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Engel A, Rishik S, Hirsch P, Keller V, Fehlmann T, Kern F, Keller A. SingmiR: a single-cell miRNA alignment and analysis tool. Nucleic Acids Res 2024:gkae225. [PMID: 38572750 DOI: 10.1093/nar/gkae225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/08/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. However, most of the gene regulatory processes on the single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like the established single-cell gene expression analysis, advanced computational expertise is required to comprehensively process newly emerging single-cell miRNA-seq datasets. A web server providing a workflow tailored for single-cell miRNA-seq data with a self-explanatory interface is currently not available. Here, we present SingmiR, enabling the rapid (pre-)processing and quantification of human miRNAs from noncoding single-cell samples. It performs read trimming for different library preparation protocols, generates automated quality control reports and provides feature-normalized count files. Numerous standard and advanced analyses such as dimension reduction, clustered feature heatmaps, sample correlation heatmaps and differential expression statistics are implemented. We aim to speed up the prototyping pipeline for biologists developing single-cell miRNA-seq protocols on small to medium-sized datasets. SingmiR is freely available to all users without the need for a login at https://www.ccb.uni-saarland.de/singmir.
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Affiliation(s)
- Annika Engel
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Shusruto Rishik
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Clinical Bioinformatics (CLIB), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany
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2
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Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Martinez-Castillo M, M. Elsayed A, López-Berestein G, Amero P, Rodríguez-Aguayo C. An Overview of the Immune Modulatory Properties of Long Non-Coding RNAs and Their Potential Use as Therapeutic Targets in Cancer. Noncoding RNA 2023; 9:70. [PMID: 37987366 PMCID: PMC10660772 DOI: 10.3390/ncrna9060070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play pivotal roles in regulating immune responses, immune cell differentiation, activation, and inflammatory processes. In cancer, they are gaining prominence as potential therapeutic targets due to their ability to regulate immune checkpoint molecules and immune-related factors, suggesting avenues for bolstering anti-tumor immune responses. Here, we explore the mechanistic insights into lncRNA-mediated immune modulation, highlighting their impact on immunity. Additionally, we discuss their potential to enhance cancer immunotherapy, augmenting the effectiveness of immune checkpoint inhibitors and adoptive T cell therapies. LncRNAs as therapeutic targets hold the promise of revolutionizing cancer treatments, inspiring further research in this field with substantial clinical implications.
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Affiliation(s)
- Moises Martinez-Castillo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Liver, Pancreas and Motility Laboratory, Unit of Research in Experimental Medicine, School of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City 06726, Mexico
| | - Abdelrahman M. Elsayed
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11754, Egypt;
- Havener Eye Institute, Department of Ophthalmology and Visual Science, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Gabriel López-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
| | - Cristian Rodríguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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Ahmad M, Weiswald LB, Poulain L, Denoyelle C, Meryet-Figuiere M. Involvement of lncRNAs in cancer cells migration, invasion and metastasis: cytoskeleton and ECM crosstalk. J Exp Clin Cancer Res 2023; 42:173. [PMID: 37464436 PMCID: PMC10353155 DOI: 10.1186/s13046-023-02741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer is the main cause of death worldwide and metastasis is a major cause of poor prognosis and cancer-associated mortality. Metastatic conversion of cancer cells is a multiplex process, including EMT through cytoskeleton remodeling and interaction with TME. Tens of thousands of putative lncRNAs have been identified, but the biological functions of most are still to be identified. However, lncRNAs have already emerged as key regulators of gene expression at transcriptional and post-transcriptional level to control gene expression in a spatio-temporal fashion. LncRNA-dependent mechanisms can control cell fates during development and their perturbed expression is associated with the onset and progression of many diseases including cancer. LncRNAs have been involved in each step of cancer cells metastasis through different modes of action. The investigation of lncRNAs different roles in cancer metastasis could possibly lead to the identification of new biomarkers and innovative cancer therapeutic options.
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Affiliation(s)
- Mohammad Ahmad
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
- Biochemistry Division, Chemistry Department, Faculty of Science, Damanhour University, Damanhour, 14000, Egypt
| | - Louis-Bastien Weiswald
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Laurent Poulain
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Christophe Denoyelle
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Matthieu Meryet-Figuiere
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France.
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France.
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Stabile R, Cabezas MR, Verhagen MP, Tucci FA, van den Bosch TPP, De Herdt MJ, van der Steen B, Nigg AL, Chen M, Ivan C, Shimizu M, Koljenović S, Hardillo JA, Verrijzer CP, Baatenburg de Jong RJ, Calin GA, Fodde R. The deleted in oral cancer (DOC1 aka CDK2AP1) tumor suppressor gene is downregulated in oral squamous cell carcinoma by multiple microRNAs. Cell Death Dis 2023; 14:337. [PMID: 37217493 DOI: 10.1038/s41419-023-05857-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Cyclin-dependent kinase 2-associated protein 1 (CDK2AP1; also known as deleted in oral cancer or DOC1) is a tumor suppressor gene known to play functional roles in both cell cycle regulation and in the epigenetic control of embryonic stem cell differentiation, the latter as a core subunit of the nucleosome remodeling and histone deacetylation (NuRD) complex. In the vast majority of oral squamous cell carcinomas (OSCC), expression of the CDK2AP1 protein is reduced or lost. Notwithstanding the latter (and the DOC1 acronym), mutations or deletions in its coding sequence are extremely rare. Accordingly, CDK2AP1 protein-deficient oral cancer cell lines express as much CDK2AP1 mRNA as proficient cell lines. Here, by combining in silico and in vitro approaches, and by taking advantage of patient-derived data and tumor material in the analysis of loss of CDK2AP1 expression, we identified a set of microRNAs, namely miR-21-5p, miR-23b-3p, miR-26b-5p, miR-93-5p, and miR-155-5p, which inhibit its translation in both cell lines and patient-derived OSCCs. Of note, no synergistic effects were observed of the different miRs on the CDK2AP1-3-UTR common target. We also developed a novel approach to the combined ISH/IF tissue microarray analysis to study the expression patterns of miRs and their target genes in the context of tumor architecture. Last, we show that CDK2AP1 loss, as the result of miRNA expression, correlates with overall survival, thus highlighting the clinical relevance of these processes for carcinomas of the oral cavity.
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Affiliation(s)
- Roberto Stabile
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mario Román Cabezas
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mathijs P Verhagen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Francesco A Tucci
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy
| | | | - Maria J De Herdt
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Berdine van der Steen
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex L Nigg
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Meng Chen
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristina Ivan
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Caris Life Science, Irving, TX, USA
| | - Masayoshi Shimizu
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Senada Koljenović
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Antwerp University Hospital, 2650, Edegem, Belgium
| | - Jose A Hardillo
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert J Baatenburg de Jong
- Department of Otorhinolaryngology and Head & Neck Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - George A Calin
- Department of Translational Molecular Pathology and Center of Department of Translational Molecular Pathology, and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Riccardo Fodde
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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Wu Y, Xu X. Long non-coding RNA signature in colorectal cancer: research progression and clinical application. Cancer Cell Int 2023; 23:28. [PMID: 36797749 PMCID: PMC9936661 DOI: 10.1186/s12935-023-02867-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023] Open
Abstract
Colorectal cancer is one of the top-ranked human malignancies. The development and progression of colorectal cancer are associated with aberrant expression of multiple coding and non-coding genes. Long non-coding RNAs (lncRNAs) have an important role in regulating gene stability as well as gene expression. Numerous current studies have shown that lncRNAs are promising biomarkers and therapeutic targets for colorectal cancer. In this review, we have searched the available literature to list lncRNAs involved in the pathogenesis and regulation of colorectal cancer. We focus on the role of lncRNAs in cancer promotion or suppression, their value in tumor diagnosis, and their role in treatment response and prognosis prediction. In addition, we will discuss the signaling pathways that these lncRNAs are mainly associated with in colorectal cancer. We also summarize the role of lncRNAs in colorectal precancerous lesions and colorectal cancer consensus molecular subgroups. We hope this review article will bring you the latest research progress and outlook on lncRNAs in colorectal cancer.
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Affiliation(s)
- Yudi Wu
- grid.33199.310000 0004 0368 7223GI Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, People’s Republic of China ,grid.33199.310000 0004 0368 7223Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 People’s Republic of China
| | - Xiangshang Xu
- GI Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, People's Republic of China. .,Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China.
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7
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Telonis AG, Yang Q, Huang HT, Figueroa ME. MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia. Nat Commun 2022; 13:6524. [PMID: 36316347 DOI: 10.1038/s41467-022-34211-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
DNMT3A and IDH1/2 mutations combinatorically regulate the transcriptome and the epigenome in acute myeloid leukemia; yet the mechanisms of this interplay are unknown. Using a systems approach within topologically associating domains, we find that genes with significant expression-methylation correlations are enriched in signaling and metabolic pathways. The common denominator across these methylation-regulated genes is the density in MIR retrotransposons of their introns. Moreover, a discrete number of CpGs overlapping enhancers are responsible for regulating most of these genes. Established mouse models recapitulate the dependency of MIR-rich genes on the balanced expression of epigenetic modifiers, while projection of leukemic profiles onto normal hematopoiesis ones further consolidates the dependencies of methylation-regulated genes on MIRs. Collectively, MIR elements on genes and enhancers are susceptible to changes in DNA methylation activity and explain the cooperativity of proteins in this pathway in normal and malignant hematopoiesis.
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Wang Y, Wang Y, Liang D, Hu H, Li G, Meng X, Zhu B, Zhong W. MIR31HG polymorphisms are related to steroid-induced osteonecrosis of femoral head among Chinese Han population. BMC Musculoskelet Disord 2022; 23:836. [PMID: 36057712 PMCID: PMC9440494 DOI: 10.1186/s12891-022-05785-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/30/2022] [Indexed: 11/11/2022] Open
Abstract
Backgrounds MIR31 host gene (MIR31HG) polymorphisms play important roles in the occurrence of osteonecrosis. However, the association of MIR31HG polymorphisms with the risk of steroid-induced osteonecrosis of the femoral head (SONFH) remains unclear. In this study, we aimed to investigate the correlation between MIR31HG polymorphisms and SONFH susceptibility in the Chinese Han population. Methods A total of 708 volunteers were recruited to detect the effect of seven single nucleotide polymorphisms (SNPs) in the MIR31HG gene on SONFH risk in the Chinese Han population. Genotyping of MIR31HG polymorphisms was performed using the Agena MassARRAY platform. The odds ratio (OR) and 95% confidence interval (95% CI) were used to evaluate the correlation between MIR31HG polymorphisms and SONFH risk using logistic regression model. Results According to the results of genetic model, rs10965059 in MIR31HG was significantly correlated with the susceptibility to SONFH (OR = 0.56, p = 0.002). Interestingly, the stratified analysis showed that rs10965059 was associated with the reduced risk of SONFH in subjects aged > 40 years (OR = 0.30, p < 0.001) and male populations (OR = 0.35, p < 0 .001). Moreover, rs10965059 was associated with the reduced risk of bilateral SONFH (OR = 0.50, p = 0.002). Finally, multi-factor dimension reduction (MDR) results showed that the combination of rs1332184, rs72703442, rs2025327, rs55683539, rs2181559, rs10965059 and rs10965064 was the best model for predicting SONFH occurrence (p < 0.0001). Conclusion The study indicated that rs10965059 could be involved in SONFH occurrence in the Chinese Han population, which might provide clues for investigating the role of MIR31HG in the pathogenesis of SONFH. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-022-05785-w.
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Affiliation(s)
- Yuan Wang
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China
| | - Yexin Wang
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China
| | - Da Liang
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China
| | - Hongtao Hu
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China.,Department of Spine Surgery, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, 261031, China
| | - Guangwei Li
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China
| | - Xiaoguang Meng
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China
| | - Bing Zhu
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China
| | - Wei Zhong
- Department of Joint Surgery, Affiliated Hospital of Weifang Medical University, #2428 Yuhe Road, Weifang, 261031, Shandong, China.
