251
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Zhu M, Lv Q, Huang H, Sun C, Pang D, Wu J. Identification of a four-long non-coding RNA signature in predicting breast cancer survival. Oncol Lett 2019; 19:221-228. [PMID: 31897133 PMCID: PMC6924049 DOI: 10.3892/ol.2019.11063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 10/04/2019] [Indexed: 01/14/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) serve key roles in tumorigenesis and are differentially expressed in cancer. Using bioinformatics and statistical methods, the present study aimed to identify an lncRNA signature to predict breast cancer survival. The gene expression data of 768 patients with breast cancer were downloaded from The Cancer Genome Atlas database, and Cox regression, Kaplan-Meier and receiver operating characteristic (ROC) analyses were performed to construct and validate a predictive model. Gene Ontology term enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis were employed to predict the functions of the indicated lncRNAs. A signature consisting of four lncRNAs, including PVT1, MAPT-AS1, LINC00667 and LINC00938, was identified, and patients were subsequently divided into high- and low-risk groups according to the median risk score. Kaplan-Meier analysis confirmed that patients in the high-risk group exhibited significantly poorer overall survival rate in both the training (P=0.0151) and the validation set (P=0.0016); furthermore, ROC analysis confirmed that the model could predict patient survival with a certain sensitivity and specificity. In conclusion, the four-lncRNA signature presents a potential prognostic biomarker for breast cancer that may be relevant for clinical application.
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Affiliation(s)
- Mingjie Zhu
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214035, P.R. China
| | - Qing Lv
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214035, P.R. China
| | - Hu Huang
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214035, P.R. China
| | - Chunlei Sun
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214035, P.R. China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Junqiang Wu
- Department of Breast Surgery, The Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214035, P.R. China
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252
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Boloix A, Masanas M, Jiménez C, Antonelli R, Soriano A, Roma J, Sánchez de Toledo J, Gallego S, Segura MF. Long Non-coding RNA PVT1 as a Prognostic and Therapeutic Target in Pediatric Cancer. Front Oncol 2019; 9:1173. [PMID: 31781490 PMCID: PMC6853055 DOI: 10.3389/fonc.2019.01173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022] Open
Abstract
In recent decades, biomedical research has focused on understanding the functionality of the human translated genome, which represents a minor part of all genetic information transcribed from the human genome. However, researchers have become aware of the importance of non-coding RNA species that constitute the vast majority of the transcriptome. In addition to their crucial role in tissue development and homeostasis, mounting evidence shows non-coding RNA to be deregulated and functionally contributing to the development and progression of different types of human disease including cancer both in adults and children. Small non-coding RNAs (i.e., microRNA) are in the vanguard of clinical research which revealed that RNA could be used as disease biomarkers or new therapeutic targets. Furthermore, many more expectations have been raised for long non-coding RNAs, by far the largest fraction of non-coding transcripts, and still fewer findings have been translated into clinical applications. In this review, we center on PVT1, a large and complex long non-coding RNA that usually confers oncogenic properties on different tumor types. We focus on the compilation of early advances in the field of pediatric tumors which often lags behind clinical improvements in adult tumors, and provide a rationale to continue studying PVT1 as a possible functional contributor to pediatric malignancies and as a potential prognostic marker or therapeutic target.
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Affiliation(s)
- Ariadna Boloix
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Esfera UAB, Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Marc Masanas
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Carlos Jiménez
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Roberta Antonelli
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Aroa Soriano
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Roma
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Josep Sánchez de Toledo
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Soledad Gallego
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Miguel F Segura
- Group of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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253
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Jamal M, Song T, Chen B, Faisal M, Hong Z, Xie T, Wu Y, Pan S, Yin Q, Shao L, Zhang Q. Recent Progress on Circular RNA Research in Acute Myeloid Leukemia. Front Oncol 2019; 9:1108. [PMID: 31781482 PMCID: PMC6851197 DOI: 10.3389/fonc.2019.01108] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/07/2019] [Indexed: 12/26/2022] Open
Abstract
Acute myeloid leukemia (AML) is a myeloid malignancy characterized by the proliferation of abnormal and immature myeloid blasts in the bone marrow. Circular RNA (circRNA) is a novel class of long non-coding RNA with a stable circular conformation that regulates various biological processes. The aberrant expression of circRNA and its impact on AML progression has been reported by a number of studies. Despite recent advances in circRNA research, our understanding of the leukemogenic mechanism of circRNA remains very limited, and translating the current circRNA-related research into clinical practice is challenging. This review provides an update on the functional roles of and research progress on circRNAs in AML with an emphasis on mechanistic insights. The challenges and opportunities associated with circRNA-based diagonostic and therapeutic development in AML are also outlined.
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Affiliation(s)
- Muhammad Jamal
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Tianbao Song
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Bei Chen
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Muhammad Faisal
- Institute of Pathology, Hannover Medical School, Hanover, Germany
| | - Zixi Hong
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Tian Xie
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Yingjie Wu
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Shan Pan
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Qian Yin
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Liang Shao
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuping Zhang
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan, China
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254
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Jin K, Wang S, Zhang Y, Xia M, Mo Y, Li X, Li G, Zeng Z, Xiong W, He Y. Long non-coding RNA PVT1 interacts with MYC and its downstream molecules to synergistically promote tumorigenesis. Cell Mol Life Sci 2019; 76:4275-4289. [PMID: 31309249 PMCID: PMC6803569 DOI: 10.1007/s00018-019-03222-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/22/2019] [Accepted: 07/05/2019] [Indexed: 02/06/2023]
Abstract
Numerous studies have shown that non-coding RNAs play crucial roles in the development and progression of various tumor cells. Plasmacytoma variant translocation 1 (PVT1) mainly encodes a long non-coding RNA (lncRNA) and is located on chromosome 8q24.21, which constitutes a fragile site for genetic aberrations. PVT1 is well-known for its interaction with its neighbor MYC, which is a qualified oncogene that plays a vital role in tumorigenesis. In the past several decades, increasing attention has been paid to the interaction mechanism between PVT1 and MYC, which will benefit the clinical treatment and prognosis of patients. In this review, we summarize the coamplification of PVT1 and MYC in cancer, the positive feedback mechanism, and the latest promoter competition mechanism of PVT1 and MYC, as well as how PVT1 participates in the downstream signaling pathway of c-Myc by regulating key molecules. We also briefly describe the treatment prospects and research directions of PVT1 and MYC.
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Affiliation(s)
- Ke Jin
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shufei Wang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yazhuo Zhang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Mengfang Xia
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yongzhen Mo
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yi He
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.
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255
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Choudhari R, Sedano MJ, Harrison AL, Subramani R, Lin KY, Ramos EI, Lakshmanaswamy R, Gadad SS. Long noncoding RNAs in cancer: From discovery to therapeutic targets. Adv Clin Chem 2019; 95:105-147. [PMID: 32122521 DOI: 10.1016/bs.acc.2019.08.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently gained considerable attention as key players in biological regulation; however, the mechanisms by which lncRNAs govern various disease processes remain mysterious and are just beginning to be understood. The ease of next-generation sequencing technologies has led to an explosion of genomic information, especially for the lncRNA class of noncoding RNAs. LncRNAs exhibit the characteristics of mRNAs, such as polyadenylation, 5' methyl capping, RNA polymerase II-dependent transcription, and splicing. These transcripts comprise more than 200 nucleotides (nt) and are not translated into proteins. Directed interrogation of annotated lncRNAs from RNA-Seq datasets has revealed dramatic differences in their expression, largely driven by alterations in transcription, the cell cycle, and RNA metabolism. The fact that lncRNAs are expressed cell- and tissue-specifically makes them excellent biomarkers for ongoing biological events. Notably, lncRNAs are differentially expressed in several cancers and show a distinct association with clinical outcomes. Novel methods and strategies are being developed to study lncRNA function and will provide researchers with the tools and opportunities to develop lncRNA-based therapeutics for cancer.
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Affiliation(s)
- Ramesh Choudhari
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Melina J Sedano
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Alana L Harrison
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Ramadevi Subramani
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Ken Y Lin
- The Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Enrique I Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Rajkumar Lakshmanaswamy
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Shrikanth S Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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256
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Xiong X, Yuan J, Zhang N, Zheng Y, Liu J, Yang M. Silencing of lncRNA PVT1 by miR-214 inhibits the oncogenic GDF15 signaling and suppresses hepatocarcinogenesis. Biochem Biophys Res Commun 2019; 521:478-484. [PMID: 31677796 DOI: 10.1016/j.bbrc.2019.10.137] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
Abstract
The prognosis for hepatocellular carcinoma (HCC) is dismal. Long noncoding RNA PVT1 has been linked to malignancies and might be a deleterious therapy target. However, the key events controlling its expression in HCC remain undetermined. Here, we address how PVT1 is fine-regulated and its downstream signaling in hepatoma cells. Interestingly, we found that c-Myc and P53 could divergently regulate PVT1 transcription. Oncoprotein c-Myc enhances PVT1 expression, whereas P53 suppresses its expression. We also identified miR-214 as a crucial, negative regulator of PVT1. Consistently, high miR-214 levels were significantly correlated with diminished PVT1 expression in HCC specimens. Silencing of PVT1 by ectopic miR-214 or siRNAs markedly inhibited viability and invasion of HCC cells. In opposition, inhibition of endogenous miR-214 promoted PVT1 expression and enhanced cell proliferation. Notably, oncogenic GDF15 is a potential downstream target of the miR-214-PVT1 signaling. Collectively, our results show that the c-Myc/P53/miR-214-PVT1-GDF15 axis is implicated in HCC development, shedding light on the mechanistic actions of PVT1 and representing potential targets for HCC clinical intervention.
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Affiliation(s)
- Xiangyu Xiong
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Jupeng Yuan
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Nasha Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Yan Zheng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Jibing Liu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
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257
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N 6-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis. Nat Commun 2019; 10:4695. [PMID: 31619685 PMCID: PMC6795808 DOI: 10.1038/s41467-019-12651-2] [Citation(s) in RCA: 437] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 09/22/2019] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) have been implicated in cancer progression through largely unknown mechanisms. Herein, we identify an N6-methyladenosine (m6A) modified circRNA, circNSUN2, frequently upregulated in tumor tissues and serum samples from colorectal carcinoma (CRC) patients with liver metastasis (LM) and predicts poorer patient survival. The upregulated expression of circNSUN2 promotes LM in PDX metastasis models in vivo and accelerates cancer cells invasion in vitro. Importantly, N6-methyladenosine modification of circNSUN2 increases export to the cytoplasm. By forming a circNSUN2/IGF2BP2/HMGA2 RNA-protein ternary complex in the cytoplasm, circNSUN2 enhances the stability of HMGA2 mRNA to promote CRC metastasis progression. Clinically, the upregulated expressions of circNSUN2 and HMGA2 are more prevalent in LM tissues than in primary CRC tissues. These findings elucidate that N6-methyladenosine modification of circNSUN2 modulates cytoplasmic export and stabilizes HMGA2 to promote CRC LM, and suggest that circNSUN2 could represent a critical prognostic marker and/or therapeutic target for the disease.
