - Shi-Hao Ni
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.,Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China
| | - Ming-Qing Wang
- Cancer Research Institute, Southern Medical University, 510515, Guangzhou, China.,School of Traditional Chinese Medicine, Southern Medical University, 510515, Guangzhou, China
| | - Yi Yang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.,Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China
| | - Yu-Sheng Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.,Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China
| | - Wen-Jun Feng
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China
| | - Wei Xiao
- School of Traditional Chinese Medicine, Southern Medical University, 510515, Guangzhou, China.
| | - Da-Jian Zhu
- Department of Gastrointestinal Surgery, Guangdong Medical University Affiliated Women and Children Hospital, 528300, Foshan, China.
| | - Shao-Xiang Xian
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China. .,Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.
| | - Lu Lu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China. .,Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, 510407, Guangzhou, Guangdong, China.
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Dai G, Yao X, Zhang Y, Gu J, Geng Y, Xue F, Zhang J. Colorectal cancer cell-derived exosomes containing miR-10b regulate fibroblast cells via the PI3K/Akt pathway. Bull Cancer 2018; 105:336-349. [PMID: 29496262 DOI: 10.1016/j.bulcan.2017.12.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/08/2017] [Accepted: 12/16/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) contribute to the proliferation of colorectal cancer(CRC) cells. However, the mechanism by which CAFs develop in the tumor microenvironment remains unknown. Exosomes may be involved in activating CAFs. METHODS Using a miRNA expression profiling array, we determined the miRNA expression profile of secretory exosomes in CRC cells and then identified potential miRNAs with significant differential expression compared to normal cells via enrichment analysis. Predicted targets of candidate miRNAs were then assessed via bioinformatics analysis. Realtime qPCR, western blot, and cell cycle analyses were performed to evaluate the role of candidate exosomal miRNAs. Luciferase reporter assays were applied to confirm whether candidate exosomal miRNAs control target pathway expression. A CRC xenograft mouse model was constructed to evaluate tumor growth in vivo. RESULTS Exosomes from CRC cells contained significantly higher levels of miR-10b than did exosomes from normal colorectal epithelial cells. Moreover, exosomes containing miR-10b were transferred to fibroblasts. Bioinformatics analysis identified PIK3CA, as a potential target of miR-10b. Luciferase reporter assays confirmed that miR-10b directly inhibited PIK3CA expression. Co-culturing fibroblasts with exosomes containing miR-10b significantly suppressed PIK3CA expression and decreased PI3K/Akt/mTOR pathway activity. Finally, exosomes containing miR-10b reduced fibroblast proliferation but promoted expression of TGF-β and SM α-actin, suggesting that exosomal miR-10b may activate fibroblasts to become CAFs that express myofibroblast markers. These activated fibroblasts were able to promote CRC growth in vitro and in vivo. CONCLUSION CRC-derived exosomes actively promote disease progression by modulating surrounding stromal cells, which subsequently acquire features of CAFs.
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Affiliation(s)
- Guangyao Dai
- First Hospital of Shijiazhuang City, Department of General Surgery, Shijiazhuang, China
| | - Xiaoguang Yao
- Hebei University of Chinese Medicine, Hebei Key Laboratory of Integrative Medicine on Liver-kidney Patterns, Shijiazhuang, China; Hebei University of Chinese Medicine, College of Integrative Medicine, Shijiazhuang, China
| | - Yubin Zhang
- First Hospital of Shijiazhuang City, Department of General Surgery, Shijiazhuang, China
| | - Jianbin Gu
- First Hospital of Shijiazhuang City, Department of General Surgery, Shijiazhuang, China
| | - Yunfeng Geng
- First Hospital of Shijiazhuang City, Department of General Surgery, Shijiazhuang, China
| | - Fei Xue
- First Hospital of Shijiazhuang City, Department of General Surgery, Shijiazhuang, China
| | - Jingcheng Zhang
- First Hospital of Shijiazhuang City, Department of General Surgery, Shijiazhuang, China.
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11
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Single nucleotide variant in Nucleoporin 107 may be predictive of sensitivity to chemotherapy in patients with ovarian cancer. Pharmacogenet Genomics 2018; 27:264-269. [PMID: 28562428 DOI: 10.1097/fpc.0000000000000288] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Alterations in nuclear pore complex (NPC) genes have been previously associated with response to chemotherapy. Using agnostic exome sequencing, we envisioned that new alleles in NPC genes, predictive of sensitivity to platinum treatment, could be discovered. METHODS Twenty-two platinum-sensitive and six platinum-resistant ovarian cancer patients were tested. Platinum sensitivity was defined as disease-free survival greater than 6 months. Next-generation sequencing of exomes was used to compare platinum-sensitive and platinum-resistant patients. Single nucleotide variants (SNVs) associated with platinum sensitivity in NPC genes (n=30 genes) were identified. RESULTS SNVs in three NPC genes were associated with response to platinum on univariate analysis. SNV rs79419059 (10T>C) in Nucleoporin 107 (Nup107) was associated with platinum resistance (P=0.0061), whereas rs2302811 (3662-4A>G) in Nucleoporin 188 (Nup188) and rs77246077 (3420-67T>A) in Nucleoporin 214 (Nup214) were associated with platinum sensitivity (P=0.0483 and 0.0091, respectively). Controlling for other confounders, multivariate age-adjusted Cox proportional hazard analysis showed rs79419059 to be significantly associated with platinum resistance (odds ratio: 4.519, 95% confidence interval: 1.317-15.501, P=0.0457). CONCLUSION We identified a variant in the 3'-UTR region Nup107 unique to sensitivity to platinum in ovarian cancer. With validation of this variant, it is possible that a new marker predictive of patient response may be identified.