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Jha A, Quesnel-Vallières M, Wang D, Thomas-Tikhonenko A, Lynch KW, Barash Y. Identifying common transcriptome signatures of cancer by interpreting deep learning models. Genome Biol 2022; 23:117. [PMID: 35581644 PMCID: PMC9112525 DOI: 10.1186/s13059-022-02681-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/27/2022] [Indexed: 01/01/2023] Open
Abstract
Background Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute to oncogenesis vary widely between tumor types, but common gene signatures that relate to core cancer pathways have also been identified. It is not clear, however, whether there exist additional sets of genes or transcriptomic features that are less well known in cancer biology but that are also commonly deregulated across several cancer types. Results Here, we agnostically identify transcriptomic features that are commonly shared between cancer types using 13,461 RNA-seq samples from 19 normal tissue types and 18 solid tumor types to train three feed-forward neural networks, based either on protein-coding gene expression, lncRNA expression, or splice junction use, to distinguish between normal and tumor samples. All three models recognize transcriptome signatures that are consistent across tumors. Analysis of attribution values extracted from our models reveals that genes that are commonly altered in cancer by expression or splicing variations are under strong evolutionary and selective constraints. Importantly, we find that genes composing our cancer transcriptome signatures are not frequently affected by mutations or genomic alterations and that their functions differ widely from the genes genetically associated with cancer. Conclusions Our results highlighted that deregulation of RNA-processing genes and aberrant splicing are pervasive features on which core cancer pathways might converge across a large array of solid tumor types. Supplementary Information The online version contains supplementary material available at (10.1186/s13059-022-02681-3).
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Affiliation(s)
- Anupama Jha
- Department of Computer and Information Science, School of Engineering and Applied Science, Philadelphia, USA.
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Philadelphia, USA. .,Department of Biochemistry and Biophysics, Philadelphia, USA.
| | - David Wang
- Department of Genetics, Philadelphia, USA
| | - Andrei Thomas-Tikhonenko
- Department of Pathology and Laboratory Medicine, Philadelphia, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.,Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Philadelphia, USA
| | - Yoseph Barash
- Department of Computer and Information Science, School of Engineering and Applied Science, Philadelphia, USA. .,Department of Genetics, Philadelphia, USA.
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Pavlič A, Hauptman N, Boštjančič E, Zidar N. Long Non-Coding RNAs as Potential Regulators of EMT-Related Transcription Factors in Colorectal Cancer—A Systematic Review and Bioinformatics Analysis. Cancers (Basel) 2022; 14:cancers14092280. [PMID: 35565409 PMCID: PMC9105237 DOI: 10.3390/cancers14092280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Emerging evidence highlights long non-coding RNAs as important regulators of epithelial–mesenchymal transition. Numerous studies have attempted to define their possible diagnostic, prognostic and therapeutic values in various human cancers. The aim of this review is to summarize long non-coding RNAs involved in the regulation of epithelial–mesenchymal transition in colorectal carcinoma. Additional candidate long non-coding RNAs are identified through a bioinformatics analysis. Abstract Epithelial–mesenchymal transition (EMT) plays a pivotal role in carcinogenesis, influencing cancer progression, metastases, stemness, immune evasion, metabolic reprogramming and therapeutic resistance. EMT in most carcinomas, including colorectal carcinoma (CRC), is only partial, and can be evidenced by identification of the underlying molecular drivers and their regulatory molecules. During EMT, cellular reprogramming is orchestrated by core EMT transcription factors (EMT-TFs), namely ZEB1/2, TWIST1/2, SNAI1 (SNAIL) and SNAI2 (SLUG). While microRNAs have been clearly defined as regulators of EMT, the role of long non-coding RNAs (lncRNAs) in EMT is poorly defined and controversial. Determining the role of lncRNAs in EMT remains a challenge, because they are involved in a number of cellular pathways and are operating through various mechanisms. Adding to the complexity, some lncRNAs have controversial functions across different tumor types, acting as EMT promotors in some tumors and as EMT suppressors in others. The aim of this review is to summarize the role of lncRNAs involved in the regulation of EMT-TFs in human CRC. Additional candidate lncRNAs were identified through a bioinformatics analysis.
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Chen B, Dragomir MP, Yang C, Li Q, Horst D, Calin GA. Targeting non-coding RNAs to overcome cancer therapy resistance. Signal Transduct Target Ther 2022; 7:121. [PMID: 35418578 DOI: 10.1038/s41392-022-00975-3] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
It is now well known that non-coding RNAs (ncRNAs), rather than protein-coding transcripts, are the preponderant RNA transcripts. NcRNAs, particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are widely appreciated as pervasive regulators of multiple cancer hallmarks such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Despite recent discoveries in cancer therapy, resistance to chemotherapy, radiotherapy, targeted therapy, and immunotherapy continue to be a major setback. Recent studies have shown that ncRNAs also play a major role in resistance to different cancer therapies by rewiring essential signaling pathways. In this review, we present the intricate mechanisms through which dysregulated ncRNAs control resistance to the four major types of cancer therapies. We will focus on the current clinical implications of ncRNAs as biomarkers to predict treatment response (intrinsic resistance) and to detect resistance to therapy after the start of treatment (acquired resistance). Furthermore, we will present the potential of targeting ncRNA to overcome cancer treatment resistance, and we will discuss the challenges of ncRNA-targeted therapy—especially the development of delivery systems.
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Lee H, Jeong SH, Lee H, Kim C, Nam YJ, Kang JY, Song MO, Choi JY, Kim J, Park EK, Baek YW, Lee JH. Analysis of lung cancer-related genetic changes in long-term and low-dose polyhexamethylene guanidine phosphate (PHMG-p) treated human pulmonary alveolar epithelial cells. BMC Pharmacol Toxicol 2022; 23:19. [PMID: 35354498 PMCID: PMC8969249 DOI: 10.1186/s40360-022-00559-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lung injury elicited by respiratory exposure to humidifier disinfectants (HDs) is known as HD-associated lung injury (HDLI). Current elucidation of the molecular mechanisms related to HDLI is mostly restricted to fibrotic and inflammatory lung diseases. In our previous report, we found that lung tumors were caused by intratracheal instillation of polyhexamethylene guanidine phosphate (PHMG-p) in a rat model. However, the lung cancer-related genetic changes concomitant with the development of these lung tumors have not yet been fully defined. We aimed to discover the effect of long-term exposure of PHMG-p on normal human lung alveolar cells. METHODS We investigated whether PHMG-p could increase distorted homeostasis of oncogenes and tumor-suppressor genes, with long-term and low-dose treatment, in human pulmonary alveolar epithelial cells (HPAEpiCs). Total RNA sequencing was performed with cells continuously treated with PHMG-p and harvested after 35 days. RESULTS After PHMG-p treatment, genes with transcriptional expression changes of more than 2.0-fold or less than 0.5-fold were identified. Within 10 days of exposure, 2 protein-coding and 5 non-coding genes were selected, whereas in the group treated for 27-35 days, 24 protein-coding and 5 non-coding genes were identified. Furthermore, in the long-term treatment group, 11 of the 15 upregulated genes and 9 of the 14 downregulated genes were reported as oncogenes and tumor suppressor genes in lung cancer, respectively. We also found that 10 genes of the selected 24 protein-coding genes were clinically significant in lung adenocarcinoma patients. CONCLUSIONS Our findings demonstrate that long-term exposure of human pulmonary normal alveolar cells to low-dose PHMG-p caused genetic changes, mainly in lung cancer-associated genes, in a time-dependent manner.
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Affiliation(s)
- Hong Lee
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Sang Hoon Jeong
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Hyejin Lee
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Cherry Kim
- Department of Radiology, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Yoon Jeong Nam
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Ja Young Kang
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Myeong Ok Song
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Jin Young Choi
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Jaeyoung Kim
- Medical Science Research Center, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea
| | - Eun-Kee Park
- Department of Medical Humanities and Social Medicine, College of Medicine, Kosin University, Busan, Republic of Korea
| | - Yong-Wook Baek
- Environmental Health Research Department, Humidifier Disinfectant Health Center, National Institute of Environmental Research, Incheon, Republic of Korea
| | - Ju-Han Lee
- Department of Pathology, Ansan Hospital, Korea University College of Medicine, Ansan-si, Gyeonggi, Republic of Korea.
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Hamidi AA, Khalili-Tanha G, Nasrpour Navaei Z, Moghbeli M. Long non-coding RNAs as the critical regulators of epithelial mesenchymal transition in colorectal tumor cells: an overview. Cancer Cell Int 2022; 22:71. [PMID: 35144601 PMCID: PMC8832734 DOI: 10.1186/s12935-022-02501-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/30/2022] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer mortality and a major health challenge worldwide. Despite advances in therapeutic and diagnostic methods, there is still a poor prognosis in CRC patients. Tumor recurrence and metastasis are the main causes of high mortality rate in these patients, which are due to late diagnosis in advanced tumor stages. Epithelial-mesenchymal transition (EMT) is known to be the most important cause of CRC metastasis, during which tumor cells obtain metastasis ability by losing epithelial features and gaining mesenchymal features. Long non-coding RNAs (lncRNAs) are pivotal regulators of EMT process. Regarding the higher stability of lncRNAs compared with coding RNAs in body fluids, they can be used as non-invasive diagnostic markers for EMT process. In the present review, we summarized all of the lncRNAs involved in regulation of EMT process during CRC progression and metastasis. It was observed that lncRNAs mainly induced the EMT process in CRC cells by regulation of EMT-related transcription factors, Poly comb repressive complex (PRC), and also signaling pathways such as WNT, NOTCH, MAPK, and Hippo.
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Affiliation(s)
- Amir Abbas Hamidi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghazaleh Khalili-Tanha
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Nasrpour Navaei
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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14
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Su T, Wang T, Zhang N, Shen Y, Li W, Xing H, Yang M. Long non-coding RNAs in gastrointestinal cancers: implications for protein phosphorylation. Biochem Pharmacol 2022; 197:114907. [PMID: 35007523 DOI: 10.1016/j.bcp.2022.114907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 12/24/2022]
Abstract
Phosphorylation of proteins is one of the most extensively investigated post-translational protein modifications. Threonine, serine and tyrosine in proteins are the most commonly phosphorylated amino acids. Dysregulated cancer-related signaling pathways due to aberrant phosphorylation status of the key protein(s) in these pathways exist in most malignancies. Intensive studies in the recent decade have implicated long non-coding RNAs (lncRNAs) in the precise regulation of protein phosphorylation in cancers. In this review, we systematically delve into recent advance that underlines the multidimensional role of lncRNAs in modulating protein phosphorylation, regulating cancerous signaling and impacting prognosis of gastrointestinal (GI) cancers including hepatocellular carcinoma, colorectal cancer, gastric cancer, esophageal cancer, and pancreatic cancer. LncRNAs regulate protein phosphorylation via directly binding to the target protein(s), interacting with the partner protein(s) of the target protein(s) or lncRNAs-encoded small peptides. Although there are still extensive studies on disclosing the intricate interactions between lncRNAs and proteins and their impacts on protein phosphorylation, we believe that targeting lncRNAs controlling phosphorylation of key protein(s) in cancerous signaling pathways might provide novel paths for precision therapeutics of GI cancers in the future.
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Affiliation(s)
- Tao Su
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Teng Wang
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Nasha Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Jinan, Shandong Province, China
| | - Yue Shen
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wenwen Li
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Jinan, Shandong Province, China
| | - Huaixin Xing
- Department of Anesthesiology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
| | - Ming Yang
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Jinan, Shandong Province, China.