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258
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Xu Y, Li Y, Jin J, Han G, Sun C, Pizzi MP, Huo L, Scott A, Wang Y, Ma L, Lee JH, Bhutani MS, Weston B, Vellano C, Yang L, Lin C, Kim Y, MacLeod AR, Wang L, Wang Z, Song S, Ajani JA. LncRNA PVT1 up-regulation is a poor prognosticator and serves as a therapeutic target in esophageal adenocarcinoma. Mol Cancer 2019; 18:141. [PMID: 31601234 PMCID: PMC6785865 DOI: 10.1186/s12943-019-1064-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
Background PVT1 has emerged as an oncogene in many tumor types. However, its role in Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) is unknown. The aim of this study was to assess the role of PVT1 in BE/EAC progression and uncover its therapeutic value against EAC. Methods PVT1 expression was assessed by qPCR in normal, BE, and EAC tissues and statistical analysis was performed to determine the association of PVT1 expression and EAC (stage, metastases, and survival). PVT1 antisense oligonucleotides (ASOs) were tested for their antitumor activity in vitro and in vivo. Results PVT1 expression was up-regulated in EACs compared with paired BEs, and normal esophageal tissues. High expression of PVT1 was associated with poor differentiation, lymph node metastases, and shorter survival. Effective knockdown of PVT1 in EAC cells using PVT1 ASOs resulted in decreased cell proliferation, invasion, colony formation, tumor sphere formation, and reduced proportion of ALDH1A1+ cells. Mechanistically, we discovered mutual regulation of PVT1 and YAP1 in EAC cells. Inhibition of PVT1 by PVT1 ASOs suppressed YAP1 expression through increased phosphor-LATS1and phosphor-YAP1 while knockout of YAP1 in EAC cells significantly suppressed PVT1 levels indicating a positive regulation of PVT1 by YAP1. Most importantly, we found that targeting both PVT1 and YAP1 using their specific ASOs led to better antitumor activity in vitro and in vivo. Conclusions Our results provide strong evidence that PVT1 confers an aggressive phenotype to EAC and is a poor prognosticator. Combined targeting of PVT1 and YAP1 provided the highest therapeutic index and represents a novel therapeutic strategy. Electronic supplementary material The online version of this article (10.1186/s12943-019-1064-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Xu
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.,Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Yuan Li
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.,Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Jiankang Jin
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Guangchun Han
- Departments of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chengcao Sun
- Departments of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Melissa Pool Pizzi
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Longfei Huo
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Ailing Scott
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Ying Wang
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Lang Ma
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Jeffrey H Lee
- Departments of Gastroenterology&Hepatology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Manoop S Bhutani
- Departments of Gastroenterology&Hepatology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Brian Weston
- Departments of Gastroenterology&Hepatology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Christopher Vellano
- Center for Co-Clinical Trial, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Liuqing Yang
- Departments of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chunru Lin
- Departments of Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Youngsoo Kim
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| | - A Robert MacLeod
- Ionis Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| | - Linghua Wang
- Departments of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhenning Wang
- Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, Shenyang, 110001, People's Republic of China.
| | - Shumei Song
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
| | - Jaffer A Ajani
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA.
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259
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Begolli R, Sideris N, Giakountis A. LncRNAs as Chromatin Regulators in Cancer: From Molecular Function to Clinical Potential. Cancers (Basel) 2019; 11:E1524. [PMID: 31658672 PMCID: PMC6826483 DOI: 10.3390/cancers11101524] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/28/2019] [Accepted: 10/06/2019] [Indexed: 12/15/2022] Open
Abstract
During the last decade, high-throughput sequencing efforts in the fields of transcriptomics and epigenomics have shed light on the noncoding part of the transcriptome and its potential role in human disease. Regulatory noncoding RNAs are broadly divided into short and long noncoding transcripts. The latter, also known as lncRNAs, are defined as transcripts longer than 200 nucleotides with low or no protein-coding potential. LncRNAs form a diverse group of transcripts that regulate vital cellular functions through interactions with proteins, chromatin, and even RNA itself. Notably, an important regulatory aspect of these RNA species is their association with the epigenetic machinery and the recruitment of its regulatory apparatus to specific loci, resulting in DNA methylation and/or post-translational modifications of histones. Such epigenetic modifications play a pivotal role in maintaining the active or inactive transcriptional state of chromatin and are crucial regulators of normal cellular development and tissue-specific gene expression. Evidently, aberrant expression of lncRNAs that interact with epigenetic modifiers can cause severe epigenetic disruption and is thus is closely associated with altered gene function, cellular dysregulation, and malignant transformation. Here, we survey the latest breakthroughs concerning the role of lncRNAs interacting with the epigenetic machinery in various forms of cancer.
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Affiliation(s)
- Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
| | - Nikos Sideris
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.
- B.S.R.C "Alexander Fleming", 34 Fleming str, 16672 Vari, Greece.
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260
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Joshi P, Katsushima K, Zhou R, Meoded A, Stapleton S, Jallo G, Raabe E, Eberhart CG, Perera RJ. The therapeutic and diagnostic potential of regulatory noncoding RNAs in medulloblastoma. Neurooncol Adv 2019; 1:vdz023. [PMID: 31763623 PMCID: PMC6859950 DOI: 10.1093/noajnl/vdz023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Medulloblastoma, a central nervous system tumor that predominantly affects children, always requires aggressive therapy. Nevertheless, it frequently recurs as resistant disease and is associated with high morbidity and mortality. While recent efforts to subclassify medulloblastoma based on molecular features have advanced our basic understanding of medulloblastoma pathogenesis, optimal targets to increase therapeutic efficacy and reduce side effects remain largely undefined. Noncoding RNAs (ncRNAs) with known regulatory roles, particularly long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), are now known to participate in medulloblastoma biology, although their functional significance remains obscure in many cases. Here we review the literature on regulatory ncRNAs in medulloblastoma. In providing a comprehensive overview of ncRNA studies, we highlight how different lncRNAs and miRNAs have oncogenic or tumor suppressive roles in medulloblastoma. These ncRNAs possess subgroup specificity that can be exploited to personalize therapy by acting as theranostic targets. Several of the already identified ncRNAs appear specific to medulloblastoma stem cells, the most difficult-to-treat component of the tumor that drives metastasis and acquired resistance, thereby providing opportunities for therapy in relapsing, disseminating, and therapy-resistant disease. Delivering ncRNAs to tumors remains challenging, but this limitation is gradually being overcome through the use of advanced technologies such as nanotechnology and rational biomaterial design.
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Affiliation(s)
- Piyush Joshi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Rui Zhou
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Avner Meoded
- Pediatric Neuroradiology, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Stacie Stapleton
- Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - George Jallo
- Institute Brain Protection Sciences, Johns Hopkins All Children's Hospital, St. Petersburg, Florida
| | - Eric Raabe
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Charles G Eberhart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland.,Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, St. Petersburg, Florida.,Sanford Burnham Prebys Medical Discovery Institute, NCI-Designated Cancer Center, La Jolla, California
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261
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Ogunwobi OO, Kumar A. Chemoresistance Mediated by ceRNA Networks Associated With the PVT1 Locus. Front Oncol 2019; 9:834. [PMID: 31508377 PMCID: PMC6718704 DOI: 10.3389/fonc.2019.00834] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/13/2019] [Indexed: 12/24/2022] Open
Abstract
Competitive endogenous RNA (ceRNA) networks have emerged as critical regulators of carcinogenesis. Their activity is mediated by various non-coding RNAs (ncRNAs), including long non-coding RNAs and microRNAs, which competitively bind to targets, thereby modulating gene expression and activity of proteins. Of particular interest, ncRNAs encoded by the 8q24 chromosomal region are associated with the development and progression of several human cancers, most prominently lncPVT1. Chemoresistance presents a significant obstacle in the treatment of cancer and is associated with dysregulation of normal cell processes, including abnormal proliferation, differentiation, and epithelial-mesenchymal transition. CeRNA networks have been shown to regulate these processes via both direct sponging/repression and epigenetic mechanisms. Here we present a review of recent literature examining the contribution of ncRNAs encoded by the PVT1 locus and their associated ceRNA networks to the development of resistance to common chemotherapeutic agents used to treat human cancers.
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Affiliation(s)
- Olorunseun O. Ogunwobi
- Department of Biological Sciences, Hunter College of the City University of New York, New York, NY, United States
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Adithya Kumar
- Department of Biological Sciences, Hunter College of the City University of New York, New York, NY, United States
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262
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Li MY, Tang XH, Fu Y, Wang TJ, Zhu JM. Regulatory Mechanisms and Clinical Applications of the Long Non-coding RNA PVT1 in Cancer Treatment. Front Oncol 2019; 9:787. [PMID: 31497532 PMCID: PMC6712078 DOI: 10.3389/fonc.2019.00787] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/05/2019] [Indexed: 12/24/2022] Open
Abstract
Cancer is the second leading cause of death worldwide, and no obvious decline in incidence and mortality has occurred in recent years. It is imperative to further investigate the mechanisms underlying tumor progression. Long non-coding RNAs have received considerable attention in recent years because of their major regulatory roles in gene expression. Among them, PVT1 is well-studied, and substantial evidence indicates that PVT1 plays critical roles in the onset and development of cancers. Normally, PVT1 acts as an oncogenic factor by promoting cancer cell proliferation, invasion, metastasis, and drug resistance. Herein, we summarize current knowledge regarding the regulatory effects of PVT1 in cancer progression, as well as the related underlying mechanisms, such as interaction with Myc, modulation of miRNAs, and regulation of gene transcription and protein expression. In extracellular fluid, PVT1 mainly promotes cancer initiation, and it normally enhances cellular cancer characteristics in the cytoplasm and cell nucleus. Regarding clinical applications, its role in drug resistance and its potential use as a diagnostic and prognostic marker have received increasing attention. We hope that this review will contribute to a better understanding of the regulatory role of PVT1 in cancer progression, paving the way for the development of PVT1-based therapeutic approaches in cancer treatment.
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Affiliation(s)
- Meng-Yuan Li
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Xiao-Huan Tang
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yan Fu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Tie-Jun Wang
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Jia-Ming Zhu
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
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263
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Yang F, Wu Q, Zhang L, Xie W, Sun X, Zhang Y, Wang L, Dai Q, Yu H, Chen Q, Sheng H, Qiu J, He X, Miao H, He F, Zhang K. The long noncoding RNA KCNQ1DN suppresses the survival of renal cell carcinoma cells through downregulating c-Myc. J Cancer 2019; 10:4662-4670. [PMID: 31528231 PMCID: PMC6746116 DOI: 10.7150/jca.29280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/28/2019] [Indexed: 01/29/2023] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) have been demonstrated to play essential roles in renal cell carcinoma (RCC). However, the role of lncRNA KCNQ1DN in RCC remains unclear. Methods: The expression of KCNQ1DN in RCC and the corresponding adjacent tissues was measured by qPCR. RNA fluorescence in situ hybridization (FISH) assay, methylation analysis, reporter gene assays and functional tests were performed to reveal the effects of KCNQ1DN on RCC. Results: In the present study, we found that lncRNA KCNQ1DN was notably decreased in RCC tissues and cell lines. RNA FISH assay showed that KCNQ1DN mainly localized to the cytoplasm. Methylation analysis revealed that the proximal region of KCNQ1DN promoter was hypermethylated in RCC tissues relative to the adjacent normal ones. Functional studies clarified that KCNQ1DN repressed the RCC cell growth and cell cycle progression. Mechanistically, KCNQ1DN inhibited the expression of c-Myc, which might further upregulate cyclin D1 and suppress p27 at mRNA and protein levels in RCC cells. Reporter gene assays revealed that the transcriptional activity of c-Myc promoter was inhibited by KCNQ1DN. The in vivo experiments in nude mice showed that KCNQ1DN overexpression dramatically repressed the growth of xenograft tumors and the expression of corresponding c-Myc. Conclusion: These results indicated that KCNQ1DN inhibit the growth of RCC cells in vitro and in vivo through repressing the oncogene c-myc, suggesting that KCNQ1DN may serve as a novel target for the treatment of RCC.