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Shirafkan N, Mansoori B, Mohammadi A, Shomali N, Ghasbi M, Baradaran B. MicroRNAs as novel biomarkers for colorectal cancer: New outlooks. Biomed Pharmacother 2018; 97:1319-1330. [DOI: 10.1016/j.biopha.2017.11.046] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/04/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
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13
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Greene J, Nguyen A, Bagby SM, Jones GN, Tai WM, Quackenbush KS, Schreiber A, Messersmith WA, Devaraj KM, Blatchford P, Eckhardt SG, Cadogan EB, Hughes GD, Smith A, Pitts TM, Arcaroli JJ. The novel ATM inhibitor (AZ31) enhances antitumor activity in patient derived xenografts that are resistant to irinotecan monotherapy. Oncotarget 2017; 8:110904-110913. [PMID: 29340025 PMCID: PMC5762293 DOI: 10.18632/oncotarget.22920] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/09/2017] [Indexed: 12/22/2022] Open
Abstract
Irinotecan, a standard of care therapy for CRC, elicits cytotoxic effects by generating double strand breaks resulting in DNA damage. The activation of the ATM pathway plays a fundamental role in regulating the cellular response and repair to DNA damage. The objective of this preclinical study was to determine whether ATM inhibition would enhance sensitivity to irinotecan treatment. Treatment effects of AZ31, irinotecan or AZ31 + irinotecan were investigated in CRC cell lines and CRC patient derived xenografts. Activation of ATM and downstream targets p-RAD50 and p-H2AX were evaluated by immunohistochemistry. Combinational effects were demonstrated in 4 out of 8 CRC explants. Interestingly, each of the combinational sensitive CRC PDX models were shown to be more resistant to irinotecan single agent therapy. Treatment with irinotecan significantly elevated the ATM pathway evident by an increase in the activation of H2AX and RAD50. Combinational therapy reduced the activation of H2AX and RAD50 when compared to irinotecan alone in the combination sensitive CRC098. AZ31 + irinotecan was effective at reducing tumor growth in tumors that exhibited resistance to irinotecan in our CRC PDX model. These findings support further investigation of this combinational therapy for the treatment of CRC patients.
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Affiliation(s)
- Justin Greene
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - Anna Nguyen
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - Stacey M. Bagby
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - Gemma N. Jones
- Innovative Medicines and Early Development, Oncology, AstraZeneca, Cambridge, UK
| | - WM. Tai
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Kevin S. Quackenbush
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - Anna Schreiber
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - Wells A. Messersmith
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - Kalpana M. Devaraj
- Pathology Department, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Patrick Blatchford
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - S. Gail Eckhardt
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - Elaine B. Cadogan
- Innovative Medicines and Early Development, Oncology, AstraZeneca, Cambridge, UK
| | - Gareth D. Hughes
- Innovative Medicines and Early Development, Oncology, AstraZeneca, Cambridge, UK
| | - Aaron Smith
- Innovative Medicines and Early Development, Oncology, AstraZeneca, Cambridge, UK
| | - Todd M. Pitts
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
| | - John J. Arcaroli
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus and University of Colorado Cancer Center, Aurora, CO, USA
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Zhou K, Diebel KW, Holy J, Skildum A, Odean E, Hicks DA, Schotl B, Abrahante JE, Spillman MA, Bemis LT. A tRNA fragment, tRF5-Glu, regulates BCAR3 expression and proliferation in ovarian cancer cells. Oncotarget 2017; 8:95377-95391. [PMID: 29221134 PMCID: PMC5707028 DOI: 10.18632/oncotarget.20709] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/31/2017] [Indexed: 12/28/2022] Open
Abstract
Ovarian cancer is a complex disease marked by tumor heterogeneity, which contributes to difficulties in diagnosis and treatment. New molecular targets and better molecular profiles defining subsets of patients are needed. tRNA fragments (tRFs) offer a recently identified group of noncoding RNAs that are often as abundant as microRNAs in cancer cells. Initially their presence in deep sequencing data sets was attributed to the breakdown of mature tRNAs, however, it is now clear that they are actively generated and function in multiple regulatory events. One such tRF, a 5’ fragment of tRNA-Glu-CTC (tRF5-Glu), is processed from the mature tRNA-Glu and is shown in this study to be expressed in ovarian cancer cells. We confirmed that tRF5-Glu binds directly to a site in the 3’UTR of the Breast Cancer Anti-Estrogen Resistance 3 (BCAR3) mRNA thereby down regulating its expression. BCAR3 has not previously been studied in ovarian cancer cells and our studies demonstrate that inhibiting BCAR3 expression suppresses ovarian cancer cell proliferation. Furthermore, mimics of tRF5-Glu were found to inhibit proliferation of ovarian cancer cells. In summary, BCAR3 and tRF5-Glu contribute to the complex tumor heterogeneity of ovarian cancer cells and may provide new targets for therapeutic intervention.
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Affiliation(s)
- Kun Zhou
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Kevin W Diebel
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Jon Holy
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Andrew Skildum
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Evan Odean
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Douglas A Hicks
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Brent Schotl
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Monique A Spillman
- Texas A&M University Medical School, Baylor University Medical Center, Dallas, TX, 75206 USA
| | - Lynne T Bemis
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
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Epigenome Aberrations: Emerging Driving Factors of the Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2017; 18:ijms18081774. [PMID: 28812986 PMCID: PMC5578163 DOI: 10.3390/ijms18081774] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/29/2017] [Accepted: 08/12/2017] [Indexed: 12/13/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC. Although VHL mutations are considered as drivers of ccRCC, they are not sufficient to cause the disease. Recent genome-wide sequencing studies of ccRCC have revealed that mutations of genes coding for epigenome modifiers and chromatin remodelers, including PBRM1, SETD2 and BAP1, are the most common somatic genetic abnormalities after VHL mutations in these tumors. Moreover, recent research has shed light on the extent of abnormal epigenome alterations in ccRCC tumors, including aberrant DNA methylation patterns, abnormal histone modifications and deregulated expression of non-coding RNAs. In this review, we discuss the epigenetic modifiers that are commonly mutated in ccRCC, and our growing knowledge of the cellular processes that are impacted by them. Furthermore, we explore new avenues for developing therapeutic approaches based on our knowledge of epigenome aberrations of ccRCC.