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15
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Veiga RN, Zambalde ÉP, Cox L, Jucoski TS, Kohler AF, Carvalho TM, Rodrigues AC, Ludwig B, Crowley K, de Oliveira JC, Cortez MA. Regulation of Immune Cells by microRNAs and microRNA-Based Cancer Immunotherapy. Advances in Experimental Medicine and Biology 2022. [DOI: 10.1007/978-3-031-08356-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Lu S, Ding X, Wang Y, Hu X, Sun T, Wei M, Wang X, Wu H. The Relationship Between the Network of Non-coding RNAs-Molecular Targets and N6-Methyladenosine Modification in Colorectal Cancer. Front Cell Dev Biol 2021; 9:772542. [PMID: 34938735 PMCID: PMC8685436 DOI: 10.3389/fcell.2021.772542] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/11/2021] [Indexed: 12/11/2022] Open
Abstract
Recent accumulating researches implicate that non-coding RNAs (ncRNAs) including microRNA (miRNA), circular RNA (circRNA), and long non-coding RNA (lncRNAs) play crucial roles in colorectal cancer (CRC) initiation and development. Notably, N6-methyladenosine (m6A) methylation, the critical posttranscriptional modulators, exerts various functions in ncRNA metabolism such as stability and degradation. However, the interaction regulation network among ncRNAs and the interplay with m6A-related regulators has not been well documented, particularly in CRC. Here, we summarize the interaction networks and sub-networks of ncRNAs in CRC based on a data-driven approach from the publications (IF > 6) in the last quinquennium (2016–2021). Further, we extend the regulatory pattern between the core m6A regulators and m6A-related ncRNAs in the context of CRC metastasis and progression. Thus, our review will highlight the clinical potential of ncRNAs and m6A modifiers as promising biomarkers and therapeutic targets for improving the diagnostic precision and treatment of CRC.
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Affiliation(s)
- Senxu Lu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Xiangyu Ding
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Yuanhe Wang
- Department of Medical Oncology, Cancer Hospital of China Medical University, Shenyang, China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Tong Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China.,Shenyang Kangwei Medical Laboratory Analysis Co. Ltd., Liaoning, China
| | - Xiaobin Wang
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
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17
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Hu D, Shao W, Liu L, Wang Y, Yuan S, Liu Z, Liu J, Zhang J. Intricate crosstalk between MYB and noncoding RNAs in cancer. Cancer Cell Int 2021; 21:653. [PMID: 34876130 PMCID: PMC8650324 DOI: 10.1186/s12935-021-02362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/24/2021] [Indexed: 11/10/2022] Open
Abstract
MYB is often overexpressed in malignant tumors and plays a carcinogenic role in the initiation and development of cancer. Deletion of the MYB regulatory C-terminal domain may be a driving mutation leading to tumorigenesis, therefore, different tumor mechanisms produce similar MYB proteins. As MYB is a transcription factor, priority has been given to identifying the genes that it regulates. All previous attention has been focused on protein-coding genes. However, an increasing number of studies have suggested that MYB can affect the complexity of cancer progression by regulating tumor-associated noncoding RNAs (ncRNAs), such as microRNAs, long-non-coding RNAs and circular RNAs. ncRNAs can regulate the expression of numerous downstream genes at the transcription, RNA processing and translation levels, thereby having various biological functions. Additionally, ncRNAs play important roles in regulating MYB expression. This review focuses on the intricate crosstalk between oncogenic MYB and ncRNAs, which play a pivotal role in tumorigenesis, including proliferation, apoptosis, angiogenesis, metastasis, senescence and drug resistance. In addition, we discuss therapeutic strategies for crosstalk between MYB and ncRNAs to prevent the occurrence and development of cancer.
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Affiliation(s)
- Dingyu Hu
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Wenjun Shao
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Li Liu
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Yanyan Wang
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Shunling Yuan
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Zhaoping Liu
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Jing Liu
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
| | - Ji Zhang
- The First Affiliated Hospital, Department of Rheumatology, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China. .,Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033, Guangdong, China.
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18
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Li Y, Zou J, Li B, Du J. Anticancer effects of melatonin via regulating lncRNA JPX-Wnt/β-catenin signalling pathway in human osteosarcoma cells. J Cell Mol Med 2021; 25:9543-9556. [PMID: 34547170 PMCID: PMC8505851 DOI: 10.1111/jcmm.16894] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Osteosarcoma (OS) is a type of malignant primary bone cancer, which is highly aggressive and occurs more commonly in children and adolescents. Thus, novel potential drugs and therapeutic methods are urgently needed. In the present study, we aimed to elucidate the effects and mechanism of melatonin on OS cells to provide a potential treatment strategy for OS. The cell survival rate, cell viability, proliferation, migration, invasion and metastasis were examined by trypan blue assay, MTT, colony formation, wound healing, transwell invasion and attachment/detachment assay, respectively. The expression of relevant lncRNAs in OS cells was determined by real-time qPCR analysis. The functional roles of lncRNA JPX in OS cells were further examined by gain and loss of function assays. The protein expression was measured by western blot assay. Melatonin inhibited the cell viability, proliferation, migration, invasion and metastasis of OS cells (Saos-2, MG63 and U2OS) in a dose-dependent manner. Melatonin treatment significantly downregulated the expression of lncRNA JPX in Saos-2, MG63 and U2OS cells. Overexpression of lncRNA JPX into OS cell lines elevated the cell viability and proliferation, which was accompanied by the increased metastasis. We also found that melatonin inhibited the OS progression by suppressing the expression of lncRNA JPX via regulating the Wnt/β-catenin pathway. Our results suggested that melatonin inhibited the biological functions of OS cells by repressing the expression of lncRNA JPX through regulating the Wnt/β-catenin signalling pathway, which indicated that melatonin might be applied as a potentially useful and effective natural agent in the treatment of OS.
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Affiliation(s)
- Yuan Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Suzhou Research Institute, Shandong University, Suzhou, Jiangsu, China
| | - Jilong Zou
- Department of Orthopedics, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bo Li
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jianyang Du
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Abstract
Therapeutic targeting of noncoding RNAs (ncRNAs), such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), represents an attractive approach for the treatment of cancers, as well as many other diseases. Over the past decade, substantial effort has been made towards the clinical application of RNA-based therapeutics, employing mostly antisense oligonucleotides and small interfering RNAs, with several gaining FDA approval. However, trial results have so far been ambivalent, with some studies reporting potent effects whereas others demonstrated limited efficacy or toxicity. Alternative entities such as antimiRNAs are undergoing clinical testing, and lncRNA-based therapeutics are gaining interest. In this Perspective, we discuss key challenges facing ncRNA therapeutics - including issues associated with specificity, delivery and tolerability - and focus on promising emerging approaches that aim to boost their success.
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Affiliation(s)
- Melanie Winkle
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
| | - Sherien M El-Daly
- Medical Biochemistry Department, Medical Research Division - Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences - National Research Centre, Cairo, Egypt
| | - Muller Fabbri
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - George A Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
- The RNA Interference and Non-codingRNA Center, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
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20
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Tang C, Liu J, Hu Q, Zeng S, Yu L. Metastatic colorectal cancer: Perspectives on long non-coding RNAs and promising therapeutics. Eur J Pharmacol 2021; 908:174367. [PMID: 34303661 DOI: 10.1016/j.ejphar.2021.174367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 01/06/2023]
Abstract
Metastatic colorectal cancer (mCRC) has long been lethal despite the continuous efforts of researchers worldwide to discover and improve therapeutic regimens. Thanks to the emergence of long non-coding RNAs (lncRNAs), which has strongly reshaped our inherent perspectives on the pathophysiological patterns of disease, research in the field has been reinvigorated. Here, we focus on current understanding of the modes of action of lncRNAs, and review their regulatory roles in metastatic colorectal cancer, and discuss correlated potential lncRNA-based therapeutics. All of the discussed studies share clear and promising perspectives on future diagnostic and therapeutic remedies for metastatic colorectal cancer.
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Affiliation(s)
- Chunyuan Tang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Junqing Liu
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310022, China
| | - Qingqing Hu
- The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Jinhua, 322023, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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21
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Sabo AA, Dudau M, Constantin GL, Pop TC, Geilfus CM, Naccarati A, Dragomir MP. Two Worlds Colliding: The Interplay Between Natural Compounds and Non-Coding Transcripts in Cancer Therapy. Front Pharmacol 2021; 12:652074. [PMID: 34295245 PMCID: PMC8290364 DOI: 10.3389/fphar.2021.652074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/07/2021] [Indexed: 12/25/2022] Open
Abstract
Cancer is a devastating disease and has recently become the leading cause of death in western countries, representing an immense public health burden. When it comes to cancer treatment, chemotherapy is one of the main pillars, especially for advanced stage tumors. Over the years, natural compounds have emerged as one of the most valuable resources for new chemotherapies. It is estimated that more than half of the currently used chemotherapeutic agents are derived from natural compounds. Usually, natural compounds are discovered empirically and an important limitation of introducing new anti-cancer natural products is lack of knowledge with regard to their mechanism of action. Recent data has proven that several natural compounds may function via modulating the expression and function of non-coding RNAs (ncRNAs). NcRNAs are a heterogenous class of RNA molecules which are usually not translated into proteins but have an important role in gene expression regulation and are involved in multiple tumorigenic processes, including response/resistance to pharmacotherapy. In this review, we will discuss how natural compounds function via ncRNAs while summarizing the available data regarding their effects on over 15 types of cancer. Moreover, we will critically analyze the current advances and limitations in understanding the way natural compounds exert these health-promoting effects by acting on ncRNAs. Finally, we will propose several hypotheses that may open new avenues and perspectives regarding the interaction between natural compounds and ncRNAs, which could lead to improved natural compound-based therapeutic strategies in cancer.
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Affiliation(s)
- Alexandru A Sabo
- Pediatrics 2 (General and Special Pediatrics), Klinikum Stuttgart, Olgahospital, Zentrum für Kinder, Jugend- und Frauenmedizin, Stuttgart, Germany
| | - Maria Dudau
- Biochemistry-Proteomics Department, Victor Babes National Institute of Pathology, Bucharest, Romania.,Department of Cellular and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - George L Constantin
- Division of Soil Science and Site Science, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tudor C Pop
- Department of Pediatrics, Marie Curie Emergency Clinical Hospital for Children, Bucharest, Romania
| | - Christoph-M Geilfus
- Division of Controlled Environment Horticulture, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alessio Naccarati
- IIGM Italian Institute for Genomic Medicine, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Mihnea P Dragomir
- Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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22
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Wu D, Yin Z, Ji Y, Li L, Li Y, Meng F, Ren X, Xu M. Identification of novel autophagy-related lncRNAs associated with a poor prognosis of colon adenocarcinoma through bioinformatics analysis. Sci Rep 2021; 11:8069. [PMID: 33850225 DOI: 10.1038/s41598-021-87540-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
LncRNAs play a pivotal role in tumorigenesis and development. However, the potential involvement of lncRNAs in colon adenocarcinoma (COAD) needs to be further explored. All the data used in this study were obtained from The Cancer Genome Atlas database, and all analyses were conducted using R software. Basing on the seven prognosis-related lncRNAs finally selected, we developed a prognosis-predicting model with powerful effectiveness (training cohort, 1 year: AUC = 0.70, 95% Cl = 0.57–0.78; 3 years: AUC = 0.71, 95% Cl = 0.6–0.8; 5 years: AUC = 0.76, 95% Cl = 0.66–0.87; validation cohort, 1 year: AUC = 0.70, 95% Cl = 0.58–0.8; 3 years: AUC = 0.73, 95% Cl = 0.63–0.82; 5 years: AUC = 0.68, 95% Cl = 0.5–0.85). The VEGF and Notch pathway were analyzed through GSEA analysis, and low immune and stromal scores were found in high-risk patients (immune score, cor = − 0.15, P < 0.001; stromal score, cor = − 0.18, P < 0.001) , which may partially explain the poor prognosis of patients in the high-risk group. We screened lncRNAs that are significantly associated with the survival of patients with COAD and possibly participate in autophagy regulation. This study may provide direction for future research.