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Affiliation(s)
- Fan Yang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China.,Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Qingjian Wu
- Department of Urology, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Le Zhang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Wei Xie
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Xiaoli Sun
- Nursing division, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Yan Zhang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Lei Wang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qian Dai
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Hua Yu
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qian Chen
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Halei Sheng
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Jing Qiu
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Xiaomei He
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Hongming Miao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Fengtian He
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Kebin Zhang
- Central Laboratory, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
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264
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Lv Y, Huang S. Role of non-coding RNA in pancreatic cancer. Oncol Lett 2019; 18:3963-3973. [PMID: 31579086 PMCID: PMC6757267 DOI: 10.3892/ol.2019.10758] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/05/2019] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer is a malignant disease that develops rapidly and carries a poor prognosis. Currently, surgery is the only radical treatment. Non-coding RNAs (ncRNAs) are protein-free RNAs produced by genome transcription; they play important roles in regulating gene expression, participating in epigenetic modification, cell proliferation, differentiation and reproduction. ncRNAs also play key roles in the development of cancer; microRNA (miRNA) and long non-coding RNA (lncRNA) may lead the way to new treatments for pancreatic cancer. miRNAs are short-chain ncRNAs (19–24 nt) that inhibit the degradation of protein translation or their target gene mRNAs to regulate gene expression. lncRNAs contain >200 nt of ncRNA and play important regulatory roles in a number of malignant tumors, in terms of tumor cell proliferation, apoptosis, invasion and distant metastasis. lncRNAs can be exploited for the diagnosis and treatment of pancreatic cancer and have substantial prospects for clinical application. Nevertheless, the molecular mechanism of their regulation and function, as well as the significance of other ncRNAs, such as piwi-interacting RNA, in the pathogenesis of pancreatic cancer, are largely unknown. In this review, the structures of ncRNAs with various classifications, as well as the functions and important roles of ncRNAs in the diagnosis and treatment of pancreatic cancer are reviewed.
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Affiliation(s)
- Yinghao Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Shuai Huang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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265
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Xie G, Meng T, Luo Y, Liu Z. SKF-LDA: Similarity Kernel Fusion for Predicting lncRNA-Disease Association. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:45-55. [PMID: 31514111 PMCID: PMC6742806 DOI: 10.1016/j.omtn.2019.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/13/2019] [Accepted: 07/24/2019] [Indexed: 01/24/2023]
Abstract
Recently, prediction of lncRNA-disease associations has attracted more and more attentions. Various computational models have been proposed; however, there is still room to improve the prediction accuracy. In this paper, we propose a kernel fusion method with different types of similarities for the lncRNAs and diseases. The expression similarity and cosine similarity are used for lncRNAs, and the semantic similarity and cosine similarity are used for the diseases. To eliminate the noise effect, a neighbor constraint is enforced to refine all the similarity matrices before fusion. Experimental results show that the proposed similarity kernel fusion (SKF)-LDA method has the superiority performance in terms of AUC values and other measurements. In the schemes of LOOCV and 5-fold CV, AUC values of SKF-LDA achieve 0.9049 and 0.8743±0.0050 respectively. In addition, the conducted case studies of three diseases (hepatocellular carcinoma, lung cancer, and prostate cancer) show that SKF-LDA can predict related lncRNAs accurately.
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Affiliation(s)
- Guobo Xie
- School of Computer Science, Guangdong University of Technology, Guangzhou, China
| | - Tengfei Meng
- School of Computer Science, Guangdong University of Technology, Guangzhou, China
| | - Yu Luo
- School of Computer Science, Guangdong University of Technology, Guangzhou, China.
| | - Zhenguo Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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266
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Unfried JP, Serrano G, Suárez B, Sangro P, Ferretti V, Prior C, Boix L, Bruix J, Sangro B, Segura V, Fortes P. Identification of Coding and Long Noncoding RNAs Differentially Expressed in Tumors and Preferentially Expressed in Healthy Tissues. Cancer Res 2019; 79:5167-5180. [PMID: 31387921 DOI: 10.1158/0008-5472.can-19-0400] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/06/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022]
Abstract
The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) datasets allow unprecedented gene expression analyses. Here, using these datasets, we performed pan-cancer and pan-tissue identification of coding and long noncoding RNA (lncRNA) transcripts differentially expressed in tumors and preferentially expressed in healthy tissues and/or tumors. Pan-cancer comparison of mRNAs and lncRNAs showed that lncRNAs were deregulated in a more tumor-specific manner. Given that lncRNAs are more tissue-specific than mRNAs, we identified healthy tissues that preferentially express lncRNAs upregulated in tumors and found that testis, brain, the digestive tract, and blood/spleen were the most prevalent. In addition, specific tumors also upregulate lncRNAs preferentially expressed in other tissues, generating a unique signature for each tumor type. Most tumors studied downregulated lncRNAs preferentially expressed in their tissue of origin, probably as a result of dedifferentiation. However, the same lncRNAs could be upregulated in other tumors, resulting in "bimorphic" transcripts. In hepatocellular carcinoma (HCC), the upregulated genes identified were expressed at higher levels in patients with worse prognosis. Some lncRNAs upregulated in HCC and preferentially expressed in healthy testis or brain were predicted to function as oncogenes and were significantly associated with higher tumor burden, and poor prognosis, suggesting their relevance in hepatocarcinogenesis and/or tumor evolution. Taken together, therapies targeting oncogenic lncRNAs should take into consideration the healthy tissue, where the lncRNAs are preferentially expressed, to predict and decrease unwanted secondary effects and increase potency. SIGNIFICANCE: Comprehensive analysis of coding and noncoding genes expressed in different tumors and normal tissues, which should be taken into account to predict side effects from potential coding and noncoding gene-targeting therapies.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/20/5167/F1.large.jpg.
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Affiliation(s)
- Juan P Unfried
- University of Navarra (UNAV). Center for Applied Medical Research (CIMA). Program of Gene Therapy and Hepatology. Pamplona, Spain
| | | | - Beatriz Suárez
- University of Navarra (UNAV). Center for Applied Medical Research (CIMA). Program of Gene Therapy and Hepatology. Pamplona, Spain
| | - Paloma Sangro
- Clínica Universidad de Navarra. Liver Unit. Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain
| | - Valeria Ferretti
- University of Navarra (UNAV). Center for Applied Medical Research (CIMA). Program of Gene Therapy and Hepatology. Pamplona, Spain
| | - Celia Prior
- University of Navarra (UNAV). Center for Applied Medical Research (CIMA). Program of Gene Therapy and Hepatology. Pamplona, Spain
| | - Loreto Boix
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain.,BCLC Group, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Jordi Bruix
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain.,BCLC Group, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Bruno Sangro
- Clínica Universidad de Navarra. Liver Unit. Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain
| | - Víctor Segura
- UNAV/CIMA. Bioinformatics Platform. Pamplona, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Puri Fortes
- University of Navarra (UNAV). Center for Applied Medical Research (CIMA). Program of Gene Therapy and Hepatology. Pamplona, Spain. .,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
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267
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Zhang TN, Goodwin JE, Liu B, Li D, Wen R, Yang N, Xia J, Zhou H, Zhang T, Song WL, Liu CF. Characterization of Long Noncoding RNA and mRNA Profiles in Sepsis-Induced Myocardial Depression. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:852-866. [PMID: 31472370 PMCID: PMC6722300 DOI: 10.1016/j.omtn.2019.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 11/06/2022]
Abstract
Septic shock with heart dysfunction is very common in intensive care units. However, whether long noncoding RNA (lncRNA) and mRNA profiles differ between patients with and without myocardial depression is unknown. We generated rat models of hypodynamic septic shock induced by lipopolysaccharide. A total of 12 rat models was constructed and heart tissue from each was collected. Whole genomic RNA sequencing was performed on left ventricular tissue; 6,508 novel lncRNAs and 432 annotated lncRNAs were identified in heart samples, and 74 lncRNAs were expressed differently in the sepsis and control groups. Gene ontology term enrichment indicated apoptosis and its related pathways showed obvious enrichment, which suggested cell apoptosis could play a critical role in the process of myocardial depression. Furthermore, we focused on one lncRNA from the Pvt1 gene. By silencing this lncRNA, we demonstrated knockdown of Pvt1 expression could induce cell apoptosis in lipopolysaccharide-induced heart cells, through increasing the expression of c-Myc, Bid, Bax, and caspase-3 and decreasing the expression of Myd88 and Bcl-2, thereby proving its functional role in myocardial depression. These results demonstrate that lncRNAs both participate in and mediate the pathological process of myocardial depression. Our study improves the understanding of the basic molecular mechanisms underlying myocardial depression.
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Affiliation(s)
- Tie-Ning Zhang
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China
| | - Julie E Goodwin
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Bing Liu
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Da Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ri Wen
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China
| | - Ni Yang
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China
| | - Jing Xia
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China
| | - Han Zhou
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Tao Zhang
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China
| | - Wen-Liang Song
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China
| | - Chun-Feng Liu
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China.
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268
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Kajino T, Shimamura T, Gong S, Yanagisawa K, Ida L, Nakatochi M, Griesing S, Shimada Y, Kano K, Suzuki M, Miyano S, Takahashi T. Divergent lncRNA MYMLR regulates MYC by eliciting DNA looping and promoter-enhancer interaction. EMBO J 2019; 38:e98441. [PMID: 31361039 DOI: 10.15252/embj.201798441] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) function in a wide range of processes by diverse mechanisms, though their roles in regulation of oncogenes and/or tumor suppressors remain rather elusive. We performed a global search for lncRNAs affecting MYC activity using a systems biology-based approach with a K supercomputer and the GIMLET algorism based on local distance correlations. Consequently, MYMLR was identified and experimentally shown to maintain MYC transcriptional activity and cell cycle progression despite the low levels of expression. A proteomic search for MYMLR-binding proteins identified PCBP2, while it was also found that MYMLR places a 557-kb upstream enhancer region in the proximity of the MYC promoter in cooperation with PCBP2. These findings implicate a crucial role for MYMLR in regulation of the archetypical oncogene MYC and warrant future studies regarding the involvement of low copy number lncRNAs in regulation of other crucial oncogenes and tumor suppressor genes.
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Affiliation(s)
- Taisuke Kajino
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shuyi Gong
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kiyoshi Yanagisawa
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Lisa Ida
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Nakatochi
- Statistical Analysis Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Sebastian Griesing
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukako Shimada
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Keiko Kano
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoshi Suzuki
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takashi Takahashi
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Aichi Cancer Center, Nagoya, Japan
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269
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Wang X, Srivastava Y, Jankowski A, Malik V, Wei Y, Del Rosario RC, Cojocaru V, Prabhakar S, Jauch R. DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1. Nucleic Acids Res 2019; 46:5470-5486. [PMID: 29669022 PMCID: PMC6009666 DOI: 10.1093/nar/gky259] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/12/2018] [Indexed: 12/16/2022] Open
Abstract
FOXA1 is a transcription factor capable to bind silenced chromatin to direct context-dependent cell fate conversion. Here, we demonstrate that a compact palindromic DNA element (termed 'DIV' for its diverging half-sites) induces the homodimerization of FOXA1 with strongly positive cooperativity. Alternative structural models are consistent with either an indirect DNA-mediated cooperativity or a direct protein-protein interaction. The cooperative homodimer formation is strictly constrained by precise half-site spacing. Re-analysis of chromatin immunoprecipitation sequencing data indicates that the DIV is effectively targeted by FOXA1 in the context of chromatin. Reporter assays show that FOXA1-dependent transcriptional activity declines when homodimeric binding is disrupted. In response to phosphatidylinositol-3 kinase inhibition DIV sites pre-bound by FOXA1 such as at the PVT1/MYC locus exhibit a strong increase in accessibility suggesting a role of the DIV configuration in the chromatin closed-open dynamics. Moreover, several disease-associated single nucleotide polymorphisms map to DIV elements and show allelic differences in FOXA1 homodimerization, reporter gene expression and are annotated as quantitative trait loci. This includes the rs541455835 variant at the MAPT locus encoding the Tau protein associated with Parkinson's disease. Collectively, the DIV guides chromatin engagement and regulation by FOXA1 and its perturbation could be linked to disease etiologies.