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16
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Yang Y, Du Y, Liu X, Cho WC. Involvement of Non-coding RNAs in the Signaling Pathways of Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 937:19-51. [PMID: 27573893 DOI: 10.1007/978-3-319-42059-2_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most common diagnosed cancers worldwide. The metastasis and development of resistance to anti-cancer treatment are major challenges in the treatment of CRC. Understanding mechanisms underpinning the pathogenesis is therefore critical in developing novel agents for CRC treatments. A large number of evidence has demonstrated that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs have functional roles in both the physiological and pathological processes by regulating the expression of their target genes. These molecules are engaged in the pathobiology of neoplastic diseases and are targets for the diagnosis, prognosis and therapy of a variety of cancers, including CRC. In this regard, ncRNAs have emerged as one of the hallmarks of CRC pathogenesis and they also play key roles in metastasis, drug resistance and the stemness of CRC stem cell by regulating various signaling networks. Therefore, a better understanding the ncRNAs involved in the signaling pathways of CRC may lead to the development of novel strategy for diagnosis, prognosis and treatment of CRC. In this chapter, we summarize the latest findings on ncRNAs, with a focus on miRNAs and lncRNAs involving in signaling networks and in the regulation of pathogenic signaling pathways in CRC.
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Affiliation(s)
- Yinxue Yang
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yong Du
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Xiaoming Liu
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China.
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17
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Mohammadi A, Mansoori B, Baradaran B. The role of microRNAs in colorectal cancer. Biomed Pharmacother 2016; 84:705-713. [PMID: 27701052 DOI: 10.1016/j.biopha.2016.09.099] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 01/30/2023] Open
Abstract
Colorectal cancer (CRC) is still the third most common cancer in the world. Mechanism of CRC tumorigenesis has been widely studied at the molecular levels, and has been recently entered the area of microRNAs. MicroRNAs are small 19 to 22 nucleotides of RNA that engage in the regulation of cell differentiation, apoptosis, and cell cycle progression. MicroRNAs are similar to small interfering RNA (siRNA), that post-transcriptionally regulate gene expression and control various cellular mechanisms. They are important factors in the carcinogenesis of CRC, one of the most important factors includes microRNA. MicroRNAs have been linked to CRC development, and these molecules have been recently studied as new potential biomarkers in diagnosis and treatment of CRC. Specific microRNA expression patterns help distinguish CRC from other colon related disease, and may be used as a prognostication factor in patients after treatment with different chemotherapy drugs. More over the newest molecular therapy via tumor suppressor micro RNA replacement can be new insight in molecular therapy of CRC. This review summarizes the potential roles of microRNAs as potential biomarkers for CRC diagnosis, and treatment.
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Affiliation(s)
- Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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18
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Bagby S, Messersmith WA, Pitts TM, Capasso A, Varella-Garcia M, Klauck PJ, Kim J, Tan AC, Eckhardt SG, Tentler JJ, Arcaroli J. Development and Maintenance of a Preclinical Patient Derived Tumor Xenograft Model for the Investigation of Novel Anti-Cancer Therapies. J Vis Exp 2016. [PMID: 27768028 DOI: 10.3791/54393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Patient derived tumor xenograft (PDTX) models provide a necessary platform in facilitating anti-cancer drug development prior to human trials. Human tumor pieces are injected subcutaneously into athymic nude mice (immunocompromised, T cell deficient) to create a bank of tumors and subsequently are passaged into different generations of mice in order to maintain these tumors from patients. Importantly, cellular heterogeneity of the original tumor is closely emulated in this model, which provides a more clinically relevant model for evaluation of drug efficacy studies (single agent and combination), biomarker analysis, resistant pathways and cancer stem cell biology. Some limitations of the PDTX model include the replacement of the human stroma with mouse stroma after the first generation in mice, inability to investigate treatment effects on metastasis due to the subcutaneous injections of the tumors, and the lack of evaluation of immunotherapies due to the use of immunocompromised mice. However, even with these limitations, the PDTX model provides a powerful preclinical platform in the drug discovery process.
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Affiliation(s)
- Stacey Bagby
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | | | - Todd M Pitts
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | - Anna Capasso
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | | | - Peter J Klauck
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | - Jihye Kim
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | - Aik-Choon Tan
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | - S Gail Eckhardt
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | - John J Tentler
- Medicine, University of Colorado Denver Anschutz Medical Campus
| | - John Arcaroli
- Medicine, University of Colorado Denver Anschutz Medical Campus;
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Wang J, Wang H, Liu A, Fang C, Hao J, Wang Z. Lactate dehydrogenase A negatively regulated by miRNAs promotes aerobic glycolysis and is increased in colorectal cancer. Oncotarget 2016; 6:19456-68. [PMID: 26062441 PMCID: PMC4637298 DOI: 10.18632/oncotarget.3318] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/08/2015] [Indexed: 12/16/2022] Open
Abstract
Reprogramming metabolism of tumor cells is a hallmark of cancer. Lactate dehydrogenase A (LDHA) is frequently overexpressed in tumor cells. Previous studies has shown higher levels of LDHA is related with colorectal cancer (CRC), but its role in tumor maintenance and underlying molecular mechanisms has not been established. Here, we investigated miRNAs-induced changes in LDHA expression. We reported that colorectal cancer express higher levels of LDHA compared with adjacent normal tissue. Knockdown of LDHA resulted in decreased lactate and ATP production, and glucose uptake. Colorectal cancer cells with knockdown of LDHA had much slower growth rate than control cells. Furthermore, we found that miR-34a, miR-34c, miR-369-3p, miR-374a, and miR-4524a/b target LDHA and regulate glycolysis in cancer cells. There is a negative correlation between these miRNAs and LDHA expression in colorectal cancer tissues. More importantly, we identified a genetic loci newly associated with increased colorectal cancer progression, rs18407893 at 11p15.4 (in 3′-UTR of LDHA), which maps to the seed sequence recognized by miR-374a. Cancer cells overexpressed miR-374a has decreased levels of LDHA compared with miR-374a-MUT (rs18407893 at 11p15.4). Taken together, these novel findings provide more therapeutic approaches to the Warburg effect and therapeutic targets of cancer energy metabolism.