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Wu QN, Luo XJ, Liu J, Lu YX, Wang Y, Qi J, Liu ZX, Huang QT, Liu ZK, Lu JB, Jin Y, Pu HY, Hu PS, Zheng JB, Zeng ZL, Ju HQ, Xie D, Zhao Q, Xu R. MYC-Activated LncRNA MNX1-AS1 Promotes the Progression of Colorectal Cancer by Stabilizing YB1. Cancer Res 2021; 81:2636-2650. [PMID: 33782099 DOI: 10.1158/0008-5472.can-20-3747] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/20/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) are involved in tumorigenesis and drug resistance. However, the roles and underlying mechanisms of lncRNAs in colorectal cancer are still unknown. In this work, through transcriptomic profiling analysis of 21 paired tumor and normal samples, we identified a novel colorectal cancer-related lncRNA, MNX1-AS1. MNX1-AS1 expression was significantly upregulated in colorectal cancer and associated with poor prognosis. In vitro and in vivo gain- and loss-of-function experiments showed that MNX1-AS1 promotes the proliferation of colorectal cancer cells. MNX1-AS1 bound to and activated Y-box-binding protein 1 (YB1), a multifunctional RNA/DNA-binding protein, and prevented its ubiquitination and degradation. A marked overlap between genes that are differentially expressed in MNX1-AS1 knockdown cells and transcriptional targets of YB1 was observed. YB1 knockdown mimicked the loss of viability phenotype observed upon depletion of MNX1-AS1. In addition, MYC bound the promoter of the MNX1-AS1 locus and activated its transcription. In vivo experiments showed that ASO inhibited MNX1-AS1, which suppressed the proliferation of colorectal cancer cells in both cell-based and patient-derived xenograft models. Collectively, these findings suggest that the MYC-MNX1-AS1-YB1 axis might serve as a potential biomarker and therapeutic target in colorectal cancer. SIGNIFICANCE: This study highlights the discovery of a novel colorectal cancer biomarker and therapeutic target, MNX1-AS1, a long noncoding RNA that drives proliferation via a MYC/MNX1-AS1/YB1 signaling pathway. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2636/F1.large.jpg.
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Affiliation(s)
- Qi-Nian Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Jing Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun-Xin Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jingjing Qi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi-Tao Huang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Kun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Bin Lu
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Jin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Heng-Ying Pu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Pei-Shan Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia-Bo Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhao-Lei Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huai-Qiang Ju
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Ruihua Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, China
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24
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Telonis AG, Rigoutsos I. The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content. BMC Biol 2021; 19:60. [PMID: 33765992 PMCID: PMC7995781 DOI: 10.1186/s12915-020-00928-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic datasets from preimplantation and differentiation stages examining the architectural properties and content of genes whose abundance changes significantly across developmental time points. Results Analysis of preimplantation embryos from human and mouse showed that short genes whose introns are enriched in Alu (human) and B (mouse) elements, respectively, have higher abundance in the blastocyst compared to the zygote. These highly expressed genes encode ribosomal proteins or metabolic enzymes. On the other hand, long genes whose introns are depleted in repetitive elements have lower abundance in the blastocyst and include genes from signaling pathways. Additionally, the sequences of the genes that are differentially expressed between the blastocyst and the zygote contain distinct collections of pyknon motifs that differ between up- and down-regulated genes. Further examination of the genes that participate in the stem cell-specific protein interaction network shows that their introns are short and enriched in Alu (human) and B (mouse) elements. As organogenesis progresses, in both human and mouse, we find that the primarily short and repeat-rich expressed genes make way for primarily longer, repeat-poor genes. With that in mind, we used a machine learning-based approach to identify gene signatures able to classify human adult tissues: we find that the most discriminatory genes comprising these signatures have long introns that are repeat-poor and include transcription factors and signaling-cascade genes. The introns of widely expressed genes across human tissues, on the other hand, are short and repeat-rich, and coincide with those with the highest expression at the blastocyst stage. Conclusions Protein-coding genes that are characteristic of each trajectory, i.e., proliferation/pluripotency or differentiation, exhibit antithetical biases in their intronic and exonic lengths and in their repetitive-element content. While the respective human and mouse gene signatures are functionally and evolutionarily conserved, their introns and exons are enriched or depleted in organism-specific repetitive elements. We posit that these organism-specific repetitive sequences found in exons and introns are used to effect the corresponding genes’ regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-020-00928-8.
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Affiliation(s)
- Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, 1020 Locust Street, Suite M81, Philadelphia, PA, 19107, USA. .,Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, 1020 Locust Street, Suite M81, Philadelphia, PA, 19107, USA.
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25
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Balihodzic A, Barth DA, Prinz F, Pichler M. Involvement of Long Non-Coding RNAs in Glucose Metabolism in Cancer. Cancers (Basel) 2021; 13:977. [PMID: 33652661 PMCID: PMC7956509 DOI: 10.3390/cancers13050977] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid and uncontrolled proliferation of cancer cells is supported by metabolic reprogramming. Altered glucose metabolism supports cancer growth and progression. Compared with normal cells, cancer cells show increased glucose uptake, aerobic glycolysis and lactate production. Byproducts of adjusted glucose metabolism provide additional benefits supporting hallmark capabilities of cancer cells. Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts of more than 200 nucleotides in length. They regulate numerous cellular processes, primarily through physical interaction with other molecules. Dysregulated lncRNAs are involved in all hallmarks of cancer including metabolic alterations. They may upregulate metabolic enzymes, modulate the expression of oncogenic or tumor-suppressive genes and disturb metabolic signaling pathways favoring cancer progression. Thus, lncRNAs are not only potential clinical biomarkers for cancer diagnostics and prediction but also possible therapeutic targets. This review summarizes the lncRNAs involved in cancer glucose metabolism and highlights their underlying molecular mechanisms.
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Affiliation(s)
- Amar Balihodzic
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Oncology, Department of Internal Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (A.B.); (D.A.B.); (F.P.)
- BioTechMed-Graz, 8010 Graz, Austria
| | - Dominik A. Barth
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Oncology, Department of Internal Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (A.B.); (D.A.B.); (F.P.)
| | - Felix Prinz
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Oncology, Department of Internal Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (A.B.); (D.A.B.); (F.P.)
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Oncology, Department of Internal Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (A.B.); (D.A.B.); (F.P.)
- BioTechMed-Graz, 8010 Graz, Austria
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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26
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Si Z, Yu L, Jing H, Wu L, Wang X. Oncogenic lncRNA ZNF561-AS1 is essential for colorectal cancer proliferation and survival through regulation of miR-26a-3p/miR-128-5p-SRSF6 axis. J Exp Clin Cancer Res 2021; 40:78. [PMID: 33622363 PMCID: PMC7903733 DOI: 10.1186/s13046-021-01882-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/15/2021] [Indexed: 02/06/2023]
Abstract
Background Long non-coding RNAs (lncRNA) are reported to influence colorectal cancer (CRC) progression. Currently, the functions of the lncRNA ZNF561 antisense RNA 1 (ZNF561-AS1) in CRC are unknown. Methods ZNF561-AS1 and SRSF6 expression in CRC patient samples and CRC cell lines was evaluated through TCGA database analysis, western blot along with real-time PCR. SRSF6 expression in CRC cells was also examined upon ZNF561-AS1 depletion or overexpression. Interaction between miR-26a-3p, miR-128-5p, ZNF561-AS1, and SRSF6 was examined by dual luciferase reporter assay, as well as RNA binding protein immunoprecipitation (RIP) assay. Small interfering RNA (siRNA) mediated knockdown experiments were performed to assess the role of ZNF561-AS1 and SRSF6 in the proliferative actives and apoptosis rate of CRC cells. A mouse xenograft model was employed to assess tumor growth upon ZNF561-AS1 knockdown and SRSF6 rescue. Results We find that ZNF561-AS1 and SRSF6 were upregulated in CRC patient tissues. ZNF561-AS1 expression was reduced in tissues from treated CRC patients but upregulated in CRC tissues from relapsed patients. SRSF6 expression was suppressed and enhanced by ZNF561-AS1 depletion and overexpression, respectively. Mechanistically, ZNF561-AS1 regulated SRSF6 expression by sponging miR-26a-3p and miR-128-5p. ZNF561-AS1-miR-26a-3p/miR-128-5p-SRSF6 axis was required for CRC proliferation and survival. ZNF561-AS1 knockdown suppressed CRC cell proliferation and triggered apoptosis. ZNF561-AS1 depletion suppressed the growth of tumors in a model of a nude mouse xenograft. Similar observations were made upon SRSF6 depletion. SRSF6 overexpression reversed the inhibitory activities of ZNF561-AS1 in vivo, as well as in vitro. Conclusion In summary, we find that ZNF561-AS1 promotes CRC progression via the miR-26a-3p/miR-128-5p-SRSF6 axis. This study reveals new perspectives into the role of ZNF561-AS1 in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01882-1.
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Affiliation(s)
- Zizhen Si
- Pharmacy Department, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, People's Republic of China.,Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo, People's Republic of China
| | - Lei Yu
- Department of Colorectal Cancer Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, People's Republic of China
| | - Haoyu Jing
- Department of Colorectal Cancer Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, People's Republic of China
| | - Lun Wu
- Pharmacy Department, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, People's Republic of China
| | - Xidi Wang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, 194 XueFu Road Nangang Dist, Harbin, 150086, People's Republic of China.
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27
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Mohapatra S, Pioppini C, Ozpolat B, Calin GA. Non-coding RNAs regulation of macrophage polarization in cancer. Mol Cancer 2021; 20:24. [PMID: 33522932 PMCID: PMC7849140 DOI: 10.1186/s12943-021-01313-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/12/2021] [Indexed: 12/19/2022] Open
Abstract
Noncoding RNA (ncRNA) transcripts that did not code proteins but regulate their functions were extensively studied for the last two decades and the plethora of discoveries have instigated scientists to investigate their dynamic roles in several diseases especially in cancer. However, there is much more to learn about the role of ncRNAs as drivers of malignant cell evolution in relation to macrophage polarization in the tumor microenvironment. At the initial stage of tumor development, macrophages have an important role in directing Go/No-go decisions to the promotion of tumor growth, immunosuppression, and angiogenesis. Tumor-associated macrophages behave differently as they are predominantly induced to be polarized into M2, a pro-tumorigenic type when recruited with the tumor tissue and thereby favoring the tumorigenesis. Polarization of macrophages into M1 or M2 subtypes plays a vital role in regulating tumor progression, metastasis, and clinical outcome, highlighting the importance of studying the factors driving this process. A substantial number of studies have demonstrated that ncRNAs are involved in the macrophage polarization based on their ability to drive M1 or M2 polarization and in this review we have described their functions and categorized them into oncogenes, tumor suppressors, Juggling tumor suppressors, and Juggling oncogenes.
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Affiliation(s)
- Swati Mohapatra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA
| | - Carlotta Pioppini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Life Science Plaza, Suite: LSP9.3012, 2130 W, Holcombe Blvd, Ste. 910, Houston, TX, 77030, USA.
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28
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Huang X, Zhu X, Yu Y, Zhu W, Jin L, Zhang X, Li S, Zou P, Xie C, Cui R. Dissecting miRNA signature in colorectal cancer progression and metastasis. Cancer Lett 2020; 501:66-82. [PMID: 33385486 DOI: 10.1016/j.canlet.2020.12.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is the third most common cancer and leading cause of cancer related deaths worldwide. Despite recent advancements in surgical and molecular targeted therapies that improved the therapeutic efficacy in CRC, the 5 years survival rate of CRC patients still remains frustratingly poor. Accumulated evidences indicate that microRNAs (miRNAs) play a crucial role in the progression and metastasis of CRC. Dysregulated miRNAs are closely associated with cancerous phenotypes (e.g. enhanced proliferative and invasive ability, evasion of apoptosis, cell cycle aberration, and promotion of angiogenesis) by regulating their target genes. In this review, we provide an updated overview of tumor suppressive and oncogenic miRNAs, circulatory miRNAs, and the possible causes of dysregulated miRNAs in CRC. In addition, we discuss the important functions of miRNAs in drug resistance of CRC.
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Affiliation(s)
- Xiangjie Huang
- Cancer and Anticancer Drug Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xinping Zhu
- Cancer and Anticancer Drug Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yun Yu
- Cancer and Anticancer Drug Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Wangyu Zhu
- Affiliated Zhoushan Hospital, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Libo Jin
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang, 325035, China; Wenzhou University-Wenzhou Medical University Collaborative Innovation Center of Biomedical, Wenzhou, Zhejiang, 325035, China
| | - Xiaodong Zhang
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shaotang Li
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Peng Zou
- Cancer and Anticancer Drug Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang, 325035, China; Wenzhou University-Wenzhou Medical University Collaborative Innovation Center of Biomedical, Wenzhou, Zhejiang, 325035, China
| | - Congying Xie
- First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Ri Cui
- Cancer and Anticancer Drug Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang, 325035, China; Wenzhou University-Wenzhou Medical University Collaborative Innovation Center of Biomedical, Wenzhou, Zhejiang, 325035, China.