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Affiliation(s)
- Xuecong Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yogesh Srivastava
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aleksander Jankowski
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warszawa, Poland.,Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanjie Wei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ricardo Ch Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge MA 02142, USA
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany.,Center for Multiscale Theory and Computation, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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270
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You Z, Ge A, Pang D, Zhao Y, Xu S. Long noncoding RNA FER1L4 acts as an oncogenic driver in human pan-cancer. J Cell Physiol 2019; 235:1795-1807. [PMID: 31332783 DOI: 10.1002/jcp.29098] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/27/2019] [Indexed: 12/25/2022]
Abstract
The function of Fer-1 like family member 4 (FER1L4) in human pan-cancer is unknown. Expression of FER1L4 in tumor tissues and nontumor tissues, upstream regulation of FER1L4, and the relationship between its expression with prognosis and chemoresistance were examined by The Cancer Genome Atlas and Gene Expression Omnibus databases. Next, these results were validated in breast tumor and paired nontumor tissues in our cohort. FER1L4 expression is higher in tumor tissues compared with the adjacent nontumor tissues. High FER1L4 expression is associated with worse disease outcomes. Hypomethylation and H3K4me3 accumulation in FER1L4 promoter locus activate its transcriptional expression. Moreover, FER1L4 may trigger chemoresistance in human cancer. Gene Ontology enrichment analysis revealed that FER1L4 may be involved in processes associated with tumorigenesis. These results indicated that FER1L4 may act as an oncogenic driver and it may be a potential therapy target in human cancer.
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Affiliation(s)
- Zilong You
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Anqi Ge
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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271
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Ghafouri-Fard S, Omrani MD, Taheri M. Long noncoding RNA PVT1: A highly dysregulated gene in malignancy. J Cell Physiol 2019; 235:818-835. [PMID: 31297833 DOI: 10.1002/jcp.29060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022]
Abstract
Recent studies have verified the contribution of several long noncoding RNAs (lncRNAs) in the carcinogenesis. Among the highly acknowledged lncRNAs is the human homolog of the plasmacytoma variant translocation gene, which is called PVT1. PVT1 resides near Myc oncogene and regulates the oncogenic process through modulation of several signaling pathways, such as TGF-β, Wnt/ β-catenin, PI3K/AKT, and mTOR pathways. This lncRNA has a circular form as well. Expression analyses and functional studies have appraised the oncogenic roles of PVT1 and circPVT1. Experiments in several cancer cell lines have shown that PVT1 silencing suppresses cancer cell proliferation, whereas its overexpression has the opposite effect. Its silencing has led to the accumulation of cells in the G0/G1 phase and diminished the number of cells in the S phase. Moreover, genome-wide association studies have signified the role of single nucleotide polymorphisms of this lncRNA in conferring risk of lymphoma in different populations. In the current study, we have summarized recent data about the role of PVT1 and circPVT1 in the carcinogenesis process.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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272
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Long non-coding RNA XIST predicting advanced clinical parameters in cancer: A Meta-Analysis and case series study in a single institution. Oncol Lett 2019; 18:2192-2202. [PMID: 31404342 PMCID: PMC6676735 DOI: 10.3892/ol.2019.10592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 06/13/2019] [Indexed: 12/11/2022] Open
Abstract
Dysregulated expression of long non-coding RNA X-inactive specific transcript (lncRNA-XIST) has been indicated in various cancer types. In the present study, a meta-analysis was conducted to evaluate the potential role of lncRNA-XIST in predicting the clinicopathological parameters of patients with cancer. Eligible studies were obtained through a systematic search of PubMed, Web of Science, Embase and the Cochrane Library, of articles published prior to January 2019. The combined odds ratio and 95% confidence interval were calculated to determine the association between lncRNA-XIST expression and patient outcome. In addition, 45 pairs of osteosarcoma (OS) tissues and adjacent healthy tissues from a single institution were analyzed for the expression of lncRNA-XIST, and its association with clinicopathological features; ultimately, a total of 1,869 cancer patients from 25 studies were assessed. The results demonstrated that high expression levels of lncRNA-XIST were significantly associated with lymphatic metastasis, larger tumor size, advanced cancer stage and distant metastasis. However, sex was not associated with lncRNA-XIST expression level. In the OS patient cohort, it was demonstrated that lncRNA-XIST was highly expressed in OS tissues, which negatively correlated with patient prognosis. The present study indicated that lncRNA-XIST may serve as a potential biomarker for advanced clinical parameters in human cancer.
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273
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Ng M, Heckl D, Klusmann JH. The Regulatory Roles of Long Noncoding RNAs in Acute Myeloid Leukemia. Front Oncol 2019; 9:570. [PMID: 31338324 PMCID: PMC6629768 DOI: 10.3389/fonc.2019.00570] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/12/2019] [Indexed: 01/23/2023] Open
Abstract
In this post-genomic era, long noncoding RNAs (lncRNAs) are rapidly gaining recognition for their crucial roles across diverse biological processes and contexts. The human blood system is no exception, where dozens of lncRNAs have been established as regulators of normal and/or malignant hematopoiesis, and where ongoing works continue to uncover novel lncRNA functions. Our review focuses on lncRNAs that are involved in the pathogenesis of acute myeloid leukemia (AML) and the mechanisms through which they control gene expression in this disease context. We also comment on genome-wide sequencing or profiling studies that have implicated large sets of lncRNAs in AML pathophysiology.
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Affiliation(s)
- Michelle Ng
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dirk Heckl
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jan-Henning Klusmann
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
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274
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Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang QJ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLoS Comput Biol 2019; 15:e1007088. [PMID: 31276486 PMCID: PMC6650088 DOI: 10.1371/journal.pcbi.1007088] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/23/2019] [Accepted: 05/09/2019] [Indexed: 02/07/2023] Open
Abstract
Cancer is mainly caused by somatic genome alterations (SGAs). Precision oncology involves identifying and targeting tumor-specific aberrations resulting from causative SGAs. We developed a novel tumor-specific computational framework that finds the likely causative SGAs in an individual tumor and estimates their impact on oncogenic processes, which suggests the disease mechanisms that are acting in that tumor. This information can be used to guide precision oncology. We report a tumor-specific causal inference (TCI) framework, which estimates causative SGAs by modeling causal relationships between SGAs and molecular phenotypes (e.g., transcriptomic, proteomic, or metabolomic changes) within an individual tumor. We applied the TCI algorithm to tumors from The Cancer Genome Atlas (TCGA) and estimated for each tumor the SGAs that causally regulate the differentially expressed genes (DEGs) in that tumor. Overall, TCI identified 634 SGAs that are predicted to cause cancer-related DEGs in a significant number of tumors, including most of the previously known drivers and many novel candidate cancer drivers. The inferred causal relationships are statistically robust and biologically sensible, and multiple lines of experimental evidence support the predicted functional impact of both the well-known and the novel candidate drivers that are predicted by TCI. TCI provides a unified framework that integrates multiple types of SGAs and molecular phenotypes to estimate which genome perturbations are causally influencing one or more molecular/cellular phenotypes in an individual tumor. By identifying major candidate drivers and revealing their functional impact in an individual tumor, TCI sheds light on the disease mechanisms of that tumor, which can serve to advance our basic knowledge of cancer biology and to support precision oncology that provides tailored treatment of individual tumors.
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Affiliation(s)
- Chunhui Cai
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Gregory F. Cooper
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Kevin N. Lu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Xiaojun Ma
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Shuping Xu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Zhenlong Zhao
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Xueer Chen
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Yifan Xue
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Adrian V. Lee
- Center for Causal Discovery, Pittsburgh, PA, United States of America
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
- Magee Women’s Cancer Research Center, Pittsburgh, PA, United States of America
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Nathan Clark
- Center for Causal Discovery, Pittsburgh, PA, United States of America
- Department of Computational Biology and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Vicky Chen
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Songjian Lu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Lujia Chen
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Liyue Yu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Harry S. Hochheiser
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Xia Jiang
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
| | - Q. Jane Wang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
- * E-mail: (QJW); (XL)
| | - Xinghua Lu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
- Center for Causal Discovery, Pittsburgh, PA, United States of America
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
- * E-mail: (QJW); (XL)
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275
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Li Y, Li L, Wang Z, Pan T, Sahni N, Jin X, Wang G, Li J, Zheng X, Zhang Y, Xu J, Yi S, Li X. LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations. Nucleic Acids Res 2019; 46:1113-1123. [PMID: 29325141 PMCID: PMC5815097 DOI: 10.1093/nar/gkx1311] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/23/2017] [Indexed: 12/23/2022] Open
Abstract
Gene regulatory network perturbations contribute to the development and progression of cancer, however, molecular determinants that mediate transcriptional perturbations remain a fundamental challenge for cancer biology. We show that transcriptional perturbations are widely mediated by long noncoding RNAs (lncRNAs) via integration of genome-wide transcriptional regulation with paired lncRNA and gene expression profiles. Systematic construction of an LncRNA Modulator Atlas in Pan-cancer (LncMAP) reveals distinct types of lncRNA regulatory molecules, which are expressed in multiple tissues, exhibit higher conservation. Strikingly, cancers with similar tissue origin share lncRNA modulators which perturb the regulation of cell cycle and immune response-related functions. Furthermore, we identified a large number of pan-cancer lncRNA modulators with potential clinical significance, which are differentially expressed in cancer or are strongly correlated with drug sensitivity across cell lines. Further stratification of cancer patients based on lncRNA-mediated transcriptional perturbations identifies subtypes with distinct survival rates. Finally, we made a user-friendly web interface available for exploring lncRNA-mediated transcriptional perturbations across cancer types. Our study provides a systems-level dissection of lncRNA-mediated regulatory perturbations in cancer, and also presents a valuable tool and resource for investigating the function of lncRNAs in cancer.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.,Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lili Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zishan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tao Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Nidhi Sahni
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiyun Jin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Guangjuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiangyi Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Song Yi
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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276
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Long noncoding RNA EMS connects c-Myc to cell cycle control and tumorigenesis. Proc Natl Acad Sci U S A 2019; 116:14620-14629. [PMID: 31262817 DOI: 10.1073/pnas.1903432116] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Deregulated expression of c-Myc is an important molecular hallmark of cancer. The oncogenic function of c-Myc has been largely attributed to its intrinsic nature as a master transcription factor. Here, we report the long noncoding RNA (lncRNA) E2F1 messenger RNA (mRNA) stabilizing factor (EMS) as a direct c-Myc transcriptional target. EMS functions as an oncogenic molecule by promoting G1/S cell cycle progression. Mechanistically, EMS cooperates with the RNA binding protein RALY to stabilize E2F1 mRNA, and thereby increases E2F1 expression. Furthermore, EMS is able to connect c-Myc to cell cycle control and tumorigenesis via modulating E2F1 mRNA stability. Together, these findings reveal a previously unappreciated mechanism through which c-Myc induces E2F1 expression and also implicate EMS as an important player in the regulation of c-Myc function.