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Affiliation(s)
- Jian Wang
- Intensive Care Unit, Tianjin Hospital, Tianjin, China
| | - Hui Wang
- Department of General Surgery, Tianjin Public Security Hospital, Tianjin, China
| | - Aifen Liu
- Department of Anesthesiology, The Second Hospital Affiliated to Tianjin Medical University, Tianjin, China
| | - Changge Fang
- Advanced Personalized Diagnostics LLC, Alexandria, VA, USA
| | - Jianguo Hao
- Department of General Surgery, Taiyuan Central Hospital, Shanxi, China
| | - Zhenghui Wang
- Department of Anatomy, Histology and Embryology, Logistics University of CAPF, Tianjin, China
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20
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Cekaite L, Eide PW, Lind GE, Skotheim RI, Lothe RA. MicroRNAs as growth regulators, their function and biomarker status in colorectal cancer. Oncotarget 2016; 7:6476-505. [PMID: 26623728 PMCID: PMC4872728 DOI: 10.18632/oncotarget.6390] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023] Open
Abstract
Gene expression is in part regulated by microRNAs (miRNAs). This review summarizes the current knowledge of miRNAs in colorectal cancer (CRC); their role as growth regulators, the mechanisms that regulate the miRNAs themselves and the potential of miRNAs as biomarkers. Although thousands of tissue samples and bodily fluids from CRC patients have been investigated for biomarker potential of miRNAs (>160 papers presented in a comprehensive tables), none single miRNA nor miRNA expression signatures are in clinical use for this disease. More than 500 miRNA-target pairs have been identified in CRC and we discuss how these regulatory nodes interconnect and affect signaling pathways in CRC progression.
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Affiliation(s)
- Lina Cekaite
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Peter W. Eide
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Guro E. Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Rolf I. Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A. Lothe
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
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Jia L, Yang A. Noncoding RNAs in Therapeutic Resistance of Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:265-95. [DOI: 10.1007/978-981-10-1498-7_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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MicroRNAs as Regulator of Signaling Networks in Metastatic Colon Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:823620. [PMID: 26064956 PMCID: PMC4438141 DOI: 10.1155/2015/823620] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/06/2015] [Accepted: 04/06/2015] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a class of small, noncoding RNA molecules capable of regulating gene expression translationally and/or transcriptionally. A large number of evidence have demonstrated that miRNAs have a functional role in both physiological and pathological processes by regulating the expression of their target genes. Recently, the functionalities of miRNAs in the initiation, progression, angiogenesis, metastasis, and chemoresistance of tumors have gained increasing attentions. Particularly, the alteration of miRNA profiles has been correlated with the transformation and metastasis of various cancers, including colon cancer. This paper reports the latest findings on miRNAs involved in different signaling networks leading to colon cancer metastasis, mainly focusing on miRNA profiling and their roles in PTEN/PI3K, EGFR, TGFβ, and p53 signaling pathways of metastatic colon cancer. The potential of miRNAs used as biomarkers in the diagnosis, prognosis, and therapeutic targets in colon cancer is also discussed.
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Abstract
OBJECTIVES In this study, we identified the protein kinases that play the most distinct roles in the occurrence of acute pancreatitis (AP). METHODS Gene expression profile data were downloaded from Gene Expression Omnibus database (GSE3644). The sample was from caerulein-induced AP mice. The intersection of the differentially expressed genes in AP mice taken from a protein kinase database was obtained for screening of the protein kinase encoded genes that were differentially expressed. Database for annotation, visualization, and integrated discovery was used for the functional enrichment analysis. Kinase inhibitors that regulated these kinases were retrieved from PubMed through text mining. RESULTS Twenty-nine differentially expressed kinase encoded genes were identified through screening. The functional enrichment analysis demonstrated that the functions of these genes were primarily enriched in "mitogen-activated protein kinase signaling pathway," followed by "extracellular regulated protein kinases pathway," "neurotrophin signaling pathway," "adherens junction," and "gap junction." SRC and epidermal growth factor receptor (EGFR) were related to extracellular regulated protein kinases pathway and also related to adherens junction as well as gap junction. On the basis of the regulated kinases, the kinase inhibitors reported in the literature were classified into multiple groups. CONCLUSIONS EGFR and SRC may be coexpressed in AP. The kinase inhibitors working together in SRC and EGFR may play better efficacy in the treatment of AP.
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Igarashi H, Kurihara H, Mitsuhashi K, Ito M, Okuda H, Kanno S, Naito T, Yoshii S, Takahashi H, Kusumi T, Hasegawa T, Sukawa Y, Adachi Y, Okita K, Hirata K, Imamura Y, Baba Y, Imai K, Suzuki H, Yamamoto H, Nosho K, Shinomura Y. Association of MicroRNA-31-5p with Clinical Efficacy of Anti-EGFR Therapy in Patients with Metastatic Colorectal Cancer. Ann Surg Oncol 2014; 22:2640-8. [PMID: 25472647 DOI: 10.1245/s10434-014-4264-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND Gene mutations in the pathway downstream of epidermal growth factor receptor (EGFR) are considered to induce resistance to anti-EGFR therapy in colorectal cancer (CRC). We recently reported that microRNA-31 (miR-31)-5p may regulate BRAF activation and play a role in the signaling pathway downstream of EGFR in CRC. Therefore, we hypothesized that miR-31-5p can be a useful biomarker for anti-EGFR therapy in CRC. METHODS We evaluated miR-31-5p expression and gene mutations [KRAS (codon 61 or 146), NRAS (codon 12, 13, or 61), and BRAF (V600E)] in the EGFR downstream pathway in 102 CRC patients harboring KRAS (codon 12 or 13) wild-type who were treated with anti-EGFR therapeutics. Progression-free survival (PFS) and overall survival (OS) were evaluated. RESULTS KRAS (codon 61 or 146), NRAS, and BRAF mutations were detected in 6.9, 6.9, and 5.9 % patients, respectively. Compared with CRCs with at least one mutation (n = 20), significantly better PFS (P = 0.0003) but insignificantly better OS were observed in CRCs harboring all wild-type genes (KRAS, NRAS, and BRAF). High miR-31-5p expression was identified in 11 % (n = 11) patients and was significantly associated with shorter PFS (P = 0.003). In CRCs carrying all wild-type genes, high miR-31-5p was associated with shorter PFS (P = 0.027). CONCLUSIONS High miR-31-5p expression was associated with shorter PFS in patients with CRC treated with anti-EGFR therapeutics. Moreover, in CRCs carrying all wild-type genes, high miR-31-5p was associated with shorter PFS, suggesting that it may be a useful and additional prognostic biomarker for anti-EGFR therapy.