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29
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Evangelista AF, de Menezes WP, Berardinelli GN, Dos Santos W, Scapulatempo-Neto C, Guimarães DP, Calin GA, Reis RM. Pyknon-Containing Transcripts Are Downregulated in Colorectal Cancer Tumors, and Loss of PYK44 Is Associated With Worse Patient Outcome. Front Genet 2020; 11:581454. [PMID: 33304384 PMCID: PMC7693444 DOI: 10.3389/fgene.2020.581454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/14/2020] [Indexed: 01/19/2023] Open
Abstract
Pyknons are specific human/primate-specific DNA motifs at least 16 nucleotides long that are repeated in blocks in intergenic and intronic regions of the genome and can be located in a new class of non-coding RNAs of variable length. Recent studies reported that pyknon deregulation could be involved in the carcinogenesis process, including colorectal cancer. We evaluated the expression profile of a set of 12 pyknons in a set of molecularly characterized colorectal cancer (CRC) patients. The pyknons (PYK10, PYK14, PYK17, PYK26, PYK27, PYK40, PYK41, PYK42, PYK43, PYK44, PYK83, and PYK90) expression was determined by qRT-PCR. A pilot analysis of 20 cases was performed, and consistent results were obtained for PYK10, PYK17, PYK42, PYK44, and PYK83. Further, the expression of the selected pyknons was evaluated in 73 CRC cases. Moreover, in 52 patients, we compared the expression profile in both tumor and normal tissues. All five pyknons analyzed showed significantly lower expression levels in the tumor compared to normal tissue. It was observed an association between expression of PYK10 with TP53 mutations (p = 0.029), PYK17 to histologic grade (p = 0.035), and PYK44 to clinical staging (p = 0.016). Moreover, levels of PYK44 were significantly associated with the patient's poor overall survival (p = 0.04). We reported the significant downregulation of pyknons motifs in tumor tissue compared with the normal counterpart, and the association of lower PYK44 expression with worse patient outcome. Further studies are needed to extend and validate these findings and determine the clinical-pathological impact.
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Affiliation(s)
| | | | | | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, Brazil
| | - George A Calin
- Translational Molecular Pathology Department, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Guimarães, Portugal
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30
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Foulkes AS, Selvaggi C, Cao T, O'Reilly ME, Cynn E, Ma P, Lumish H, Xue C, Reilly MP. Nonconserved Long Intergenic Noncoding RNAs Associate With Complex Cardiometabolic Disease Traits. Arterioscler Thromb Vasc Biol 2020; 41:501-511. [PMID: 33176448 DOI: 10.1161/atvbaha.120.315045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Transcriptome profiling of human tissues has revealed thousands of long intergenic noncoding RNAs (lincRNAs) at loci identified through large-scale genome-wide studies for complex cardiometabolic traits. This raises the question of whether genetic variation at nonconserved lincRNAs has any systematic association with complex disease, and if so, how different this pattern is from conserved lincRNAs. We evaluated whether the associations between nonconserved lincRNAs and 8 complex cardiometabolic traits resemble or differ from the pattern of association for conserved lincRNAs. Approach and Results: Our investigation of over 7000 lincRNA annotations from GENCODE Release 33-GRCh38.p13 for complex trait genetic associations leveraged several large, established meta-analyses genome-wide association study summary data resources, including GIANT (Genetic Investigation of Anthropometric Traits), UK Biobank, GLGC (Global Lipids Genetics Consortium), Cardiogram (Coronary Artery Disease Genome Wide Replication and Meta-Analysis), and DIAGRAM (Diabetes Genetics Replication and Meta-Analysis)/DIAMANTE (Diabetes Meta-Analysis of Trans-Ethnic Association Studies). These analyses revealed that (1) nonconserved lincRNAs associate with a range of cardiometabolic traits at a rate that is generally consistent with conserved lincRNAs; (2) these findings persist across different definitions of conservation; and (3) overall across all cardiometabolic traits, approximately one-third of genome-wide association study-associated lincRNAs are nonconserved, and this increases to about two-thirds using a more stringent definition of conservation. CONCLUSIONS These findings suggest that the traditional notion of conservation driving prioritization for functional and translational follow-up of complex cardiometabolic genomic discoveries may need to be revised in the context of the abundance of nonconserved long noncoding RNAs in the human genome and their apparent predilection to associate with complex cardiometabolic traits.
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Affiliation(s)
- Andrea S Foulkes
- Biostatistics Center, Massachusetts General Hospital, Boston (A.S.F., C.S., T.C.).,Department of Medicine, Harvard Medical School, Boston, MA (A.S.F.).,Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA (A.S.F., T.C.)
| | - Caitlin Selvaggi
- Biostatistics Center, Massachusetts General Hospital, Boston (A.S.F., C.S., T.C.)
| | - Tingyi Cao
- Biostatistics Center, Massachusetts General Hospital, Boston (A.S.F., C.S., T.C.).,Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA (A.S.F., T.C.)
| | - Marcella E O'Reilly
- Cardiology Division, Department of Medicine (M.E.O., E.C., H.L., C.X., M.P.R.), Columbia University, New York, NY
| | - Esther Cynn
- Cardiology Division, Department of Medicine (M.E.O., E.C., H.L., C.X., M.P.R.), Columbia University, New York, NY
| | - Puyang Ma
- Data Science Institute, Stanford University, CA (P.M.)
| | - Heidi Lumish
- Cardiology Division, Department of Medicine (M.E.O., E.C., H.L., C.X., M.P.R.), Columbia University, New York, NY
| | - Chenyi Xue
- Cardiology Division, Department of Medicine (M.E.O., E.C., H.L., C.X., M.P.R.), Columbia University, New York, NY
| | - Muredach P Reilly
- Cardiology Division, Department of Medicine (M.E.O., E.C., H.L., C.X., M.P.R.), Columbia University, New York, NY.,Irving Institute for Clinical and Translational Sciences (M.P.R.), Columbia University, New York, NY
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31
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Liu R, Ju C, Zhang F, Tang X, Yan J, Sun J, Lv B, Guo Y, Liang Y, Lv XB, Zhang Z. LncRNA GSEC promotes the proliferation, migration and invasion by sponging miR-588/ EIF5A2 axis in osteosarcoma. Biochem Biophys Res Commun 2020; 532:300-307. [PMID: 32868080 DOI: 10.1016/j.bbrc.2020.08.056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 08/15/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Long noncoding RNAs (LncRNAs) show dysregulation in a variety of cancers. However, the function and specific mechanism of LncRNA GSEC in the progression of osteosarcoma remain mostly unknown. In this study, we sought to elucidate the role and mechanism of LncRNA GSEC in the occurrence and progression of osteosarcoma. METHODS we examined the expression of LncRNA GSEC in osteosarcoma cell lines by quantitative real time PCR. In vitro experiments, including transwell assays, cck8 assays, and flow cytometry analysis have biologically demonstrated the effect of LncRNA GSEC on the proliferation and migration of osteosarcoma cell lines. Furthermore, the regulation of miR-588 by LncRNA GSEC was determined by luciferase reporter assay and quantitative real time PCR. What's more, subcutaneous tumor formation was performed in nude mice to monitor the growth of the tumor in vivo. RESULTS We found that the expression of LncRNA GSEC was up-regulated in osteosarcoma cell lines. Overexpression of LncRNA GSEC promoted the proliferating and migratory capacity, and inhibited the apoptosis of osteosarcoma cells. Conversely, knockdown of LncRNA GSEC resulted in the opposite effect. Mechanistically, we identified LncRNA GSEC functioned as the sponge of miR-588, thus inhibiting the miR-588/EIF5A2 signal pathway. In addition, the expression of miR-588 was negatively correlated with LncRNA GSEC, and the effect by silencing or overexpressing LncRNA GSEC could be rescued by the introduction of miR-588 mimics or inhibitors, respectively. CONCLUSIONS In summary, this study shows that LncRNA GSEC promotes the proliferation and invasion of OS through the regulation of miR-588/EIF5A2 pathway, which might provide a new strategy for the treatment of osteosarcoma in the future.
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Affiliation(s)
- Renfeng Liu
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Department of Orthopedics, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, China; Nanchang Key Laboratory of Orthopaedics, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Medical Department of Graduate School, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Cheng Ju
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Department of Orthopedics, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, China; Nanchang Key Laboratory of Orthopaedics, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Medical Department of Graduate School, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Feifei Zhang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Xiaofeng Tang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Jinhua Yan
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Jun Sun
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Bin Lv
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Department of Orthopedics, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, China; Nanchang Key Laboratory of Orthopaedics, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Medical Department of Graduate School, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Yuhong Guo
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Department of Orthopedics, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, China; Nanchang Key Laboratory of Orthopaedics, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Medical Department of Graduate School, Nanchang University, Nanchang, Jiangxi, 330006, China.
| | - Yiping Liang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Xiao-Bin Lv
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Zhiping Zhang
- Jiangxi Key Laboratory of Cancer Metastasis and Precision Treatment, The Third Affiliated Hospital of Nanchang University, Nanchang, China; Department of Orthopedics, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, China; Nanchang Key Laboratory of Orthopaedics, The Third Affiliated Hospital of Nanchang University, Nanchang, China.
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Lin B, He H, Zhang Q, Zhang J, Xu L, Zhou L, Zheng S, Wu L. Long non-coding RNA00844 inhibits MAPK signaling to suppress the progression of hepatocellular carcinoma by targeting AZGP1. Ann Transl Med 2020; 8:1365. [PMID: 33313110 PMCID: PMC7723597 DOI: 10.21037/atm-20-3848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Previous data have confirmed that disordered long non-coding ribonucleic acid (lncRNA) expression is evident in many cancers and is correlated with tumor progression. The present study aimed to investigate the function of long non-coding RNA00844 (LINC00844) in hepatocellular carcinoma (HCC). Methods The expression levels of target genes were detected with real-time polymerase chain reaction (PCR) and western blotting. The biologic function of HCC cells was determined with cell viability assay, colony formation assay, cell cycle analysis, apoptosis detection, and Transwell migration assay in vitro. Tumorigenesis was performed with cell injection in vivo. The relationship between LINC00844 and survival outcomes was determined with the Cox proportional hazards model. A RNA precipitation assay was conducted to reveal the types of LINC00844 that potentially bind with proteins. Results LINC00844 was found to be significantly decreased in HCC tissue and was correlated with poor tumor characteristics, such as portal vein invasion, high α-fetoprotein (AFP), and a high rate of tumor recurrence. Exotic LINC00844 expression in HCC cell lines significantly suppressed proliferation and migration, as well as invasiveness, whereas LINC00844 deletion had the opposite effect. LINC00844 overexpression significantly inhibited HCC tumorigenesis in vivo. Mechanistic analyses indicated that the mitogen-activated protein kinase (MAPK) signaling pathway was remarkably inactivated by LINC00844. Furthermore, the immunoprecipitation assay verified that LINC00844 can bind to zinc-alpha-2-glycoprotein (AZGP1) and interfere with its translocation. LINC00844 can also promote AZGP1 expression, leading to the suppression of the transforming growth factor-β1 (TGF-β1)-extracellular signal-regulated kinase (ERK) pathway. Conclusions LINC00844 is a novel anti-oncogene in the development of HCC and a potentially promising therapeutic target in HCC.