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277
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Wang Y, Liu J, Yang J, Yu X, Chen Z, Chen Y, Kuang M, Zhu Y, Zhuang S. Lnc-UCID Promotes G1/S Transition and Hepatoma Growth by Preventing DHX9-Mediated CDK6 Down-regulation. Hepatology 2019; 70:259-275. [PMID: 30865310 PMCID: PMC6618099 DOI: 10.1002/hep.30613] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/10/2019] [Indexed: 12/22/2022]
Abstract
Although thousands of long noncoding RNAs (lncRNAs) have been annotated, only a limited number of them have been functionally characterized. Here, we identified an oncogenic lncRNA, named lnc-UCID (lncRNA up-regulating CDK6 by interacting with DHX9). Lnc-UCID was up-regulated in hepatocellular carcinoma (HCC), and a higher lnc-UCID level was correlated with shorter recurrence-free survival of HCC patients. Both gain-of-function and loss-of function studies revealed that lnc-UCID enhanced cyclin-dependent kinase 6 (CDK6) expression and thereby promoted G1/S transition and cell proliferation. Studies from mouse xenograft models revealed that tumors derived from lnc-UCID-silenced HCC cells had a much smaller size than those from control cells, and intratumoral injection of lnc-UCID small interfering RNA suppressed xenograft growth. Mechanistically, the 850-1030-nt domain of lnc-UCID interacted physically with DEAH (Asp-Glu-Ala-His) box helicase 9 (DHX9), an RNA helicase. On the other hand, DHX9 post-transcriptionally suppressed CDK6 expression by binding to the 3'-untranslated region (3'UTR) of CDK6 mRNA. Further investigation disclosed that lnc-UCID enhanced CDK6 expression by competitively binding to DHX9 and sequestering DHX9 from CDK6-3'UTR. In an attempt to explore the mechanisms responsible for lnc-UCID up-regulation in HCC, we found that the lnc-UCID gene was frequently amplified in HCC. Furthermore, miR-148a, whose down-regulation was associated with an increase of lnc-UCID in HCC, could bind lnc-UCID and inhibit its expression. Conclusion: Up-regulation of lnc-UCID, which may result from amplification of its gene locus and down-regulation of miR-148a, can promote HCC growth by preventing the interaction of DHX9 with CDK6 and subsequently enhancing CDK6 expression. These findings provide insights into the biological functions of lncRNAs, the regulatory network of cell cycle control, and the mechanisms of HCC development, which may be exploited for anticancer therapy.
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Affiliation(s)
- Yun‐Long Wang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Jin‐Yu Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Jin‐E Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina,Key Laboratory of Liver Disease of Guangdong ProvinceThe Third Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Xiao‐Man Yu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Zhan‐Li Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ya‐Jing Chen
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ming Kuang
- Department of Liver SurgeryThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Ying Zhu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Shi‐Mei Zhuang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen UniversityGuangzhouChina,Key Laboratory of Liver Disease of Guangdong ProvinceThe Third Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
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278
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Celebi R, Bear Don't Walk O, Movva R, Alpsoy S, Dumontier M. In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data. Sci Rep 2019; 9:8949. [PMID: 31222109 PMCID: PMC6586895 DOI: 10.1038/s41598-019-45236-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/29/2019] [Indexed: 12/14/2022] Open
Abstract
Chemotherapy is a routine treatment approach for early-stage cancers, but the effectiveness of such treatments is often limited by drug resistance, toxicity, and tumor heterogeneity. Combination chemotherapy, in which two or more drugs are applied simultaneously, offers one promising approach to address these concerns, since two single-target drugs may synergize with one another through interconnected biological processes. However, the identification of effective dual therapies has been particularly challenging; because the search space is large, combination success rates are low. Here, we present our method for DREAM AstraZeneca-Sanger Drug Combination Prediction Challenge to predict synergistic drug combinations. Our approach involves using biologically relevant drug and cell line features with machine learning. Our machine learning model obtained the primary metric = 0.36 and the tie-breaker metric = 0.37 in the extension round of the challenge which was ranked in top 15 out of 76 submissions. Our approach also achieves a mean primary metric of 0.39 with ten repetitions of 10-fold cross-validation. Further, we analyzed our model's predictions to better understand the molecular processes underlying synergy and discovered that key regulators of tumorigenesis such as TNFA and BRAF are often targets in synergistic interactions, while MYC is often duplicated. Through further analysis of our predictions, we were also ble to gain insight into mechanisms and potential biomarkers of synergistic drug pairs.
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Affiliation(s)
- Remzi Celebi
- Maastricht University, Institute of Data Science, Maastricht, Netherlands.
| | | | - Rajiv Movva
- Stanford University, Department of Genetics, Palo Alto, USA
| | - Semih Alpsoy
- Turkish-German University, Department of Molecular Biotechnology, Istanbul, Turkey
| | - Michel Dumontier
- Maastricht University, Institute of Data Science, Maastricht, Netherlands
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279
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Razavi M, Ghorbian S. Up-regulation of long non-coding RNA-PCAT-1 promotes invasion and metastasis in esophageal squamous cell carcinoma. EXCLI JOURNAL 2019; 18:422-428. [PMID: 31338011 PMCID: PMC6635722 DOI: 10.17179/excli2018-1847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022]
Abstract
Long non-coding RNA prostate cancer associated transcript-1 ncRNA (lncRNA-PCAT-1) plays an important role in the progression of prostate cancer. The present investigation was aimed to evaluate the potential roles of the lncRNA-PCAT-1 gene expression changes in esophageal squamous cell carcinoma (ESCC) between Iranian population. In the case-control investigation, we have analyzed a total of 150 fresh tissue samples, compromising of 75 cancerous tissues and 75 adjacent normal tissues from patients with ESCC. We used quantitative Real-time polymerase chain reaction (qRT-PCR) to evaluate the lncRNA-PCAT-1 gene expression levels in ESCC patients and correlation between the lncRNA-PCAT-1 expression changes and clinical characteristics. Our findings showed that the lncRNA-PCAT-1 gene was up-regulated in cancerous tissues compared with the adjacent non-cancerous tissues (p=0.0016). In addition, the results revealed a significant correlation between up-regulating of lncRNA-PCAT-1 and hot liquid drinking (p =0.017). These findings offer the potential roles of lncRNA-PCAT-1 in the pathogenesis of ESCC and may consider as a candidate prognostic biomarker for ESCC in an Iranian population.
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Affiliation(s)
- Maryam Razavi
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Saeid Ghorbian
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
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280
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Moschovis D, Vasilaki E, Tzouvala M, Karamanolis G, Katifelis H, Legaki E, Vezakis A, Aravantinos G, Gazouli M. Association between genetic polymorphisms in long non-coding RNAs and pancreatic cancer risk. Cancer Biomark 2019; 24:117-123. [PMID: 30475759 DOI: 10.3233/cbm-181959] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are emerging as candidate biomarkers of cancer, having regulatory functions in both oncogenic and tumor-suppressive pathways. Concerning pancreatic cancer (PC), deregulation of lncRNAs involved in tumor initiation, invasion, and metastasis seem to play a key role. However, data is scarce about regulatory mechanism of lncRNA expression. OBJECTIVE The aim of our study was to investigate the contribution of two lncRNAs polymorphisms (rs1561927 and rs4759313 of PVT1 and HOTAIR, respectively) in PC susceptibility. METHODS A case-control study was conducted analysing rs1561927 and rs4759313 polymorphisms using DNA collected in a population-based case-control study of pancreatic cancer (111 pancreatic ductal adenocarcinoma cases (PDAC), 56 pancreatic neuroendocrine tumor (PNET), and 125 healthy controls). RESULTS Regarding the PVT1 rs1561927 polymorphism the G allele was significantly overrepresented in both PDAC and PNET patients compared to the controls, while the presence of the HOTAIR rs4759314 G allele was found to be overrepresented in the PNET patients only compared to the controls. The PVT1 rs1561927 AG/GG genotypes were associated with poor overall survival in PDAC patients. CONCLUSIONS Our results suggested that polymorphisms of these two lncRNA polymorphisms implicated in pancreatic carcinogenesis. Further large-scale and functional studies are needed to confirm our results.
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Affiliation(s)
- D Moschovis
- Department of Gastroenterology, General Hospital of Nikea and Piraeus "Agios Panteleimon", Nikea, Greece
| | - E Vasilaki
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - M Tzouvala
- Department of Gastroenterology, General Hospital of Nikea and Piraeus "Agios Panteleimon", Nikea, Greece
| | - G Karamanolis
- Academic Department of Gastroenterology, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - H Katifelis
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - E Legaki
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - A Vezakis
- Second Department of Surgery, Aretaieion University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - G Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - M Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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281
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Zheng C, Xiao Y, Li Y, He D. Knockdown of long non-coding RNA PVT1 inhibits the proliferation of Raji cells through cell cycle regulation. Oncol Lett 2019; 18:1225-1234. [PMID: 31423183 PMCID: PMC6607259 DOI: 10.3892/ol.2019.10450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA plasmacytoma variant translocation 1 (PVT1) has been reported to be associated with oncogenesis. However, the functional role of PVT1 in Burkitt lymphoma has not yet been addressed. The purpose of the present study was to investigate the effect of PVT1 knockdown by small interfering RNA (siRNA) on the proliferation of Burkitt lymphoma Raji cells and to explore its possible mechanism of action. An effective siRNA targeting PVT1 was screened and the corresponding short hairpin RNA (shRNA) was reconstructed into a lentiviral vector. Cell proliferation and cell cycle distribution were assessed by Cell Counting kit-8 assay and flow cytometry, respectively. Protein expression levels of c-Myc, cyclin-dependent kinase inhibitor1A (CDKN1A, P21) and cyclin E1 (CCNE1) were detected by western blotting. A polymerase chain reaction (PCR) array was used to analyse the expression of genes associated with the cell cycle. PVT1 knockdown markedly suppressed proliferation, and induced cell cycle arrest at the G0/G1 phase in Raji cells. Protein expression levels of c-Myc and CCNE1 were reduced, whereas P21 protein expression was markedly increased following downregulation of PVT1 in Raji cells. The cell cycle PCR array revealed that 54 genes were upregulated and 26 genes were downregulated in Raji cells following PVT1 knockdown. Reverse transcription-quantitative PCR demonstrated that cyclin G2 (CCNG2), CDKN1A, Retinoblastoma-like 2 (RBL2, p130), HUS1 checkpoint homolog, cyclin dependent kinase inhibitor 3 (CDKN3) and cyclin dependent kinase inhibitor 1B (CDKN1B) expression were upregulated, whereas the expression levels of CCNE1, cyclin D1 (CCND1) and cell division cycle 20 (CDC20) were downregulated in Raji cells with PVT1 knockdown. In conclusion, PVT1 knockdown may inhibit the proliferation of Raji cells by arresting cells in G0/G1 phase. Furthermore, inhibition of cell proliferation may be associated with a reduction inc-Myc expression and alterations in the expression levels of cell cycle-associated genes.