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Affiliation(s)
- Hisayoshi Igarashi
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Danielsen SA, Eide PW, Nesbakken A, Guren T, Leithe E, Lothe RA. Portrait of the PI3K/AKT pathway in colorectal cancer. Biochim Biophys Acta Rev Cancer 2014; 1855:104-21. [PMID: 25450577 DOI: 10.1016/j.bbcan.2014.09.008] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/07/2014] [Indexed: 12/16/2022]
Abstract
PI3K/AKT signaling leads to reduced apoptosis, stimulates cell growth and increases proliferation. Under normal conditions, PI3K/AKT activation is tightly controlled and dependent on both extracellular growth signals and the availability of amino acids and glucose. Genetic aberrations leading to PI3K/AKT hyper-activation are observed at considerable frequency in all major nodes in most tumors. In colorectal cancer the most commonly observed pathway changes are IGF2 overexpression, PIK3CA mutations and PTEN mutations and deletions. Combined, these alterations are found in about 40% of large bowel tumors. In addition, but not mutually exclusive to these, KRAS mutations are observed at a similar frequency. There are however additional, less frequent and more poorly understood events that may also push the PI3K/AKT pathway into overdrive and thus promote malignant growth. Here we discuss aberrations of components at the genetic, epigenetic, transcriptional, post-transcriptional, translational and post-translational level where perturbations may drive excessive PI3K/AKT signaling. Integrating multiple molecular levels will advance our understanding of this cancer critical circuit and more importantly, improve our ability to pharmacologically target the pathway in view of clonal development, tumor heterogeneity and drug resistance mechanisms. In this review, we revisit the PI3K/AKT pathway cancer susceptibility syndromes, summarize the known aberrations at the different regulatory levels and the prognostic and predictive values of these alterations in colorectal cancer.
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Affiliation(s)
- Stine Aske Danielsen
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Peter Wold Eide
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Arild Nesbakken
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo, Norway
| | - Tormod Guren
- K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Edward Leithe
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.
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Hong YS, Kim J, Pectasides E, Fox C, Hong SW, Ma Q, Wong GS, Peng S, Stachler MD, Thorner AR, Van Hummelen P, Bass AJ. Src mutation induces acquired lapatinib resistance in ERBB2-amplified human gastroesophageal adenocarcinoma models. PLoS One 2014; 9:e109440. [PMID: 25350844 PMCID: PMC4211679 DOI: 10.1371/journal.pone.0109440] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/01/2014] [Indexed: 02/01/2023] Open
Abstract
ERBB2-directed therapy is now a routine component of therapy for ERBB2-amplified metastatic gastroesophageal adenocarcinomas. However, there is little knowledge of the mechanisms by which these tumors develop acquired resistance to ERBB2 inhibition. To investigate this question we sought to characterize cell line models of ERBB2-amplified gastroesophageal adenocarcinoma with acquired resistance to ERBB2 inhibition. We generated lapatinib-resistant (LR) subclones from an initially lapatinib-sensitive ERBB2-amplified esophageal adenocarcinoma cell line, OE19. We subsequently performed genomic characterization and functional analyses of resistant subclones with acquired lapatinib resistance. We identified a novel, acquired SrcE527K mutation in a subset of LR OE19 subclones. Cells with this mutant allele harbour increased Src phosphorylation. Genetic and pharmacologic inhibition of Src resensitized these subclones to lapatinib. Biochemically, Src mutations could activate both the phosphatidylinositol 3-kinase and mitogen activated protein kinase pathways in the lapatinib-treated LR OE19 cells. Ectopic expression of SrcE527K mutation also was sufficient to induce lapatinib resistance in drug-naïve cells. These results indicate that pathologic activation of Src is a potential mechanism of acquired resistance to ERBB2 inhibition in ERBB2-amplified gastroesophageal cancer. Although Src mutation has not been described in primary tumor samples, we propose that the Src hyperactivation should be investigated in the settings of acquired resistance to ERBB2 inhibition in esophageal and gastric adenocarcinoma.
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Affiliation(s)
- Yong Sang Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jihun Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eirini Pectasides
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Cameron Fox
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Seung-Woo Hong
- Innovative Cancer Research, Asan Institute for Life Science, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Qiuping Ma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Gabrielle S. Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Shouyong Peng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Matthew D. Stachler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Aaron R. Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Paul Van Hummelen
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Adam J. Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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Dong P, Konno Y, Watari H, Hosaka M, Noguchi M, Sakuragi N. The impact of microRNA-mediated PI3K/AKT signaling on epithelial-mesenchymal transition and cancer stemness in endometrial cancer. J Transl Med 2014; 12:231. [PMID: 25141911 PMCID: PMC4145234 DOI: 10.1186/s12967-014-0231-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 08/12/2014] [Indexed: 02/06/2023] Open
Abstract
Activation of the PI3K/AKT pathway, a common mechanism in all subtypes of endometrial cancers (endometrioid and non-endometrioid tumors), has important roles in contributing to epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC) features. MicroRNAs (miRNAs) are small non-coding RNA molecules that concurrently affect multiple target genes, and regulate a wide range of genes involved in modulating EMT and CSC properties. Here we overview the recent advances revealing the impact of miRNAs on EMT and CSC phenotypes in tumors including endometrial cancer via regulating PI3K/AKT pathway. MiRNAs are crucial mediators of EMT and CSC through targeting PTEN-PI3K-AKT-mTOR axis. In endometrial cancer cells, miRNAs can activate or attenuate EMT and CSC by targeting PTEN and other EMT-associated genes, such as Twist1, ZEB1 and BMI-1. More detailed studies of miRNAs will deepen our understanding of the molecular basis underlying PI3K/AKT-induced endometrial cancer initiation and progression. Targeting key signaling components of PI3K/AKT pathway by restoring or inhibiting miRNA function holds promise as a potential therapeutic approach to suppress EMT and CSC in endometrial cancer.
