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Zhang P, Xue B, Yang H, Zhang L. Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing. Genes (Basel) 2024; 15:317. [PMID: 38540376 PMCID: PMC10970011 DOI: 10.3390/genes15030317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 06/14/2024] Open
Abstract
The marine nematode Litoditis marina is widely distributed in intertidal zones around the globe, yet the mechanisms underlying its broad adaptation to salinity remain elusive. In this study, we applied ONT long-read sequencing technology to unravel the transcriptome responses to different salinity conditions in L. marina. Through ONT sequencing under 3‱, 30‱ and 60‱ salinity environments, we obtained 131.78 G clean data and 26,647 non-redundant long-read transcripts, including 6464 novel transcripts. The DEGs obtained from the current ONT lrRNA-seq were highly correlated with those identified in our previously reported Illumina short-read RNA sequencing data. When we compared the 30‱ to the 3‱ salinity condition, we found that GO terms such as oxidoreductase activity, cation transmembrane transport and ion transmembrane transport were shared between the ONT lrRNA-seq and Illumina data. Similarly, GO terms including extracellular space, structural constituents of cuticle, substrate-specific channel activity, ion transport and substrate-specific transmembrane transporter activity were shared between the ONT and Illumina data under 60‱ compared to 30‱ salinity. In addition, we found that 79 genes significantly increased, while 119 genes significantly decreased, as the salinity increased. Furthermore, through the GO enrichment analysis of 214 genes containing DAS, in 30‱ compared to 3‱ salinity, we found that GO terms such as cellular component assembly and coenzyme biosynthetic process were enriched. Additionally, we observed that GO terms such as cellular component assembly and coenzyme biosynthetic process were also enriched in 60‱ compared to 30‱ salinity. Moreover, we found that 86, 125, and 81 genes that contained DAS were also DEGs, in comparisons between 30‱ and 3‱, 60‱ and 30‱, and 60‱ and 3‱ salinity, respectively. In addition, we demonstrated the landscape of alternative polyadenylation in marine nematode under different salinity conditions This report provides several novel insights for the further study of the mechanisms by which euryhalinity formed and evolved, and it might also contribute to the investigation of salinity dynamics induced by global climate change.
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Affiliation(s)
- Pengchi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beining Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanwen Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Liusuo Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
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Naro C, Antonioni A, Medici V, Caggiano C, Jolly A, de la Grange P, Bielli P, Paronetto MP, Sette C. Splicing targeting drugs highlight intron retention as an actionable vulnerability in advanced prostate cancer. J Exp Clin Cancer Res 2024; 43:58. [PMID: 38413979 PMCID: PMC10898177 DOI: 10.1186/s13046-024-02986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Advanced prostate cancer (PC) is characterized by insensitivity to androgen deprivation therapy and chemotherapy, resulting in poor outcome for most patients. Thus, advanced PC urgently needs novel therapeutic strategies. Mounting evidence points to splicing dysregulation as a hallmark of advanced PC. Moreover, pharmacologic inhibition of the splicing process is emerging as a promising option for this disease. METHOD By using a representative androgen-insensitive PC cell line (22Rv1), we have investigated the genome-wide transcriptomic effects underlying the cytotoxic effects exerted by three splicing-targeting drugs: Pladienolide B, indisulam and THZ531. Bioinformatic analyses were performed to uncover the gene structural features underlying sensitivity to transcriptional and splicing regulation by these treatments. Biological pathways altered by these treatments were annotated by gene ontology analyses and validated by functional experiments in cell models. RESULTS Although eliciting similar cytotoxic effects on advanced PC cells, Pladienolide B, indisulam and THZ531 modulate specific transcriptional and splicing signatures. Drug sensitivity is associated with distinct gene structural features, expression levels and cis-acting sequence elements in the regulated exons and introns. Importantly, we identified PC-relevant genes (i.e. EZH2, MDM4) whose drug-induced splicing alteration exerts an impact on cell survival. Moreover, computational analyses uncovered a widespread impact of splicing-targeting drugs on intron retention, with enrichment in genes implicated in pre-mRNA 3'-end processing (i.e. CSTF3, PCF11). Coherently, advanced PC cells displayed high sensitivity to a specific inhibitor of the cleavage and polyadenylation complex, which enhances the effects of chemotherapeutic drugs that are already in use for this cancer. CONCLUSIONS Our study uncovers intron retention as an actionable vulnerability for advanced PC, which may be exploited to improve therapeutic management of this currently incurable disease.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | - Ambra Antonioni
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Vanessa Medici
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy
| | | | | | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143, Rome, Italy
- University of Rome Foro Italico, 00135, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168, Rome, Italy.