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Affiliation(s)
- Chanli Zheng
- Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Yu Xiao
- Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Yangqiu Li
- Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China.,Key Laboratory for Regenerative Medicine of Ministry of Education, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Dongmei He
- Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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282
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Adhikary J, Chakraborty S, Dalal S, Basu S, Dey A, Ghosh A. Circular PVT1: an oncogenic non-coding RNA with emerging clinical importance. J Clin Pathol 2019; 72:513-519. [PMID: 31154423 DOI: 10.1136/jclinpath-2019-205891] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022]
Abstract
The importance of circular RNAs (circRNAs) in pathological processes like cancer is evident. Among the circRNAs, recent studies have brought circPVT1 under focus as the most potent oncogenic non-coding RNA. Recent studies on various aspects of circPVT1, including its biogenesis, molecular alteration and its probable role in oncogenesis, have been conducted for research and clinical interest. In this review, a first attempt has been made to summarise the available data on circPVT1 from PubMed and other relevant databases with special emphasis on its role in development, progression and prognosis of various malignant conditions. CircPVT1 is derived from the same genetic locus encoding for long non-coding RNA lncPVT1; however, existing literature suggested circPVT1 and lncPVT1 are transcripted independently by different promoters. The interaction between circRNA and microRNA has been highlighted in majority of the few malignancies in which circPVT1 was studied. Besides its importance in diagnostic and prognostic procedures, circPVT1 seemed to have huge therapeutic potential as evident from differential drug response of cancer cell line as well as primary tumors depending on expression level of the candidate. circPVT1 in cancer therapeutics might be promising as a biomarker to make the existing treatment protocol more effective and also as potential target for designing novel therapeutic intervention.
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Affiliation(s)
- Jayashree Adhikary
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | | | - Subhamita Dalal
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University Kolkata, Kolkata, India
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283
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Liu Y, Cheng Z, Pang Y, Cui L, Qian T, Quan L, Zhao H, Shi J, Ke X, Fu L. Role of microRNAs, circRNAs and long noncoding RNAs in acute myeloid leukemia. J Hematol Oncol 2019; 12:51. [PMID: 31126316 PMCID: PMC6534901 DOI: 10.1186/s13045-019-0734-5] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/16/2019] [Indexed: 12/16/2022] Open
Abstract
Acute myeloid leukemia (AML) is a malignant tumor of the immature myeloid hematopoietic cells in the bone marrow (BM). It is a highly heterogeneous disease, with rising morbidity and mortality in older patients. Although researches over the past decades have improved our understanding of AML, its pathogenesis has not yet been fully elucidated. Long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) are three noncoding RNA (ncRNA) molecules that regulate DNA transcription and translation. With the development of RNA-Seq technology, more and more ncRNAs that are closely related to AML leukemogenesis have been discovered. Numerous studies have found that these ncRNAs play an important role in leukemia cell proliferation, differentiation, and apoptosis. Some may potentially be used as prognostic biomarkers. In this systematic review, we briefly described the characteristics and molecular functions of three groups of ncRNAs, including lncRNAs, miRNAs, and circRNAs, and discussed their relationships with AML in detail.
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Affiliation(s)
- Yan Liu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Zhiheng Cheng
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yifan Pang
- Department of Medicine, William Beaumont Hospital, Royal Oak, MI, 48073, USA
| | - Longzhen Cui
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China
| | - Tingting Qian
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Liang Quan
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Hongyou Zhao
- Department of Laser Medicine, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jinlong Shi
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China. .,Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China. .,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, 475000, China.
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284
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Lin T, Hou PF, Meng S, Chen F, Jiang T, Li ML, Shi ML, Liu JJ, Zheng JN, Bai J. Emerging Roles of p53 Related lncRNAs in Cancer Progression: A Systematic Review. Int J Biol Sci 2019; 15:1287-1298. [PMID: 31223287 PMCID: PMC6567798 DOI: 10.7150/ijbs.33218] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
p53 is the major mediator of the tumor suppressor response. It participates in apoptosis and senescence and can respond to DNA damage. As a crucial sequence-specific transcription factor, p53 regulates the expression of many genes, such as small noncoding RNAs (ncRNAs), microRNAs, and long ncRNAs (lncRNAs). Given the emergence of novel and high-throughput sequencing technologies, many lncRNAs have been discovered. LncRNAs may function as vital gene regulators in a variety of biological processes through extensive mechanisms. Recently, lncRNAs have been demonstrated to be associated with the p53 regulatory pathway. In this review, we discuss the current and fast growing knowledge about the influence of lncRNAs to the p53 signaling pathway, the different mechanisms by which they affect gene expression in cancer. Our findings show that p53-associated lncRNAs may be used as biomarkers for cancer diagnosis or targets for disease therapy.
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Affiliation(s)
- Tian Lin
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Ping-Fu Hou
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Sen Meng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Fang Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Tao Jiang
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Min-Le Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Mei-Lin Shi
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jin-Jin Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Jun-Nian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
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285
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Abstract
A diverse catalog of long noncoding RNAs (lncRNAs), which lack protein-coding potential, are transcribed from the mammalian genome. They are emerging as important regulators in gene expression networks by controlling nuclear architecture and transcription in the nucleus and by modulating mRNA stability, translation and post-translational modifications in the cytoplasm. In this Review, we highlight recent progress in cellular functions of lncRNAs at the molecular level in mammalian cells.
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286
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Mishra S, Verma SS, Rai V, Awasthee N, Chava S, Hui KM, Kumar AP, Challagundla KB, Sethi G, Gupta SC. Long non-coding RNAs are emerging targets of phytochemicals for cancer and other chronic diseases. Cell Mol Life Sci 2019; 76:1947-1966. [PMID: 30879091 PMCID: PMC7775409 DOI: 10.1007/s00018-019-03053-0] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 02/01/2019] [Accepted: 02/19/2019] [Indexed: 12/18/2022]
Abstract
The long non-coding RNAs (lncRNAs) are the crucial regulators of human chronic diseases. Therefore, approaches such as antisense oligonucleotides, RNAi technology, and small molecule inhibitors have been used for the therapeutic targeting of lncRNAs. During the last decade, phytochemicals and nutraceuticals have been explored for their potential against lncRNAs. The common lncRNAs known to be modulated by phytochemicals include ROR, PVT1, HOTAIR, MALAT1, H19, MEG3, PCAT29, PANDAR, NEAT1, and GAS5. The phytochemicals such as curcumin, resveratrol, sulforaphane, berberine, EGCG, and gambogic acid have been examined against lncRNAs. In some cases, formulation of phytochemicals has also been used. The disease models where phytochemicals have been demonstrated to modulate lncRNAs expression include cancer, rheumatoid arthritis, osteoarthritis, and nonalcoholic fatty liver disease. The regulation of lncRNAs by phytochemicals can affect multi-steps of tumor development. When administered in combination with the conventional drugs, phytochemicals can also produce synergistic effects on lncRNAs leading to the sensitization of cancer cells. Phytochemicals target lncRNAs either directly or indirectly by affecting a wide variety of upstream molecules. However, the potential of phytochemicals against lncRNAs has been demonstrated mostly by preclinical studies in cancer models. How the modulation of lncRNAs by phytochemicals produce therapeutic effects on cancer and other chronic diseases is discussed in this review.
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Affiliation(s)
- Shruti Mishra
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Sumit S Verma
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Vipin Rai
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Nikee Awasthee
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Srinivas Chava
- Department of Biochemistry and Molecular Biology, and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kam Man Hui
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, 169610, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology, and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
| | - Subash C Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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287
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Gharib E, Anaraki F, Baghdar K, Ghavidel P, Sadeghi H, Nasrabadi PN, Peyravian N, Aghdaei HA, Zali MR, Mojarad EN. Investigating the diagnostic performance of HOTTIP, PVT1, and UCA1 long noncoding RNAs as a predictive panel for the screening of colorectal cancer patients with lymph node metastasis. J Cell Biochem 2019; 120:14780-14790. [PMID: 30993787 DOI: 10.1002/jcb.28739] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/16/2019] [Accepted: 03/22/2019] [Indexed: 12/24/2022]
Abstract
Like other noncoding RNAs (ncRNAs), dysregulation of long ncRNAs (lncRNAs) has been associated with various clinicopathological features of colorectal cancer (CRC) patients such as lymph node metastasis (LNM). Recently, three aberrant expressed oncogenic lncRNA (onco-lncRNAs), including HOXA transcript at the distal tip (HOTTIP), plasmacytoma variant translocation 1 (PVT1), and urothelial carcinoma associated 1 (UCA1) have been reported in LNM. Herein, we compared the diagnostic performance of these lncRNAs as individual biomarkers and as a discriminating panel between LNM CRC patients, nonmetastatic lymph nodes (NLN) and normal healthy subjects. The lncRNAs expression level was measured by quantitative real-time PCR and analyzed by the Mann-Whitney U test. The receiver operating characteristic (ROC) curve analysis was applied to evaluate the diagnostic power. The Kaplan-Meier survival analysis was performed to outline the overall survival (OS) of CRC patients with an abnormal level of lncRNAs. The area under the ROC curve (AUC) of the overexpressed HOTTIP (0.7817; 95% CI, 0.6809-0.8824), PVT1 (0.8559; 95% CI, 0.7737-0.9382), and UCA1 (0.8135; 95% CI, 0.722-0.9051) introduced them as individual CRC biomarkers. As a predictive panel, the AUC values of the HOTTIP, PVT1, and UCA1 for training set were 0.9256 (95% CI, 0.8634-0.9879; all CRCs), 0.8708 (95% CI, 0.7709-0.9378; NLN) and 0.9804 (95% CI, 0.9585-0.9998; LNM), and for validation set were 0.9286 (95% CI, 0.8752-0.9820; all CRCs), 0.8911 (95% CI, 0.8238-0.9585; NLN), and 0.9833 (95% CI, 0.9642-1.002; LNM), respectively. Also, HOTTIP/PVT1/UCA1 panel dysregulation had a marked correlation with patient's OS in training set (logrank test P = 0.0121; hazard ratio [HR], 0.1225; 95% confidence interval [CI], 0.02376-0.6312), and in validation set (logrank test P < 0.0001, HR, 0.2003; 95% CI, 0.08942-0.4486). These data showed that the combination of HOTTIP, PVT1, and UCA1 as a predictive panel, has a better diagnostic performance than each of these lncRNAs individually, and could be used for the screening of patients with advanced CRC.
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Affiliation(s)
- Ehsan Gharib
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, hahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fakhrosadat Anaraki
- Colorectal Division of Department of Surgery, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghdar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, hahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pegah Ghavidel
- Department of Biology, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Sadeghi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, hahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parinaz Nasri Nasrabadi
- Department of Biology, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Noshad Peyravian
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, hahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, hahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, hahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, hahid Beheshti University of Medical Sciences, Tehran, Iran
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288
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Esposito R, Bosch N, Lanzós A, Polidori T, Pulido-Quetglas C, Johnson R. Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening. Cancer Cell 2019; 35:545-557. [PMID: 30827888 DOI: 10.1016/j.ccell.2019.01.019] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/20/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) represent a huge reservoir of potential cancer targets. Such "onco-lncRNAs" have resisted traditional RNAi methods, but CRISPR-Cas9 genome editing now promises functional screens at high throughput and low cost. The unique biology of lncRNAs demands screening strategies distinct from protein-coding genes. The first such screens have identified hundreds of onco-lncRNAs promoting cell proliferation and drug resistance. Ongoing developments will further improve screen performance and translational relevance. This Review aims to highlight the potential of CRISPR screening technology for discovering new onco-lncRNAs, and to guide molecular oncologists wishing to apply it to their cancer of interest.