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Affiliation(s)
- Peixin Dong
- Department of Women's Health Educational System, Hokkaido University School of Medicine, Hokkaido University, N15, W7, Sapporo 0608638, Japan.
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Increased SOX2 gene copy number is associated with FGFR1 and PIK3CA gene gain in non-small cell lung cancer and predicts improved survival in early stage disease. PLoS One 2014; 9:e95303. [PMID: 24736592 PMCID: PMC3988173 DOI: 10.1371/journal.pone.0095303] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 03/26/2014] [Indexed: 12/21/2022] Open
Abstract
Background We aimed to investigate prevalence and prognostic role of SOX2, PIK3CA, FGFR1 and BRF2 gene gain in patients with surgically resected non-small cell lung cancer (NSCLC). Methods SOX2, PIK3CA, FGFR1 and BRF2 gene copy number was assessed by fluorescence in situ hybridization (FISH) in arrayed tissue cores from 447 resected NSCLCs. Results Increased gene copy number (FISH+) for SOX2, PIK3CA, FGFR1 and BRF2 was observed in 23.6%, 29.2%, 16.6% and 14.9% of cases, respectively. FISH+ status for each gene was significantly associated with smoking history, squamous cell carcinoma (SCC) histology, and increased copy number of the other studied genes. Multivariate analysis of overall survival indicated increased SOX2 gene copy number (P = 0.008), stage I-II (P<0.001), and adenocarcinoma or SCC histology (P = 0.016) as independent, favorable prognostic factors. A statistically significant interaction was observed between stage and SOX2 gene status (P = 0.021), indicating that the prognostic impact of SOX2 gene gain differs across stages and is limited to patients with stage I-II disease (HR 0.44, 95% CI: 0.25–0.77; P = 0.004, adjusted for histology). Conclusions Increased SOX2 gene copy number is an independent and favorable prognostic factor in surgically resected, early stage NSCLC, regardless of histology. SOX2, PIK3CA, FGFR1 and BRF2 gene gains are likely to occur concurrently, with potentially relevant implications for the development of new therapeutic strategies.
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30
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Gossage L, Murtaza M, Slatter AF, Lichtenstein CP, Warren A, Haynes B, Marass F, Roberts I, Shanahan SJ, Claas A, Dunham A, May AP, Rosenfeld N, Forshew T, Eisen T. Clinical and pathological impact of VHL, PBRM1, BAP1, SETD2, KDM6A, and JARID1c in clear cell renal cell carcinoma. Genes Chromosomes Cancer 2014; 53:38-51. [PMID: 24166983 DOI: 10.1002/gcc.22116] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/16/2013] [Indexed: 12/21/2022] Open
Abstract
VHL is mutated in the majority of patients with clear cell renal cell carcinoma (ccRCC), with conflicting clinical relevance. Recent studies have identified recurrent mutations in histone modifying and chromatin remodeling genes, including BAP1, PBRM1, SETD2, KDM6A, and JARID1c. Current evidence suggests that BAP1 mutations are associated with aggressive disease. The clinical significance of the remaining genes is unknown. In this study, targeted sequencing of VHL and JARID1c (entire genes) and coding regions of BAP1, PBRM1, SETD2, and KDM6A was performed on 132 ccRCCs and matched normal tissues. Associations between mutations and clinical and pathological outcomes were interrogated. Inactivation of VHL (coding mutation or promoter methylation) was seen in 75% of ccRCCs. Somatic noncoding VHL alterations were identified in 29% of ccRCCs and may be associated with improved overall survival. BAP1 (11%), PBRM1 (33%), SETD2 (16%), JARID1c (4%), and KDM6A (3%) mutations were identified. BAP1-mutated tumors were associated with metastatic disease at presentation (P = 0.023), advanced clinical stage (P = 0.042) and a trend towards shorter recurrence free survival (P = 0.059) when compared with tumors exclusively mutated for PBRM1. Our results support those of recent publications pointing towards a role for BAP1 and PBRM1 mutations in risk stratifying ccRCCs. Further investigation of noncoding alterations in VHL is warranted.
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Affiliation(s)
- Lucy Gossage
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
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Manikandan M, Munirajan AK. Single nucleotide polymorphisms in microRNA binding sites of oncogenes: implications in cancer and pharmacogenomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 18:142-54. [PMID: 24286505 DOI: 10.1089/omi.2013.0098] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer, a complex genetic disease involving uncontrolled cell proliferation, is caused by inactivation of tumor suppressor genes and activation of oncogenes. A vast majority of these cancer causing genes are known targets of microRNAs (miRNAs) that bind to complementary sequences in 3' untranslated regions (UTR) of messenger RNAs and repress them from translation. Single Nucleotide Polymorphisms (SNPs) occurring naturally in such miRNA binding regions can alter the miRNA:mRNA interaction and can significantly affect gene expression. We hypothesized that 3'UTR SNPs in miRNA binding sites of proto-oncogenes could abrogate their post-transcriptional regulation, resulting in overexpression of oncogenic proteins, tumor initiation, progression, and modulation of drug response in cancer patients. Therefore, we developed a systematic computational pipeline that integrates data from well-established databases, followed stringent selection criteria and identified a panel of 30 high-confidence SNPs that may impair miRNA target sites in the 3' UTR of 54 mRNA transcripts of 24 proto-oncogenes. Further, 8 SNPs amidst them had the potential to determine therapeutic outcome in cancer patients. Functional annotation suggested that altogether these SNPs occur in proto-oncogenes enriched for kinase activities. We provide detailed in silico evidence for the functional effect of these candidate SNPs in various types of cancer.