- GSTeP Organoids Research Core Facility, Fondazione Policlinico Universitario A. Gemelli, IRCCS, 00168, Rome, Italy.
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Steadman K, You S, Srinivas DV, Mouakkad L, Yan Y, Kim M, Venugopal SV, Tanaka H, Freeman MR. Autonomous action and cooperativity between the ONECUT2 transcription factor and its 3' untranslated region. Front Cell Dev Biol 2023; 11:1206259. [PMID: 37484909 PMCID: PMC10356556 DOI: 10.3389/fcell.2023.1206259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/16/2023] [Indexed: 07/25/2023] Open
Abstract
The transcription factor ONECUT2 (OC2) is a master transcriptional regulator operating in metastatic castration-resistant prostate cancer that suppresses androgen receptor activity and promotes neural differentiation and tumor cell survival. OC2 mRNA possesses an unusually long (14,575 nt), evolutionarily conserved 3' untranslated region (3' UTR) with many microRNA binding sites, including up to 26 miR-9 sites. This is notable because miR-9 targets many of the same genes regulated by the OC2 protein. Paradoxically, OC2 expression is high in tissues with high miR-9 expression. The length and complex secondary structure of OC2 mRNA suggests that it is a potent master competing endogenous RNA (ceRNA) capable of sequestering miRNAs. Here, we describe a novel role for OC2 3' UTR in lethal prostate cancer consistent with a function as a ceRNA. A plausible ceRNA network in OC2-driven tumors was constructed computationally and then confirmed in prostate cancer cell lines. Genes regulated by OC2 3' UTR exhibited high overlap (up to 45%) with genes driven by the overexpression of the OC2 protein in the absence of 3' UTR, indicating a cooperative functional relationship between the OC2 protein and its 3' UTR. These overlapping networks suggest an evolutionarily conserved mechanism to reinforce OC2 transcription by protection of OC2-regulated mRNAs from miRNA suppression. Both the protein and 3' UTR showed increased polycomb-repressive complex activity. The expression of OC2 3' UTR mRNA alone (without protein) dramatically increased the metastatic potential by in vitro assays. Additionally, OC2 3' UTR increased the expression of Aldo-Keto reductase and UDP-glucuronyl transferase family genes responsible for altering the androgen synthesis pathway. ONECUT2 represents the first-described dual-modality transcript that operates as both a key transcription factor driving castration-resistant prostate cancer and a master ceRNA that promotes and protects the same transcriptional network.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Michael R. Freeman
- Division of Cancer Biology and Therapeutics, Biomedical Sciences and Pathology and Laboratory Medicine, Department of Urology, Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, United States
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Cao J, Kuyumcu-Martinez MN. Alternative polyadenylation regulation in cardiac development and cardiovascular disease. Cardiovasc Res 2023; 119:1324-1335. [PMID: 36657944 PMCID: PMC10262186 DOI: 10.1093/cvr/cvad014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 01/21/2023] Open
Abstract
Cleavage and polyadenylation of pre-mRNAs is a necessary step for gene expression and function. Majority of human genes exhibit multiple polyadenylation sites, which can be alternatively used to generate different mRNA isoforms from a single gene. Alternative polyadenylation (APA) of pre-mRNAs is important for the proteome and transcriptome landscape. APA is tightly regulated during development and contributes to tissue-specific gene regulation. Mis-regulation of APA is linked to a wide range of pathological conditions. APA-mediated gene regulation in the heart is emerging as a new area of research. Here, we will discuss the impact of APA on gene regulation during heart development and in cardiovascular diseases. First, we will briefly review how APA impacts gene regulation and discuss molecular mechanisms that control APA. Then, we will address APA regulation during heart development and its dysregulation in cardiovascular diseases. Finally, we will discuss pre-mRNA targeting strategies to correct aberrant APA patterns of essential genes for the treatment or prevention of cardiovascular diseases. The RNA field is blooming due to advancements in RNA-based technologies. RNA-based vaccines and therapies are becoming the new line of effective and safe approaches for the treatment and prevention of human diseases. Overall, this review will be influential for understanding gene regulation at the RNA level via APA in the heart and will help design RNA-based tools for the treatment of cardiovascular diseases in the future.