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Affiliation(s)
- Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Núria Bosch
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrés Lanzós
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
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289
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Chen S, Chen Y, Qian Q, Wang X, Chang Y, Ju S, Xu Y, Zhang C, Qin N, Ding H, Gu Y, Han J, Wang C, Zhang E, Hu Z. Gene amplification derived a cancer-testis long noncoding RNA PCAT6 regulates cell proliferation and migration in hepatocellular carcinoma. Cancer Med 2019; 8:3017-3025. [PMID: 30968586 PMCID: PMC6558594 DOI: 10.1002/cam4.2141] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/16/2019] [Accepted: 03/17/2019] [Indexed: 12/17/2022] Open
Abstract
Our previous work demonstrated cancer-testis (CT) genes as a new source of candidate driver of cancer. Recently, mounting evidence indicates that long noncoding RNAs (lncRNAs) with CT expression pattern could play a pivotal role in cancer biology. Here, we characterized a conserved CT long noncoding RNA (CT-lncRNA), PCAT6, which is expressed exclusively in the testis and is reactivated in liver hepatocellular carcinoma (LIHC) tissues due to the highly frequent amplification. The expression in LIHC was correlated with clinical prognosis in TCGA data. Knockdown of PCAT6 could inhibit cell proliferation and migration in hepatocellular carcinoma (LIHC) cells. Gene set enrichment analysis (GSEA) based on coexpression network revealed that PCAT6 was involved in similar cilium-related pathways in the testis and LIHC tissues. However, PCAT6 was mainly positively correlated with gametogenesis-related pathways in the testis but was coexpressed with mitotic cell cycle genes in LIHC. Together, our data demonstrated that CT-lncRNA PCAT6 represents the similarity and difference between tumorigenesis and gametogenesis. The CT expression pattern and important role in LIHC oncogenesis make PCAT6 an ideal target for LIHC diagnosis and therapy.
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Affiliation(s)
- Shuaizhou Chen
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yao Chen
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qufei Qian
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuewei Wang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuting Chang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sihan Ju
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yide Xu
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chang Zhang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Na Qin
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hui Ding
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yayun Gu
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Jing Han
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Erbao Zhang
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
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Ren Y, Huang W, Weng G, Cui P, Liang H, Li Y. LncRNA PVT1 promotes proliferation, invasion and epithelial-mesenchymal transition of renal cell carcinoma cells through downregulation of miR-16-5p. Onco Targets Ther 2019; 12:2563-2575. [PMID: 31040699 PMCID: PMC6454988 DOI: 10.2147/ott.s190239] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background LncRNAs have recently emerged as vital regulators in the pathogenesis and development of various cancers. LncRNA PVT1 is reported to function as an oncogene in some tumors. However, the role of PVT1 in RCC remains unknown. Purpose To explore the potential effects of lncPVT1 on the development of renal cell carcinoma. Methods The expression of PVT1 in renal cancer cell lines and tissues was measured by qRT-PCR. The endogenous PVT1 was silenced by RNAi. Cell viabilities were measured by the MTT assay. The migration and invasion of cells were investigated by the transwell assay. The apoptosis of cells was measured by the Nucleosome ELISA and caspase-3 activity assays. The levels of proteins were measured by the western blot. Results We found that PVT1 was upregulated in RCC tissues compared with the adjacent normal tissues. PVT1 expression was closely correlated with TNM stage, Fuhrman grade, lymph node metastasis and tumor size. Kaplan–Meier analysis revealed that high expression of PVT1 was significantly associated with poor overall survival. In accordance, overexpression of PVT1 was observed in RCC cells comto HK-2 cell. Silencing of PVT1 significantly repressed cell viability, induced apoptosis and inhibited cell migration and invasion in vitro. Furthermore, bioinformatic analysis and luciferase reporter assay confirmed that miR-16-5p was a target of PVT1. Silencing of miR-16-5p mostly reversed the regulatory effects on RCC cells induced by downregulation of PVT1. Conclusion In summary, our study indicates that targeting PVT1 might represent a rational therapeutic strategy for RCC.
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Affiliation(s)
- Yu Ren
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo 315000, Zhejiang Province, People's Republic of China
| | - Weiping Huang
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, People's Republic of China,
| | - Guobin Weng
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo 315000, Zhejiang Province, People's Republic of China
| | - Pinger Cui
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo 315000, Zhejiang Province, People's Republic of China
| | - Haote Liang
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, People's Republic of China,
| | - Yeping Li
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, People's Republic of China,
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291
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Li Y, Egranov SD, Yang L, Lin C. Molecular mechanisms of long noncoding RNAs-mediated cancer metastasis. Genes Chromosomes Cancer 2019; 58:200-207. [PMID: 30350428 PMCID: PMC10642708 DOI: 10.1002/gcc.22691] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/03/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022] Open
Abstract
Cancer metastasis is a multistep process that requires cancer cells to leave the primary site, survive in the blood stream, and finally colonize at a distant organ. It is the major cause of cancer morbidity and mortality. The organ-specific colonization requires close interaction and communication between cancer cells and host organs. Noncoding RNAs represent the majority of the transcriptome, with long noncoding RNAs (lncRNAs) making up a significant proportion. It has been suggested that lncRNAs play a key role in all stages of tumorigenesis and metastasis. This review will provide an overview of how lncRNAs are involved in cancer cell colonization in specific organ sites and the underlying mechanisms as well as therapeutic strategies.
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Affiliation(s)
- Yajuan Li
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sergey D. Egranov
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
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292
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Zheng Y, Tian X, Wang T, Xia X, Cao F, Tian J, Xu P, Ma J, Xu H, Wang S. Long noncoding RNA Pvt1 regulates the immunosuppression activity of granulocytic myeloid-derived suppressor cells in tumor-bearing mice. Mol Cancer 2019; 18:61. [PMID: 30925926 PMCID: PMC6441229 DOI: 10.1186/s12943-019-0978-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/25/2019] [Indexed: 12/26/2022] Open
Abstract
Background Myeloid-derived suppressor cells (MDSCs) participate in tumor-elicited immunosuppression by dramatically blocking T-cell-induced antitumor responses, thereby influencing the effectiveness of cancer immunotherapies. Treatments that alter the differentiation and function of MDSCs can partially restore antitumor immune responses. The long noncoding RNA plasmacytoma variant translocation 1 (lncRNA Pvt1) is a potential oncogene in a variety of cancer types. However, whether lncRNA Pvt1 is involved in the regulation of MDSCs has not been thoroughly elucidated to date. Methods MDSCs or granulocytic MDSCs (G-MDSCs) were isolated by microbeads and flow cytometry. Bone marrow derived G-MDSCs were induced by IL-6 and GM-CSF. The expression of lncRNA Pvt1 was measured by qRT-PCR. Specific siRNA was used to knockdown the expression of lncRNA Pvt1 in G-MDSCs. Results In this study, we found that knockdown of lncRNA Pvt1 significantly inhibited the immunosuppressive function of G-MDSCs in vitro. Additionally, lncRNA Pvt1 knockdown reduced the ability of G-MDSCs to delay tumor progression in tumor-bearing mice in vivo. Notably, lncRNA Pvt1 was upregulated by HIF-1α under hypoxia in G-MDSCs. Conclusions Taken together, our results demonstrate a critical role for lncRNA Pvt1 in regulating the immunosuppression activity of G-MDSCs, and lncRNA Pvt1 might thus be a potential antitumor immunotherapy target. Electronic supplementary material The online version of this article (10.1186/s12943-019-0978-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Zheng
- Department of Laboratory Medicine, the Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xinyu Tian
- Department of Laboratory Medicine, the Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tingting Wang
- Department of Laboratory Medicine, the Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi Children's Hospital, Wuxi, China
| | - Xueli Xia
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Fenghua Cao
- Department of Laboratory Medicine, Zhenjiang Hospital of Chinese Traditional and Western Medicine, Zhenjiang, China
| | - Jie Tian
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
| | - Ping Xu
- Department of Laboratory Medicine, The Fifth People's Hospital of Suzhou, Suzhou, China.
| | - Jie Ma
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Huaxi Xu
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shengjun Wang
- Department of Laboratory Medicine, the Affiliated People's Hospital, Jiangsu University, Zhenjiang, 212013, China. .,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
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293
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Shimizu N, Kapoor R, Naniwa S, Sakamaru N, Yamada T, Yamamura YK, Utani KI. Generation and maintenance of acentric stable double minutes from chromosome arms in inter-species hybrid cells. BMC Mol Cell Biol 2019; 20:2. [PMID: 31041889 PMCID: PMC6446505 DOI: 10.1186/s12860-019-0186-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extrachromosomal acentric double minutes (DMs) contribute to human malignancy by carrying amplified oncogenes. Recent cancer genomics revealed that the pulverization of defined chromosome arms (chromothripsis) may generate DMs, however, nobody had actually generated DMs from chromosome arm in culture. Human chromosomes are lost in human-rodent hybrid cells. RESULTS We found that human acentric DMs with amplified c-myc were stable in human-rodent hybrid cells, although the degree of stability depended on the specific rodent cell type. Based on this finding, stable human-rodent hybrids were efficiently generated by tagging human DMs with a plasmid with drug-resistance gene. After cell fusion, human chromosomes were specifically pulverised and lost. Consistent with chromothripsis, pulverization of human chromosome arms was accompanied by the incorporation into micronuclei. Such micronucleus showed different replication timing from the main nucleus. Surprisingly, we found that the hybrid cells retained not only the original DMs, but also new DMs without plasmid-tag and c-myc, but with human Alu. These DMs were devoid of telomeres and centromeres, and were stable in culture for more than 3 months. Microarray analysis showed that the new DMs were generated from several human chromosomal regions containing genes advantageous for cellular growth. Such regions were completely different from the original DMs. CONCLUSIONS The inter-species hybrid mimics the chromothripsis in culture. This is the first report that experimentally demonstrates the generation of multiple stable acentric DMs from the chromosome arm.
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Affiliation(s)
- Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan.
| | - Rita Kapoor
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Shuhei Naniwa
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Naoto Sakamaru
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Taku Yamada
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - You-Ki Yamamura
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Koh-Ichi Utani
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan.,Present address; Kanazawa Medical University, Uchinada, Japan
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294
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Russo F, Fiscon G, Conte F, Rizzo M, Paci P, Pellegrini M. Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer. Methods Mol Biol 2019; 1819:75-92. [PMID: 30421400 DOI: 10.1007/978-1-4939-8618-7_4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the last decade noncoding RNAs (ncRNAs) have been extensively studied in several biological processes and human diseases including cancer. microRNAs (miRNAs) are the best-known class of ncRNAs. miRNAs are small ncRNAs of around 20-22 nucleotides (nt) and are crucial posttranscriptional regulators of protein coding genes. Recently, new classes of ncRNAs, longer than miRNAs have been discovered. Those include intergenic noncoding RNAs (lincRNAs) and circular RNAs (circRNAs). These novel types of ncRNAs opened a very exciting field in biology, leading researchers to discover new relationships between miRNAs and long noncoding RNAs (lncRNAs), which act together to control protein coding gene expression. One of these new discoveries led to the formulation of the "competing endogenous RNA (ceRNA) hypothesis." This hypothesis suggests that an lncRNA acts as a sponge for miRNAs reducing their expression and causing the upregulation of miRNA targets. In this chapter we first discuss some recent discoveries in this field showing the mutual regulation of miRNAs, lncRNAs, and protein-coding genes in cancer. We then discuss the general approaches for the study of ceRNAs and present in more detail a recent computational approach to explore the ability of lncRNAs to act as ceRNAs in human breast cancer that has been shown to be, among the others, the most precise and promising.