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Affiliation(s)
- Mayakannan Manikandan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras , Taramani Campus, Chennai, Tamil Nadu, India
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32
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Nosho K, Igarashi H, Nojima M, Ito M, Maruyama R, Yoshii S, Naito T, Sukawa Y, Mikami M, Sumioka W, Yamamoto E, Kurokawa S, Adachi Y, Takahashi H, Okuda H, Kusumi T, Hosokawa M, Fujita M, Hasegawa T, Okita K, Hirata K, Suzuki H, Yamamoto H, Shinomura Y. Association of microRNA-31 with BRAF mutation, colorectal cancer survival and serrated pathway. Carcinogenesis 2013; 35:776-83. [PMID: 24242331 DOI: 10.1093/carcin/bgt374] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BRAF is an important gene in colorectal cancers (CRCs) that is associated with molecular characterization and resistance to targeted therapy. Although microRNAs (miRNAs) are useful biomarkers of various cancers, the association between miRNA and BRAF in CRCs is undefined. Therefore, this study was conducted to identify a relationship between specific miRNA molecules and BRAF mutation in CRCs and serrated lesions. miRNA array was used for the measurement of 760 miRNAs in 29 CRCs. To assess the identified miRNAs, quantitative reverse transcription-PCR was performed on 721 CRCs, 381 serrated lesions and 251 non-serrated adenomas. Moreover, proliferation and invasion assays were conducted using cell lines. miRNA array analysis revealed that microRNA-31 (miR-31)-5p was the most up-regulated miRNA in CRCs with mutated BRAF (V600E) compared with CRCs possessing wild-type BRAF (including cases with KRAS mutation). High miR-31 expression was associated with BRAF and KRAS mutations and proximal location (P < 0.0001). High miR-31 expression was related to cancer-specific mortality [multivariate hazard ratio = 2.06, 95% confidence interval: 1.36-3.09, P = 0.0008]. Functional analysis demonstrated that miR-31 inhibitor decreased cell invasion and proliferation. With regard to serrated lesions, high miR-31 expression was less frequently detected in hyperplastic polyps compared with other serrated lesions. In conclusion, associations were identified between miR-31, BRAF and prognosis in CRC. Transfection of miR-31 inhibitor had an antitumour effect. Thus, miR-31 may be a promising diagnostic biomarker and therapeutic target in colon cancers. Moreover, high miR-31 expression in serrated lesions suggested that miR-31 may be a key molecule in serrated pathway.
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Affiliation(s)
- Katsuhiko Nosho
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Ogino S, Liao X, Imamura Y, Yamauchi M, McCleary NJ, Ng K, Niedzwiecki D, Saltz LB, Mayer RJ, Whittom R, Hantel A, Benson AB, Mowat RB, Spiegelman D, Goldberg RM, Bertagnolli MM, Meyerhardt JA, Fuchs CS. Predictive and prognostic analysis of PIK3CA mutation in stage III colon cancer intergroup trial. J Natl Cancer Inst 2013; 105:1789-98. [PMID: 24231454 DOI: 10.1093/jnci/djt298] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Somatic mutations in PIK3CA (phosphatidylinositol-4,5-bisphosphonate 3-kinase [PI3K], catalytic subunit alpha gene) activate the PI3K-AKT signaling pathway and contribute to pathogenesis of various malignancies, including colorectal cancer. METHODS We examined associations of PIK3CA oncogene mutation with relapse, survival, and treatment efficacy in 627 stage III colon carcinoma case subjects within a randomized adjuvant chemotherapy trial (5-fluorouracil and leucovorin [FU/LV] vs irinotecan [CPT11], fluorouracil and leucovorin [IFL]; Cancer and Leukemia Group B 89803 [Alliance]). We detected PIK3CA mutation in exons 9 and 20 by polymerase chain reaction and pyrosequencing. Cox proportional hazards model was used to assess prognostic and predictive role of PIK3CA mutation, adjusting for clinical features and status of routine standard molecular pathology features, including KRAS and BRAF mutations and microsatellite instability (mismatch repair deficiency). All statistical tests were two-sided. RESULTS Compared with PIK3CA wild-type cases, overall status of PIK3CA mutation positivity or the presence of PIK3CA mutation in either exon 9 or 20 alone was not statistically significantly associated with recurrence-free, disease-free, or overall survival (log-rank P > .70; P > .40 in multivariable regression models). There was no statistically significant interaction between PIK3CA and KRAS (or BRAF) mutation status in survival analysis (P(interaction) > .18). PIK3CA mutation status did not appear to predict better or worse response to IFL therapy compared with FU/LV therapy (P(interaction) > .16). CONCLUSIONS Overall tumor PIK3CA mutation status is not associated with stage III colon cancer prognosis. PIK3CA mutation does not appear to serve as a predictive tumor molecular biomarker for response to irinotecan-based adjuvant chemotherapy.
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Affiliation(s)
- Shuji Ogino
- Affiliations of authors: Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA (SO, XL, YI, MY, NJM, KN, RJM, JAM, CSF); Department of Pathology (SO), Channing Division of Network Medicine, Department of Medicine (DS, CSF), and Department of Surgery (MMB), Brigham and Women's Hospital and Harvard Medical School, Boston, MA (SO); Department of Epidemiology (SO, DS) and Department of Biostatistics (DS) , Harvard School of Public Health, Boston, MA; Alliance Statistics and Data Center, Duke University Medical Center, Durham, NC (DN); Memorial Sloan-Kettering Cancer Center, New York, NY (LBS); Hôpital du Sacré-Coeur de Montréal, Montreal, Canada (RW); Loyola University Stritch School of Medicine, Maywood, IL (AH); current: Edward Cancer Center, Naperville, IL (AH); Northwestern University, Chicago, IL (ABB); Toledo Community Hospital Oncology Program, Toledo, OH (RBM); Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH (RMG)
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Klempner SJ, Myers AP, Mills GB, Westin SN. Clinical investigation of receptor and non-receptor tyrosine kinase inhibitors for the treatment of epithelial ovarian cancer. Expert Opin Pharmacother 2013; 14:2171-82. [PMID: 23937415 PMCID: PMC4103698 DOI: 10.1517/14656566.2013.826650] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Epithelial ovarian cancer (EOC) is the second most common gynecologic malignancy and the leading cause of death from gynecologic cancer in the USA. EOC is an exquisitely chemo-sensitive disease with response rates of over 75% in the upfront setting. Despite this, due to high rates of recurrence and development of chemo-resistance, the overall survival of EOC remains about 25%. Thus, there is a great need for new therapeutic approaches to render more durable responses. Based on preclinical and early phase clinical studies, key targeted pathways include targets that drive angiogenesis and chemo-resistance. Receptor tyrosine kinases and non-receptor tyrosine kinases play important roles in these processes and several small molecule tyrosine kinase inhibitors (TKIs) are in clinical development. AREAS COVERED This review summarizes clinical rationale, mechanisms of action and clinical data for the TKIs under evaluation in the Phase III setting for EOC. EXPERT OPINION Despite reasonable preclinical activity, small molecule TKIs are unlikely to improve patient survival as single agent therapies in an unselected EOC population. Incorporation of tissue evaluation during ongoing clinical trials is required to identify molecularly defined groups that respond to single agents and direct rational combination strategies based on mechanisms of resistance to improve outcomes in EOC.