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Affiliation(s)
- Bingyi Lin
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Hui He
- Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Qijun Zhang
- Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Jie Zhang
- Department of Hepatobiliary Surgery, First Hospital of Jiaxing, Jiaxing University, China
| | - Liu Xu
- Department of Hepatobiliary Surgery, First Hospital of Jiaxing, Jiaxing University, China
| | - Lin Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Shusen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China
| | - Liming Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Li H, Hu Y, Jin Y, Zhu Y, Hao Y, Liu F, Yang Y, Li G, Song X, Ye Y, Xiang S, Gao Y, Zhu J, Zhang Y, Jiang L, Huang W, Zhu J, Wu X, Liu Y. Long noncoding RNA lncGALM increases risk of liver metastasis in gallbladder cancer through facilitating N-cadherin and IL-1β-dependent liver arrest and tumor extravasation. Clin Transl Med 2020; 10:e201. [PMID: 33252861 PMCID: PMC7653798 DOI: 10.1002/ctm2.201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/19/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNA) represent significant factors of the mammalian transcriptome that mediates varied biological and pathological processes. The liver is the most common site for gallbladder cancer (GBC) distant metastasis and contributes to the majority of GBC-related death. How lncRNA affects GBC metastasis is not completely understood. RESULTS A novel lncRNA termed lncGALM (lncRNA in GBC associated with liver metastasis) was discovered to be highly expressed in cancer patients and xenografted tumors with liver metastasis. Elevated lncGALM in GBC patients also correlated to decreased survival. Invasion and migration of GBC cells were enhanced through lncGALM, both in vitro and in vivo. lncGALM functioned as sponges by competitively binding to and inactivating miR-200 family members, which increase epithelial-mesenchymal transition-associated transcription factor ZEB1 and ZEB2, leading to a fibroblastic phenotype and increased expression of N-cadherin. In addition, lncGALM bound to IL-1β mRNA and stabilized the IL-1β gene that mediates liver sinusoidal endothelial cell (LSECs) apoptosis. lncGALM-expressing LiM2-NOZ cells acquired a strong ability to migrate and adhere to LSECs, promoting LSECs apoptosis and therefore facilitating tumor cell extravasation and dissemination. CONCLUSIONS lncGALM promotes GBC liver metastasis by facilitating GBC cell migration, invasion, liver arrest, and extravasation via the invasion-metastasis cascade. Targeting lncGALM may be protective against the development of liver metastasis in GBC patients.
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Affiliation(s)
- Huaifeng Li
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yunping Hu
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yunpeng Jin
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yidi Zhu
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yajuan Hao
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Fatao Liu
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yang Yang
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Department of Biliary‐Pancreatic SurgeryRenji Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
- State Key Laboratory of Oncogenes and Related GenesShanghaiChina
| | - Guoqiang Li
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Department of Biliary‐Pancreatic SurgeryRenji Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
- State Key Laboratory of Oncogenes and Related GenesShanghaiChina
| | - Xiaoling Song
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yuanyuan Ye
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Shanshan Xiang
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yuan Gao
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Department of Biliary‐Pancreatic SurgeryRenji Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
- State Key Laboratory of Oncogenes and Related GenesShanghaiChina
| | - Jinhui Zhu
- Department of General Surgery and Laparoscopic CenterThe Second Affiliated Hospital Zhejiang University School of MedicineHangzhouChina
| | - Yijian Zhang
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Department of Biliary‐Pancreatic SurgeryRenji Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
| | - Lin Jiang
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Wen Huang
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Jian Zhu
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Xiangsong Wu
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
| | - Yingbin Liu
- Department of General Surgery, Xinhua HospitalAffiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Department of Biliary‐Pancreatic SurgeryRenji Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory of Biliary Tract Disease ResearchShanghaiChina
- Shanghai Research Center of Biliary Tract DiseaseShanghaiChina
- State Key Laboratory of Oncogenes and Related GenesShanghaiChina
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Pichler M, Rodriguez-Aguayo C, Nam SY, Dragomir MP, Bayraktar R, Anfossi S, Knutsen E, Ivan C, Fuentes-Mattei E, Lee SK, Ling H, Ivkovic TC, Huang G, Huang L, Okugawa Y, Katayama H, Taguchi A, Bayraktar E, Bhattacharya R, Amero P, He WR, Tran AM, Vychytilova-Faltejskova P, Klec C, Bonilla DL, Zhang X, Kapitanovic S, Loncar B, Gafà R, Wang Z, Cristini V, Hanash S, Bar-Eli M, Lanza G, Slaby O, Goel A, Rigoutsos I, Lopez-Berestein G, Calin GA. Therapeutic potential of FLANC, a novel primate-specific long non-coding RNA in colorectal cancer. Gut 2020; 69:1818-1831. [PMID: 31988194 PMCID: PMC7382985 DOI: 10.1136/gutjnl-2019-318903] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/21/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the function of a novel primate-specific long non-coding RNA (lncRNA), named FLANC, based on its genomic location (co-localised with a pyknon motif), and to characterise its potential as a biomarker and therapeutic target. DESIGN FLANC expression was analysed in 349 tumours from four cohorts and correlated to clinical data. In a series of multiple in vitro and in vivo models and molecular analyses, we characterised the fundamental biological roles of this lncRNA. We further explored the therapeutic potential of targeting FLANC in a mouse model of colorectal cancer (CRC) metastases. RESULTS FLANC, a primate-specific lncRNA feebly expressed in normal colon cells, was significantly upregulated in cancer cells compared with normal colon samples in two independent cohorts. High levels of FLANC were associated with poor survival in two additional independent CRC patient cohorts. Both in vitro and in vivo experiments demonstrated that the modulation of FLANC expression influenced cellular growth, apoptosis, migration, angiogenesis and metastases formation ability of CRC cells. In vivo pharmacological targeting of FLANC by administration of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine nanoparticles loaded with a specific small interfering RNA, induced significant decrease in metastases, without evident tissue toxicity or pro-inflammatory effects. Mechanistically, FLANC upregulated and prolonged the half-life of phosphorylated STAT3, inducing the overexpression of VEGFA, a key regulator of angiogenesis. CONCLUSIONS Based on our findings, we discovered, FLANC as a novel primate-specific lncRNA that is highly upregulated in CRC cells and regulates metastases formation. Targeting primate-specific transcripts such as FLANC may represent a novel and low toxic therapeutic strategy for the treatment of patients.
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Affiliation(s)
- Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Research Unit of Non-Coding RNA and Genome Editing, Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Su Youn Nam
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Gastroenterology Department, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enrique Fuentes-Mattei
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sang Kil Lee
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina Catela Ivkovic
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Guoliang Huang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: China-America Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, Guangdong, P.R. China
| | - Li Huang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ayumu Taguchi
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Emine Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajat Bhattacharya
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Ruixian He
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anh M. Tran
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Petra Vychytilova-Faltejskova
- Molecular Oncology II - Solid Cancers, Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Czech Republic
| | - Christiane Klec
- Research Unit of Non-Coding RNA and Genome Editing, Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Diana L. Bonilla
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinna Zhang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Medical and Molecular Genetics Department, Indiana University, Indianapolis, IN, USA
| | - Sanja Kapitanovic
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Bozo Loncar
- Department of Surgery, Clinical Hospital Dubrava, Zagreb, Croatia
| | - Roberta Gafà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Zhihui Wang
- Mathematics in Medicine Program, The Houston Methodist Research Institute HMRI R8-122, 6670 Bertner Ave, Houston, TX 77030
| | - Vittorio Cristini
- Mathematics in Medicine Program, The Houston Methodist Research Institute HMRI R8-122, 6670 Bertner Ave, Houston, TX 77030
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giovanni Lanza
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Ondrej Slaby
- Molecular Oncology II - Solid Cancers, Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX,Present address: Department of Molecular Diagnostics, Therapeutics and Translational Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center and Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Corresponding authors George A. Calin, M.D., Ph.D. Professor, Department of Experimental Therapeutics, Center for RNA Interference and Non-Coding RNAs, Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, P.O. Box 301429, Houston, Texas 77030-1429, and Gabriel Lopez-Berestein, M.D., Professor, Department of Experimental Therapeutics, Center for RNA Interference and Non-Coding RNAs, Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, P.O. Box 301429, Houston, Texas 77030-1429,
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Elsayed AM, Amero P, Salama SA, Abdelaziz AH, Lopez-Berestein G, Rodriguez-Aguayo C. Back to the Future: Rethinking the Great Potential of lncRNA S for Optimizing Chemotherapeutic Response in Ovarian Cancer. Cancers (Basel) 2020; 12:E2406. [PMID: 32854207 DOI: 10.3390/cancers12092406] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 01/17/2023] Open
Abstract
Ovarian cancer (OC) is one of the most fatal cancers in women worldwide. Currently, platinum- and taxane-based chemotherapy is the mainstay for the treatment of OC. Yet, the emergence of chemoresistance results in therapeutic failure and significant relapse despite a consistent rate of primary response. Emerging evidence substantiates the potential role of lncRNAs in determining the response to standard chemotherapy in OC. The objective of this narrative review is to provide an integrated, synthesized overview of the current state of knowledge regarding the role of lncRNAs in the emergence of resistance to platinum- and taxane-based chemotherapy in OC. In addition, we sought to develop conceptual frameworks for harnessing the therapeutic potential of lncRNAs in strategies aimed at enhancing the chemotherapy response of OC. Furthermore, we offered significant new perspectives and insights on the interplay between lncRNAs and the molecular circuitries implicated in chemoresistance to determine their impacts on therapeutic response. Although this review summarizes robust data concerning the involvement of lncRNAs in the emergence of acquired resistance to platinum- and taxane-based chemotherapy in OC, effective approaches for translating these lncRNAs into clinical practice warrant further investigation.
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Barth DA, Juracek J, Slaby O, Pichler M, Calin GA. lncRNA and Mechanisms of Drug Resistance in Cancers of the Genitourinary System. Cancers (Basel) 2020; 12:cancers12082148. [PMID: 32756406 PMCID: PMC7463785 DOI: 10.3390/cancers12082148] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 02/08/2023] Open
Abstract
Available systemic treatment options for cancers of the genitourinary system have experienced great progress in the last decade. However, a large proportion of patients eventually develop resistance to treatment, resulting in disease progression and shorter overall survival. Biomarkers indicating the increasing resistance to cancer therapies are yet to enter clinical routine. Long non-coding RNAs (lncRNA) are non-protein coding RNA transcripts longer than 200 nucleotides that exert multiple types of regulatory functions of all known cellular processes. Increasing evidence supports the role of lncRNAs in cancer development and progression. Additionally, their involvement in the development of drug resistance across various cancer entities, including genitourinary malignancies, are starting to be discovered. Consequently, lncRNAs have been suggested as factors in novel therapeutic strategies to overcome drug resistance in cancer. In this review, the existing evidences on lncRNAs and their involvement in mechanisms of drug resistance in cancers of the genitourinary system, including renal cell carcinoma, bladder cancer, prostate cancer, and testicular cancer, will be highlighted and discussed to facilitate and encourage further research in this field. We summarize a significant number of lncRNAs with proposed pathways in drug resistance and available reported studies.
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Affiliation(s)
- Dominik A. Barth
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (D.A.B.); (M.P.)
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Jaroslav Juracek
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 62500 Brno, Czech Republic;
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Ondrej Slaby
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 62500 Brno, Czech Republic;
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (D.A.B.); (M.P.)
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Correspondence:
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O'Brien SJ, Bishop C, Hallion J, Fiechter C, Scheurlen K, Paas M, Burton J, Galandiuk S. Long non-coding RNA (lncRNA) and epithelial-mesenchymal transition (EMT) in colorectal cancer: a systematic review. Cancer Biol Ther 2020; 21:769-781. [PMID: 32730165 PMCID: PMC7515495 DOI: 10.1080/15384047.2020.1794239] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a leading cause of cancer-related death. Epithelial-mesenchymal transition (EMT) is a major process in tumor metastasis development. This systematic review aims to describe the role of long non-coding RNA (lncRNA) in EMT in CRC. METHODS The electronic databases, PubMed, Cochrane, and EMBASE, were searched from January1990 to June 2019 to identify studies examining lncRNA and their role in mediating EMT in CRC. Studies examining clinical specimens and/or in vitro experiments were included. RESULTS In 61 identified studies, 54 lncRNAs were increased in CRC compared to normal colorectal epithelium. Increased lncRNA expression was frequently associated with worse survival. Many lncRNAs mediate their effect through competitive endogenous RNA or transcription factor regulation. The ZEB1, 2/E-cadherin, Wnt/β-catenin signaling, and chromatin remodeling pathways are discussed in particular. CONCLUSIONS lncRNAs are major regulators of EMT and predictor adverse outcome in CRC patients. Future research must focus on delineating lncRNA function prior to potential clinical use.