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Affiliation(s)
- Francesco Russo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Milena Rizzo
- Institute of Clinical Physiology, National Research Council (CNR), Pisa, Italy.,Istituto Toscano Tumori (ITT), Firenze, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, Italy
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296
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Chen J, Yu Y, Li H, Hu Q, Chen X, He Y, Xue C, Ren F, Ren Z, Li J, Liu L, Duan Z, Cui G, Sun R. Long non-coding RNA PVT1 promotes tumor progression by regulating the miR-143/HK2 axis in gallbladder cancer. Mol Cancer 2019; 18:33. [PMID: 30825877 PMCID: PMC6397746 DOI: 10.1186/s12943-019-0947-9] [Citation(s) in RCA: 265] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The long non-coding RNA PVT1 (lncRNA PVT1) has been reported to act as an oncogenic regulator of several cancers. However, its expression and function in gallbladder cancer (GBC) remain largely unknown. METHODS In situ hybridization (ISH) and quantitative real-time PCR (qPCR) were performed to detect the expression of PVT1 and miR-143 in GBC tissues and cell lines. Immunohistochemistry (IHC) assays were performed to assess the expression of the hexokinase 2 (HK2) protein. The relationships among PVT1, miR-143 and HK2 were evaluated using dual-luciferase reporter, RNA immunoprecipitation (RIP) and biotin pull-down assays. The biological functions of PVT1, miR-143 and HK2 in GBC cells were explored with cell counting kit 8 (CCK-8), 5-ethynyl-20-deoxyuridine (EdU), colony formation, transwell, wound healing and glucose metabolism assays in vitro. For in vivo experiments, a xenograft model was used to investigate the effects of PVT1 and HK2 on GBC. RESULTS PVT1 was upregulated in GBC tissues and cells and was positively associated with malignancies and worse overall survival. PVT1 knockdown inhibited cell proliferation, migration, and invasion in vitro and restrained tumor growth in vivo. Further studies demonstrated that PVT1 positively regulated HK2 expression via its competing endogenous RNA (ceRNA) activity on miR-143. Additionally, HK2 expression and function were positively correlated with PVT1. Furthermore, we observed that the PVT1/miR-143/HK2 axis promoted cell proliferation and metastasis by regulating aerobic glucose metabolism in GBC cells. CONCLUSIONS The results of our study reveal a potential ceRNA regulatory pathway in which PVT1 modulates HK2 expression by competitively binding to endogenous miR-143 in GBC cells, which may provide new insights into novel molecular therapeutic targets for GBC.
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Affiliation(s)
- Jianan Chen
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Yan Yu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Hua Li
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Qiuyue Hu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaolong Chen
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Yuting He
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Chen Xue
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Fang Ren
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Zhigang Ren
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Juan Li
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Liwen Liu
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Zhenfeng Duan
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Guangying Cui
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Ranran Sun
- Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
- National Engineering Laboratory for Internet Medical System and Application, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
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Arnes L, Liu Z, Wang J, Maurer HC, Sagalovskiy I, Sanchez-Martin M, Bommakanti N, Garofalo DC, Balderes DA, Sussel L, Olive KP, Rabadan R. Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Gut 2019; 68:499-511. [PMID: 29440233 PMCID: PMC6086768 DOI: 10.1136/gutjnl-2017-314353] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 12/22/2017] [Accepted: 01/01/2018] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDA) is a highly metastatic disease with limited therapeutic options. Genome and transcriptome analyses have identified signalling pathways and cancer driver genes with implications in patient stratification and targeted therapy. However, these analyses were performed in bulk samples and focused on coding genes, which represent a small fraction of the genome. DESIGN We developed a computational framework to reconstruct the non-coding transcriptome from cross-sectional RNA-Seq, integrating somatic copy number alterations (SCNA), common germline variants associated to PDA risk and clinical outcome. We validated the results in an independent cohort of paired epithelial and stromal RNA-Seq derived from laser capture microdissected human pancreatic tumours, allowing us to annotate the compartment specificity of their expression. We employed systems and experimental biology approaches to interrogate the function of epithelial long non-coding RNAs (lncRNAs) associated with genetic traits and clinical outcome in PDA. RESULTS We generated a catalogue of PDA-associated lncRNAs. We showed that lncRNAs define molecular subtypes with biological and clinical significance. We identified lncRNAs in genomic regions with SCNA and single nucleotide polymorphisms associated with lifetime risk of PDA and associated with clinical outcome using genomic and clinical data in PDA. Systems biology and experimental functional analysis of two epithelial lncRNAs (LINC00673 and FAM83H-AS1) suggest they regulate the transcriptional profile of pancreatic tumour samples and PDA cell lines. CONCLUSIONS Our findings indicate that lncRNAs are associated with genetic marks of pancreatic cancer risk, contribute to the transcriptional regulation of neoplastic cells and provide an important resource to design functional studies of lncRNAs in PDA.
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Affiliation(s)
- Luis Arnes
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Zhaoqi Liu
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Jiguang Wang
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Division of Life Science and Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - H. Carlo Maurer
- Columbia University Medical Center, New York, United States
- Department of Medicine, Division of Digestive and Liver Diseases, University of Colorado, Denver, United States
| | - Irina Sagalovskiy
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Marta Sanchez-Martin
- Columbia University Medical Center, New York, United States
- Institute for Cancer Genetics, University of Colorado, Denver, United States
| | - Nikhil Bommakanti
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Diana C. Garofalo
- Columbia University Medical Center, New York, United States
- Department of Genetics & Development, University of Colorado, Denver, United States
| | - Dina A. Balderes
- Columbia University Medical Center, New York, United States
- Department of Genetics & Development, University of Colorado, Denver, United States
| | - Lori Sussel
- Columbia University Medical Center, New York, United States
- Department of Genetics & Development, University of Colorado, Denver, United States
- Barbara Davis Center, University of Colorado, Denver, United States
| | - Kenneth P. Olive
- Columbia University Medical Center, New York, United States
- Department of Medicine, Division of Digestive and Liver Diseases, University of Colorado, Denver, United States
- Department of Pathology and Cell Biology
- Herbert Irving Comprehensive Cancer Center
| | - Raul Rabadan
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
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298
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Alessio E, Buson L, Chemello F, Peggion C, Grespi F, Martini P, Massimino ML, Pacchioni B, Millino C, Romualdi C, Bertoli A, Scorrano L, Lanfranchi G, Cagnin S. Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network. Nucleic Acids Res 2019; 47:1653-1670. [PMID: 30649422 PMCID: PMC6393313 DOI: 10.1093/nar/gkz007] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/05/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important players in the regulation of several aspects of cellular biology. For a better comprehension of their function, it is fundamental to determine their tissue or cell specificity and to identify their subcellular localization. In fact, the activity of lncRNAs may vary according to cell and tissue specificity and subcellular compartmentalization. Myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism. How lncRNAs are expressed in different myofibers, participate in metabolism regulation and muscle atrophy or how they are compartmentalized within a single myofiber is still unknown. We compiled a comprehensive catalog of lncRNAs expressed in skeletal muscle, associating the fiber-type specificity and subcellular location to each of them, and demonstrating that many lncRNAs can be involved in the biological processes de-regulated during muscle atrophy. We demonstrated that the lncRNA Pvt1, activated early during muscle atrophy, impacts mitochondrial respiration and morphology and affects mito/autophagy, apoptosis and myofiber size in vivo. This work corroborates the importance of lncRNAs in the regulation of metabolism and neuromuscular pathologies and offers a valuable resource to study the metabolism in single cells characterized by pronounced plasticity.
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Affiliation(s)
- Enrico Alessio
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesca Grespi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Paolo Martini
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Beniamina Pacchioni
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Chiara Romualdi
- Department of Biology, University of Padova, 35131 Padova, Italy
| | - Alessandro Bertoli
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, 35131 Padova, Italy
- Venetian Institute of Molecular Medicine, 35131 Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
- CIR-Myo Myology Center, University of Padova, 35131 Padova, Italy
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299
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MicroRNA-1205, encoded on chromosome 8q24, targets EGLN3 to induce cell growth and contributes to risk of castration-resistant prostate cancer. Oncogene 2019; 38:4820-4834. [PMID: 30808975 PMCID: PMC6565506 DOI: 10.1038/s41388-019-0760-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 01/06/2019] [Accepted: 02/12/2019] [Indexed: 12/27/2022]
Abstract
The chromosome 8q24.21 locus, which contains the proto-oncogene c-MYC, long non-coding RNA PVT1, and microRNAs (miRs), is the most commonly amplified region in human prostate cancer. A long-range interaction of genetic variants with c-MYC or long non-coding PVT1 at this locus contributes to the genetic risk of prostate cancer. At this locus is a cluster of genes for six miRs (miR-1204, −1205, −1206, −1207–3p, −1207–5p, and −1208), but their functional role remains elusive. Here, the copy numbers and expressions of miRs-1204~1208 were investigated using quantitative PCR for prostate cancer cell lines and primary tumors. The data revealed that copy numbers and expression of miR-1205 were increased in both castration-resistant prostate cancer cell lines and in primary tumors. In castration-resistant prostate cancer specimens, the copy number at the miR-1205 locus correlated with expression of miR-1205. Furthermore, functional analysis with an miR-1205 mimic, an miR-1205 inhibitor, and CRISPR/Cas9 knockout revealed that, in human prostate cancer cells, miR-1205 promoted cell proliferation and cell cycle progression and inhibited hydrogen peroxide-induced apoptosis. In these cells, miR-1205 downregulated expression of the Egl-9 family hypoxia inducible factor 3 (EGLN3) gene and targeted a site in its 3’-untranslated region to downregulate its transcriptional activity. Thus, by targeting EGLN3, miR-1205 has an oncogenic role and may contribute to the genetic risk of castration-resistant prostate cancer.
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300
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Saleembhasha A, Mishra S. Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach. PeerJ 2019; 7:e6388. [PMID: 30809433 PMCID: PMC6387586 DOI: 10.7717/peerj.6388] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/04/2019] [Indexed: 12/18/2022] Open
Abstract
Despite years of research, we are still unraveling crucial stages of gene expression regulation in cancer. On the basis of major biological hallmarks, we hypothesized that there must be a uniform gene expression pattern and regulation across cancer types. Among non-coding genes, long non-coding RNAs (lncRNAs) are emerging as key gene regulators playing powerful roles in cancer. Using TCGA RNAseq data, we analyzed coding (mRNA) and non-coding (lncRNA) gene expression across 15 and 9 common cancer types, respectively. 70 significantly differentially expressed genes common to all 15 cancer types were enlisted. Correlating with protein expression levels from Human Protein Atlas, we observed 34 positively correlated gene sets which are enriched in gene expression, transcription from RNA Pol-II, regulation of transcription and mitotic cell cycle biological processes. Further, 24 lncRNAs were among common significantly differentially expressed non-coding genes. Using guilt-by-association method, we predicted lncRNAs to be involved in same biological processes. Combining RNA-RNA interaction prediction and transcription regulatory networks, we identified E2F1, FOXM1 and PVT1 regulatory path as recurring pan-cancer regulatory entity. PVT1 is predicted to interact with SYNE1 at 3′-UTR; DNAJC9, RNPS1 at 5′-UTR and ATXN2L, ALAD, FOXM1 and IRAK1 at CDS sites. The key findings are that through E2F1, FOXM1 and PVT1 regulatory axis and possible interactions with different coding genes, PVT1 may be playing a prominent role in pan-cancer development and progression.
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Affiliation(s)
- Asanigari Saleembhasha
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Seema Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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