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Affiliation(s)
- Samuel J. Klempner
- Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | - Andrea P. Myers
- Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215
- Department of Gynecologic Oncology, Dana Farber Cancer Institute, Boston, MA, 02215
| | - Gordon B. Mills
- Department of Systems Biology, University of Texas M. D. Anderson Cancer Center, Houston TX, 77030
| | - Shannon N. Westin
- Departments of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, 77030
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Bennett PE, Bemis L, Norris DA, Shellman YG. miR in melanoma development: miRNAs and acquired hallmarks of cancer in melanoma. Physiol Genomics 2013; 45:1049-59. [PMID: 24046283 DOI: 10.1152/physiolgenomics.00116.2013] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Melanoma is a very aggressive skin cancer with increasing incidence worldwide. MicroRNAs are small, noncoding RNAs that regulate gene expression of targeted gene(s). The hallmark of cancer model outlined by Hanahan and Weinberg offers a meaningful framework to consider the roles of microRNAs in melanoma development and progression. In this systematic review of the literature, we associate what is known about deregulation of microRNAs and their targeted genes in melanoma development with the hallmarks and characteristics of cancer. The diagnostic and therapeutic potential of microRNAs for future melanoma management will also be discussed.
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Affiliation(s)
- Paige E Bennett
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Mlcochova J, Faltejskova P, Nemecek R, Svoboda M, Slaby O. MicroRNAs targeting EGFR signalling pathway in colorectal cancer. J Cancer Res Clin Oncol 2013; 139:1615-24. [PMID: 23817698 DOI: 10.1007/s00432-013-1470-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/21/2013] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are short, 18-25-nucleotide long, non-coding single-stranded RNAs, which are capable to regulate gene expression on post-transcriptional level through binding to their target protein-encoding mRNAs. miRNAs regulate individual components of multiple oncogenic pathways. One of them is epidermal growth factor receptor (EGFR) signalling pathway that regulates cell proliferation, differentiation, migration, angiogenesis and apoptosis. All these processes are deregulated in colorectal cancer (CRC). Moreover, EGFR has been validated as the therapeutic target in CRC, and monoclonal antibodies cetuximab and panitumumab are used in the therapy of patients with metastatic CRC. Because of the extensive involvement of miRNAs in the regulation of EGFR signalling, it seems they could also serve as promising predictive biomarkers to anti-EGFR therapy. In this review, we summarize current knowledge about miRNAs targeting EGFR signalling pathway, their functioning in CRC pathogenesis and potential usage as biomarkers.
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Affiliation(s)
- Jitka Mlcochova
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic, Europe
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Arcaroli J, Quackenbush K, Dasari A, Powell R, McManus M, Tan AC, Foster NR, Picus J, Wright J, Nallapareddy S, Erlichman C, Hidalgo M, Messersmith WA. Biomarker-driven trial in metastatic pancreas cancer: feasibility in a multicenter study of saracatinib, an oral Src inhibitor, in previously treated pancreatic cancer. Cancer Med 2012; 1:207-17. [PMID: 23342270 PMCID: PMC3544442 DOI: 10.1002/cam4.27] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/23/2012] [Accepted: 07/24/2012] [Indexed: 12/16/2022] Open
Abstract
Src tyrosine kinases are overexpressed in pancreatic cancers, and the oral Src inhibitor saracatinib has shown antitumor activity in preclinical models of pancreas cancer. We performed a CTEP-sponsored Phase II clinical trial of saracatinib in previously treated pancreas cancer patients, with a primary endpoint of 6-month survival. A Simon MinMax two-stage phase II design was used. Saracatinib (175 mg/day) was administered orally continuously in 28-day cycles. In the unselected portion of the study, 18 patients were evaluable. Only two (11%) patients survived for at least 6 months, and three 6-month survivors were required to move to second stage of study as originally designed. The study was amended as a biomarker-driven trial (leucine rich repeat containing protein 19 [LRRC19] > insulin-like growth factor-binding protein 2 [IGFBP2] "top scoring pairs" polymerase chain reaction [PCR] assay, and PIK3CA mutant) based on preclinical data in a human pancreas tumor explant model. In the biomarker study, archival tumor tissue or fresh tumor biopsies were tested. Biomarker-positive patients were eligible for the study. Only one patient was PIK3CA mutant in a 3' untranslated region (UTR) portion of the gene. This patient was enrolled in the study and failed to meet the 6-month survival endpoint. As the frequency of biomarker-positive patients was very low (<3%), the study was closed. Although we were unable to conclude whether enriching for a subset of second/third line pancreatic cancer patients treated with a Src inhibitor based on a biomarker would improve 6-month survival, we demonstrate that testing pancreatic tumor samples for a biomarker-driven, multicenter study in metastatic pancreas cancer is feasible.
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Affiliation(s)
- John Arcaroli
- University of Colorado Cancer Center, Denver, Colorado 80045, USA
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