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Affiliation(s)
- Jun Cao
- Faculty of Environment and Life, Beijing University of Technology, Xueyuan Road, Haidian District, Beijing 100124, PR China
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Translational Sciences, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
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UBE3D Regulates mRNA 3'-End Processing and Maintains Adipogenic Potential in 3T3-L1 Cells. Mol Cell Biol 2022; 42:e0017422. [PMID: 36519931 PMCID: PMC9753722 DOI: 10.1128/mcb.00174-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We have previously described the role of an essential Saccharomyces cerevisiae gene, important for cleavage and polyadenylation 1 (IPA1), in the regulation of gene expression through its interaction with Ysh1, the endonuclease subunit of the mRNA 3'-end processing complex. Through a similar mechanism, the mammalian homolog ubiquitin protein ligase E3D (UBE3D) promotes the migratory and invasive potential of breast cancer cells, but its role in the regulation of gene expression during normal cellular differentiation has not previously been described. In this study, we show that CRISPR/Cas9-mediated knockout of Ube3d in 3T3-L1 cells blocks their ability to differentiate into mature adipocytes. Consistent with previous studies in other cell types, Ube3d knockout leads to decreased levels of CPSF73 and global changes in cellular mRNAs indicative of a loss of 3'-end processing capacity. Ube3d knockout cells also display decreased expression of known preadipogenic markers. Overexpression of either UBE3D or CPSF73 rescues the differentiation defect and partially restores protein levels of these markers. These results support a model in which UBE3D is necessary for the maintenance of the adipocyte-committed state via its regulation of the mRNA 3'-end processing machinery.
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Pieraccioli M, Caggiano C, Mignini L, Zhong C, Babini G, Lattanzio R, Di Stasi S, Tian B, Sette C, Bielli P. The transcriptional terminator XRN2 and the RNA-binding protein Sam68 link alternative polyadenylation to cell cycle progression in prostate cancer. Nat Struct Mol Biol 2022; 29:1101-1112. [PMID: 36344846 PMCID: PMC9872553 DOI: 10.1038/s41594-022-00853-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Alternative polyadenylation (APA) yields transcripts differing in their 3'-end, and its regulation is altered in cancer, including prostate cancer. Here we have uncovered a mechanism of APA regulation impinging on the interaction between the exonuclease XRN2 and the RNA-binding protein Sam68, whose increased expression in prostate cancer is promoted by the transcription factor MYC. Genome-wide transcriptome profiling revealed a widespread impact of the Sam68/XRN2 complex on APA. XRN2 promotes recruitment of Sam68 to its target transcripts, where it competes with the cleavage and polyadenylation specificity factor for binding to strong polyadenylation signals at distal ends of genes, thus promoting usage of suboptimal proximal polyadenylation signals. This mechanism leads to 3' untranslated region shortening and translation of transcripts encoding proteins involved in G1/S progression and proliferation. Thus, our findings indicate that the APA program driven by Sam68/XRN2 promotes cell cycle progression and may represent an actionable target for therapeutic intervention.
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Affiliation(s)
- Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy.,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy.,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Luca Mignini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Chuwei Zhong
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Gabriele Babini
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Rossano Lattanzio
- Department of Innovative Technologies in Medicine & Dentistry, G. d’Annunzio University, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), G. d’Annunzio University, Chieti, Italy
| | - Savino Di Stasi
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Bin Tian
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy. .,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy.