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Affiliation(s)
- Stephen J O'Brien
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
| | - Campbell Bishop
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
| | - Jacob Hallion
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
| | - Casey Fiechter
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
| | - Katharina Scheurlen
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
| | - Mason Paas
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
| | - James Burton
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
| | - Susan Galandiuk
- Price Institute of Surgical Research, Department of Surgery, University of Louisville , Louisville, KY, USA
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Zheng S, Wan L, Ge D, Jiang F, Qian Z, Tang J, Yang J, Yao Y, Yan J, Zhao L, Li H, Yang L. LINC00266-1/miR-548c-3p/SMAD2 feedback loop stimulates the development of osteosarcoma. Cell Death Dis 2020; 11:576. [PMID: 32709857 DOI: 10.1038/s41419-020-02764-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 07/04/2020] [Accepted: 07/09/2020] [Indexed: 11/09/2022]
Abstract
Osteosarcoma (OS) is one of the most common primary bone malignancies and accounts for 3.4% of pediatric tumors. Its 5-year survival is as low as about 20%. Differentially expressed lncRNAs in OS profiling were searched in the downloaded profile of GSE12865. As a result, LINC00266-1 was detected to be upregulated in both GSE12865 and OS tissues we collected. SMAD2 was the downstream target binding to promoter sites of LINC00266-1, displaying a positive regulatory interaction. Knockdown of LINC00266-1 suppressed the proliferative and metastatic abilities, and promoted the apoptosis in OS cells. Besides, knockdown of LINC00266-1 significantly alleviated the growth of OS in vivo. MiR-548c-3p was the sponge miRNA of LINC00266-1, which was able to reverse the regulatory effects of LINC00266-1 on OS cell phenotypes. Moreover, miR-548c-3p bound to the 3'-UTR of SMAD2 and thus downregulated SMAD2. Overexpression of SMAD2 partially reversed the regulatory effects of LINC00266-1 on OS cell phenotypes. Finally, we have identified that LINC00266-1/miR-548c-3p/SMAD2 feedback loop was responsible for stimulating the development of OS.
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Zhang Y, Huang W, Yuan Y, Li J, Wu J, Yu J, He Y, Wei Z, Zhang C. Long non-coding RNA H19 promotes colorectal cancer metastasis via binding to hnRNPA2B1. J Exp Clin Cancer Res 2020; 39:141. [PMID: 32698890 PMCID: PMC7412843 DOI: 10.1186/s13046-020-01619-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022]
Abstract
Background Long non-coding RNA H19 was demonstrated to be significantly correlated with tumor metastasis. However, the specific functions of H19 in colorectal cancer (CRC) metastasis and the underlying mechanism are still largely unclear. Methods Use public database to screen the potential lncRNA crucial for metastasis in colorectal cancer. The expression of H19 in clinical CRC specimens was detected by qRT-PCR. The effect of H19 on the metastasis of CRC cells was investigated by transwell, wound healing assays, CCK-8 assays and animal studies. The potential proteins binding to H19 were identified by LC-MS and verified by RNA immunoprecipitation (RIP). The expression of indicated RNA and proteins were measured by qRT-PCR or western blot. Results We found the expression of lncRNA H19 was significantly upregulated in primary tumor and metastatic tissues, correlated with poor prognosis in CRC. Ectopic H19 expression promoted the metastasis of colorectal cancer cells in vitro and in vivo, and induced epithelial-to-mesenchymal transition (EMT). Mechanistically, H19 directly bound to hnRNPA2B1. Knockdown of hnRNPA2B1 attenuated the H19-induce migration and invasion in CRC cells. Furthermore, H19 stabilized and upregulated the expression of Raf-1 by facilitated the interaction between hnRNPA2B1 and Raf-1 mRNA, resulting in activation of Raf-ERK signaling. Conclusions Our findings demonstrate the role of H19/hnRNPA2B1/EMT axis in regulation CRC metastasis, suggested H19 could be a potential biomarker to predict prognosis as well as a therapeutic strategy for CRC.
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Affiliation(s)
- Yuhui Zhang
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Weibin Huang
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Yujie Yuan
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Jin Li
- Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University, 628 Zhenyuan Road, Shenzhen, 518000, Guangdong, China
| | - Jing Wu
- Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University, 628 Zhenyuan Road, Shenzhen, 518000, Guangdong, China
| | - Jie Yu
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Yulong He
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China. .,Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University, 628 Zhenyuan Road, Shenzhen, 518000, Guangdong, China.
| | - Zhewei Wei
- Department of Gastrointestinal Surgery, the First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
| | - Changhua Zhang
- Center for Digestive Disease, the Seventh Affiliated Hospital of Sun Yat-sen University, 628 Zhenyuan Road, Shenzhen, 518000, Guangdong, China.
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Fabrizio FP, Sparaneo A, Fontana A, Mazza T, Graziano P, Pantalone A, Parente P, Centra F, Orlando N, Trombetta D, Torre A, Ferretti GM, Taurchini M, Micco CMD, Maiello E, Fazio VM, Rossi A, Muscarella LA. Potential Prognostic Role of SPARC Methylation in Non-Small-Cell Lung Cancer. Cells 2020; 9:E1523. [PMID: 32580473 DOI: 10.3390/cells9061523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/14/2020] [Accepted: 06/17/2020] [Indexed: 12/29/2022] Open
Abstract
The silencing of SPARC (secreted protein acid and rich in cysteine) gene through methylation of its promoter region represents a common event in many solid tumors and it is frequently associated with tumor progression and an aggressive clinical outcome. Anyhow, the data concerning the epigenetic mechanism of SPARC deregulation and its prognostic value in lung cancer are still incomplete. We explored the aberrant methylation of SPARC and its effects in 4 non-small cell lung cancer (NSCLC) cell lines and 59 NSCLC tissues and correlated the methylation levels with clinical-pathological features and disease outcome of patients. In 3 out of 4 tumor cell lines high SPARC methylation levels were observed. An inverse correlation between the epigenetic silencing and SPARC expression was confirmed by 5-Aza-2′-deoxycytidine ((5-Aza-CdR) treatment that also significantly induced a reduction in cell viability, proliferation and tumor cell migration. In tissues, the DNA methylation levels of the SPARC gene were significantly lower in paired non-neoplastic lungs (NLs) and normal lungs distant from tumor (NLDTs) than in NSCLCs (p = 0.002 and p = 0.0034 respectively). A promoter hypermethylation was detected in 68% of squamous cell carcinoma (SqCCs, 17/25) and 56% of adenocarcinoma (ADCs, 19/34), with SqCC showing the highest levels of methylation. Higher SPARC methylation levels were significantly associated with higher mortality risk both in all NSCLCs early stage patients (Hazard Ratio, HR = 1.97; 95% Confidence Interval, CI: 1.32–2.93; p = 0.001) and in those with SqCC (HR = 2.96; 95% CI: 1.43–6.12; p = 0.003). Promoter methylation of SPARC gene should represent an interesting prognostic biomarker in NSCLC, with potential application in the squamous early-stage context. Further research in this setting on larger independent cohorts of lung patients with different histologies and stages of disease are warranted.
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Iurca I, Tirpe A, Zimta AA, Moldovan C, Gulei D, Slabý O, Condorelli G, Berindan-Neagoe I. Macrophages Interaction and MicroRNA Interplay in the Modulation of Cancer Development and Metastasis. Front Immunol 2020; 11:870. [PMID: 32477352 PMCID: PMC7235377 DOI: 10.3389/fimmu.2020.00870] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/15/2020] [Indexed: 12/24/2022] Open
Abstract
Advancement in cancer research has shown that the tumor microenvironment plays a crucial role in the installation, progression, and dissemination of cancer cells. Among the heterogeneous panel of cells within the malignant microenvironment are tumor-associated macrophages that are sustaining the malignant cells through strict feedback mechanisms and spatial distribution. Considering that the presence of metastasis is one of the main feature associated with decreased survival rates among patients, in the present article we briefly present the involvement of tumor-associated macrophages in the hallmarks of metastasis and their microRNA-related regulation with a focus on lung cancer in order to coordinate the vast information under one pathology. As shown, these cells have emerged as coordinators of immunosuppression, angiogenesis and lymphangiogenesis, vessel intravasation and extravasation of cancer cells, and premetastatic niche formation, transforming the macrophages in potential therapeutic targets and also prognostic markers according to their density within the tumor and polarization phenotype. An indirect therapeutic approach on tumor-associated macrophages can be also represented by regulation of microRNAs involved in their polarization and implicit oncogenic features. Examples of these microRNAs consist in the highly studied miR-21 and miR-155, but also other microRNA with less feedback in the literature: miR-1207-5p, miR-193b, miR-320a, and others.
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Affiliation(s)
- Ioana Iurca
- Tumor Biology Department, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania.,Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandru Tirpe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina-Andreea Zimta
- Research Center for Advanced Medicine-Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristian Moldovan
- Research Center for Advanced Medicine-Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Gulei
- Research Center for Advanced Medicine-Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ondřej Slabý
- Centre for Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk Memorial Cancer Institute, Masaryk University, Brno, Czech Republic
| | - Gerolama Condorelli
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Naples, Italy
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Research Center for Advanced Medicine-Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta," Cluj-Napoca, Romania
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Jonas K, Calin GA, Pichler M. RNA-Binding Proteins as Important Regulators of Long Non-Coding RNAs in Cancer. Int J Mol Sci 2020; 21:E2969. [PMID: 32340118 DOI: 10.3390/ijms21082969] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
The majority of the genome is transcribed into pieces of non-(protein) coding RNA, among which long non-coding RNAs (lncRNAs) constitute a large group of particularly versatile molecules that govern basic cellular processes including transcription, splicing, RNA stability, and translation. The frequent deregulation of numerous lncRNAs in cancer is known to contribute to virtually all hallmarks of cancer. An important regulatory mechanism of lncRNAs is the post-transcriptional regulation mediated by RNA-binding proteins (RBPs). So far, however, only a small number of known cancer-associated lncRNAs have been found to be regulated by the interaction with RBPs like human antigen R (HuR), ARE/poly(U)-binding/degradation factor 1 (AUF1), insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), and tristetraprolin (TTP). These RBPs regulate, by various means, two aspects in particular, namely the stability and the localization of lncRNAs. Importantly, these RBPs themselves are commonly deregulated in cancer and might thus play a major role in the deregulation of cancer-related lncRNAs. There are, however, still many open questions, for example regarding the context specificity of these regulatory mechanisms that, in part, is based on the synergistic or competitive interaction between different RBPs. There is also a lack of knowledge on how RBPs facilitate the transport of lncRNAs between different cellular compartments.
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Bekric D, Neureiter D, Ritter M, Jakab M, Gaisberger M, Pichler M, Kiesslich T, Mayr C. Long Non-Coding RNAs in Biliary Tract Cancer-An Up-to-Date Review. J Clin Med 2020; 9:jcm9041200. [PMID: 32331331 PMCID: PMC7231154 DOI: 10.3390/jcm9041200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
The term long non-coding RNA (lncRNA) describes non protein-coding transcripts with a length greater than 200 base pairs. The ongoing discovery, characterization and functional categorization of lncRNAs has led to a better understanding of the involvement of lncRNAs in diverse biological and pathological processes including cancer. Aberrant expression of specific lncRNA species was demonstrated in various cancer types and associated with unfavorable clinical characteristics. Recent studies suggest that lncRNAs are also involved in the development and progression of biliary tract cancer, a rare disease with high mortality and limited therapeutic options. In this review, we summarize current findings regarding the manifold roles of lncRNAs in biliary tract cancer and give an overview of the clinical and molecular consequences of aberrant lncRNA expression as well as of underlying regulatory functions of selected lncRNA species in the context of biliary tract cancer.
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Affiliation(s)
- Dino Bekric
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria;
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Markus Ritter
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Jakab
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Martin Gaisberger
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria;
| | - Tobias Kiesslich
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
| | - Christian Mayr
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
- Correspondence:
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Zimta AA, Tigu AB, Braicu C, Stefan C, Ionescu C, Berindan-Neagoe I. An Emerging Class of Long Non-coding RNA With Oncogenic Role Arises From the snoRNA Host Genes. Front Oncol 2020; 10:389. [PMID: 32318335 PMCID: PMC7154078 DOI: 10.3389/fonc.2020.00389] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/04/2020] [Indexed: 12/24/2022] Open
Abstract
The small nucleolar RNA host genes (SNHGs) are a group of long non-coding RNAs, which are reported in many studies as being overexpressed in various cancers. With very few exceptions, the SNHGs (SNHG1, SNHG3, SNHG5, SNHG6, SNHG7, SNHG12, SNHG15, SNHG16, SNHG20) are recognized as inducing increased proliferation, cell cycle progression, invasion, and metastasis of cancer cells, which makes this class of transcripts a viable biomarker for cancer development and aggressiveness. Through our literature research, we also found that silencing of SNHGs through small interfering RNAs or short hairpin RNAs is very effective in both in vitro and in vivo experiments by lowering the aggressiveness of solid cancers. The knockdown of SNHG as a new cancer therapeutic option should be investigated more in the future.
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Affiliation(s)
- Alina-Andreea Zimta
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adrian Bogdan Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Stefan
- African Organisation for Research and Training in Cancer, Cape Town, South Africa
| | - Calin Ionescu
- Surgical Department, Municipal Hospital, Cluj-Napoca, Romania
- Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. I. Chiricuta”, Cluj-Napoca, Romania
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Yao X, Lan Z, Lai Q, Li A, Liu S, Wang X. LncRNA SNHG6 plays an oncogenic role in colorectal cancer and can be used as a prognostic biomarker for solid tumors. J Cell Physiol 2020; 235:7620-7634. [PMID: 32239696 DOI: 10.1002/jcp.29672] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/06/2020] [Indexed: 12/15/2022]
Abstract
Small nucleolar RNA host gene 6 (SNHG6) has been recognized as an oncogene in numerous cancers and overexpression of SNHG6 was found to promote colorectal cancer (CRC). Hence, we performed a meta-analysis to examine the clinical importance of the long noncoding RNA (lncRNA) SNHG6. Moreover, comprehensive identification of RNA-binding proteins-mass spectrometry (ChIRP-MS) was conducted to explore the carcinogenic mechanism of lncRNA SNHG6 in CRC. Fourteen studies conducted on 1,139 patients were included in this meta-analysis. We also constructed the protein-protein interactive (PPI) network in string based on the ChIRP-MS results and cytoscape was used to identify core modules in the PPI network, which were then analyzed using the bioinformatics websites, cancer single-cell state atlas (CancerSEA) and G:profilter. The clinical outcomes of the meta-analysis indicated that higher expression of SNHG6 was related with a poorer survival outcome (overall survival: hazard ratio (HR) = 1.92; 95% confidence interval [Cl]: 1.48, 2.49; p < .0001; disease-free survival: HR = 1.84; 95% Cl: 1.02, 3.34; p = .044), higher tumor stage (odds ratio [OR] = 3.35; 95% Cl: 2.57, 4.37; p < .0001), distant metastasis (OR = 1.83; 95% Cl: 1.11, 2.99; p = .017) and lymph node metastasis (OR = 1.33; 95% Cl: 0.93, 1.89; p = .119). The ChIRP-MS results showed that core Module 1 of the PPI was significant in ribosomes and core Module 2 was mainly related to spliceosomes and messenger RNA processing. In conclusion, a higher expression of SNHG6 was found to be associated with a poorer survival outcome, high tumor stage, and distant metastasis in various solid tumors. SNHG6 was also found to be able to affect the processes of transcription and translation to promote CRC.
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Affiliation(s)
- Xiang Yao
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhixian Lan
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qiuhua Lai
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Aimin Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Side Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xinke Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Dragomir MP, Kopetz S, Ajani JA, Calin GA. Non-coding RNAs in GI cancers: from cancer hallmarks to clinical utility. Gut 2020; 69:748-763. [PMID: 32034004 DOI: 10.1136/gutjnl-2019-318279] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 12/11/2022]
Abstract
One of the most unexpected discoveries in molecular oncology, in the last decades, was the identification of a new layer of protein coding gene regulation by transcripts that do not codify for proteins, the non-coding RNAs. These represent a heterogeneous category of transcripts that interact with many types of genetic elements, including regulatory DNAs, coding and other non-coding transcripts and directly to proteins. The final outcome, in the malignant context, is the regulation of any of the cancer hallmarks. Non-coding RNAs represent the most abundant type of hormones that contribute significantly to cell-to cell communication, revealing a complex interplay between tumour cells, tumour microenvironment cells and immune cells. Consequently, profiling their abundance in bodily fluids became a mainstream of biomarker identification. Therapeutic targeting of non-coding RNAs represents a new option for clinicians that is currently under development. This review will present the biology and translational value of three of the most studied categories on non-coding RNAs, the microRNAs, the long non-coding RNAs and the circular RNAs. We will also focus on some aspirational concepts that can help in the development of clinical applications related to non-coding RNAs, including using pyknons to discover new non-coding RNAs, targeting human-specific transcripts which are expressed specifically in the tumour cell and using non-coding RNAs to increase the efficiency of immunotherapy.
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Affiliation(s)
- Mihnea Paul Dragomir
- Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George Adrian Calin
- Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Lan Z, Yao X, Sun K, Li A, Liu S, Wang X. The Interaction Between lncRNA SNHG6 and hnRNPA1 Contributes to the Growth of Colorectal Cancer by Enhancing Aerobic Glycolysis Through the Regulation of Alternative Splicing of PKM. Front Oncol 2020; 10:363. [PMID: 32296635 PMCID: PMC7136466 DOI: 10.3389/fonc.2020.00363] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Small nucleolar RNA host gene 6 (SNHG6) acts as a carcinogenic gene in colorectal cancer (CRC). However, previous studies on the mechanism by which long non-coding RNA (lncRNA) SNHG6 exerts its carcinogenic effect in CRC have not involved the direct interaction between SNHG6 and proteins, which is a very important carcinogenic mechanism of lncRNAs. Hence, our study conducted a comprehensive RNA-binding proteins-mass spectrometry (ChIRP-MS) analysis on SNHG6 to further explore its carcinogenic mechanism in CRC. Methods: Proteins that interact with SNHG6 were found using ChIRP-MS analysis and were used to construct the protein-protein interactive (PPI) network using STRING, while the core module of the PPI network was identified using the MCODE plugin in Cytoscape. Pathway enrichment analyses, using WebGestalt, were performed on proteins and RNAs that were found to be associated with the expression of SNHG6 or which directly interacted with SNHG6. Finally, CatRAPID, miRbase, and TargetScanHuman were used to identify the sites of interaction between SNHG6, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), and pyruvate kinase M (PKM) mRNA. Results: The expression of SNHG6 in CRC was found to be higher than that of normal tissues and was positively correlated with a poor prognosis (p < 0.05). A total of 467 proteins that are able to interact with SNHG6 in CRC cells were identified using ChIRP-MS analysis and were used to create a PPI network, within which a core module composed of 44 proteins that performed the function of splicing mRNA, including hnRNPA1, was found to be positively correlated with SNHG6 (p < 0.05). The results of the pathway enrichment analyses suggested that SNHG6 played an important role in the metabolism of CRC by affecting the expression of PKM and SNHG6. The increase in the ratio of PKM2/PKM1 was proven using quantitative real-time polymerase chain reaction analysis. Further exploration suggested that SNHG6 could bind to hnRNPA1 and PKM. Conclusion: SNHG6 was found to be able to target the mRNA of PKM as well as induce hnRNPA1 to specifically splice PKM mRNA, which increased the proportion of PKM2/PKM1, which may be an important carcinogenic mechanism in CRC that proceeds through the enhancement of aerobic glycolysis in CRC cells.
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Affiliation(s)
- Zhixian Lan
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiang Yao
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kangyue Sun
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Aimin Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Side Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xinke Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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48
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Abstract
Non-coding RNAs (ncRNAs) are reported to be expressed in human cancers, including pancreatic ductal adenocarcinoma (PDAC). These ncRNAs affect the growth, migration and invasion of tumor cells by regulating cell cycle and apoptosis, as well as playing important roles in epigenetic processes, transcription and post-transcriptional regulation. It is still unclear whether alterations in ncRNAs influence PDAC development and progression. Because of this, analysis based on existing data on ncRNAs, which are crucial for modulating pancreatic tumorigenesis, will be important for future research on PDAC. Here, we summarize ncRNAs with tumor-promoting functions: HOTAIR, HOTTIP, MALAT1, lncRNA H19, lncRNA PVT1, circ-RNA ciRS-7, circ-0030235, circ-RNA_100782, circ-LDLRAD3, circ-0007534, circRHOT1, circZMYM2, circ-IARS, circ-RNA PDE8A, miR-21, miR-155, miR-221/222, miR-196b, miR-10a. While others including GAS5, MEG3, and lncRNA ENST00000480739, has_circ_0001649, miR-34a, miR-100, miR-217, miR-143 inhibit the proliferation and invasion of PDAC. Hence, we summarize the functions of ncRNAs in the occurrence, development and metastasis of PDAC, with the goal to provide guidance in the clinical diagnosis and treatment of PDAC.
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Affiliation(s)
- Ruining Gong
- Department of Gastroenterology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yueping Jiang
- Department of Gastroenterology, Affiliated Hospital of Qingdao University, Qingdao, China
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Drula R, Braicu C, Harangus A, Nabavi SM, Trif M, Slaby O, Ionescu C, Irimie A, Berindan-Neagoe I. Critical function of circular RNAs in lung cancer. Wiley Interdiscip Rev RNA 2020; 11:e1592. [PMID: 32180372 DOI: 10.1002/wrna.1592] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/12/2022]
Abstract
Lung cancer is one of the main causes of cancer-related death in the world, especially due to its frequency and ineffective therapeutically approaches in the late stages of the disease. Despite the recent advent of promising new targeted therapies, lung cancer diagnostic strategies still have difficulty in identifying the disease at an early stage. Therefore, the characterizations of more sensible and specific cancer biomarkers have become an important goal for clinicians. Circular RNAs (circRNAs), a type of RNA with covalently closed continuous loop structures that display high structural resistance and tissue specificity pointed toward a potential biomarker role. Current investigations have identified that circRNAs have a prominent function in the regulation of oncogenic pathways, by regulating gene expression both at transcriptional and post-transcriptional level. The aim of this review is to provide novel information regarding the implications of circRNAs in lung cancer, with an emphasis on the role in disease development and progression. Initially, we explored the potential utility of circRNAs as biomarkers, focusing on function, mechanisms, and correlation with disease progression in lung cancer. Further, we will describe the interaction between circRNAs and other non-coding species of RNA (particularly microRNA) and their biological significance in lung cancer. Describing the nature of these interactions and their therapeutic potential will provide additional insight regarding the altered molecular landscape of lung cancer and consolidate the potential clinical value of these circular transcripts. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Rares Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Antonia Harangus
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,"Leon Daniello" Pneumology Clinic, Cluj-Napoca, Romania
| | - Seyed M Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Calin Ionescu
- 5th Surgical Department, Municipal Hospital, Cluj-Napoca, Romania.,Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandru Irimie
- Department of Surgery, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania.,Department of Surgical Oncology and Gynecological Oncology, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca, Romania.,Department of Functional Genomics and Experimental Pathology, The Oncology Institute Prof. Dr. Ion Chiricuta, Cluj-Napoca, Romania
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50
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Abstract
A new concept is emerging in the non-coding RNA (ncRNA) field: an increasing number of ncRNAs in fact codify for short peptides that have biological activities. In this issue of JEM, Wang et al. (https://doi.org/10.1084/jem.20190950) report the identification of a long ncRNA (lncRNA)-encoded 60-amino acid polypeptide that they name ASRPS, as well as its ability to inhibit angiogenesis in the deadly triple-negative breast cancer (TNBC).
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Affiliation(s)
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
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