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy. .,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome, Italy.
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A ceRNA Network Composed of Survival-Related lncRNAs, miRNAs, and mRNAs in Clear Cell Renal Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8504441. [PMID: 35529267 PMCID: PMC9071875 DOI: 10.1155/2022/8504441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 12/02/2022]
Abstract
Clear cell renal carcinoma (ccRCC) is one of the most common renal carcinomas worldwide, which has worse prognosis compared with other subtypes of tumors. We propose a potential RNA regulatory mechanism associated with ccRCC progression. Accordingly, we screened out clinical factors and the expression of RNAs and miRNAs of ccRCC from the TCGA database. 9 lncRNAs (FGF12-AS2, WT1-AS, TRIM36-IT1, AC009093.1, LINC00443, TCL6, COL18A1-AS1, AC110619.1, HOTTIP), 2 miRNAs (mir-155 and mir-21), and 3 mRNAs (COL4A4, ERMP1, PRELID2) were selected from differential expression RNAs and built predictive survival models. The survival models performed very well in predicting prognosis and were found to be highly correlated with tumor stage. In addition, the survival-related lncRNA-miRNA-mRNA (ceRNA) network was constructed by 18 RNAs including 12 mRNAs, 2 miRNAs, and 4 lncRNAs. It is found that the “ECM-receptor interaction,” “Pathways in cancer,” and “Chemokine signaling pathway” as the main pathways in KEGG pathway analysis. Overall, we established predictive survival model and ceRNA network based on multivariate Cox regression analysis. It may open a new approach and potential biomarkers for clinical prognosis and treatment of ccRCC patients.
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8
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Alternative polyadenylation associated with prognosis and therapy in colorectal cancer. Sci Rep 2022; 12:7036. [PMID: 35487956 PMCID: PMC9054804 DOI: 10.1038/s41598-022-11089-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 04/11/2022] [Indexed: 11/24/2022] Open
Abstract
Colorectal cancer (CRC) is among the most widely spread cancers globally. Aberrant alternative polyadenylation (APA) plays a role in cancer onset and its progression. Consequently, this study focused on highlighting the role of APA events and signals in the prognosis of patients with CRC. The APA events, RNA sequencing (RNA-seq), somatic mutations, copy number variants (CNVs), and clinical information of the CRC cohort were obtained from The Cancer Genome Atlas (TCGA) database and UCSC (University of California-Santa Cruz) Xena database. The whole set was sorted into two sets: a training set and a test set in a ratio of 7:3. 197 prognosis-related APA events were collected by performing univariate Cox regression signature in patients with CRC. Subsequently, a signature for APA events was established by least absolute shrinkage and selection operator (LASSO) and multivariate Cox analysis. The risk scores were measured for individual patients on the basis of the signature and patients were sorted into two groups; the high-risk group and the low-risk group as per their median risk scores. Kaplan–Meier curves, principal component analysis (PCA), and time-dependent receiver operator characteristic (ROC) curves revealed that the signature was able to predict patient prognosis effectively and further validation was provided in the test set and the whole set. The high-risk and low-risk groups displayed various distributions of mutations and CNVs. Tumor mutation burden (TMB) alone and in combination with the signature predicted the prognosis of CRC patients, but the gene frequencies of TMBs and CNVs did not change in the low- and high-risk groups. Moreover, immunotherapy and chemotherapy treatments showed different responses to PD-1 inhibitors and multiple chemotherapeutic agents in the low and high-risk groups based on the tumor immune dysfunction and exclusion (TIDE) and genomics of drugs sensitivity in cancer (GDSC) databases. This study may help in understanding the potential roles of APA in CRC, and the signature for prognosis-related APA events can work as a potential predictor for survival and treatment in patients with CRC.
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Li J, Chen W, Cao Y, Li ZR. The Identification of Alternative Polyadenylation in Stomach Adenocarcinomas Using the Genotype-Tissue Expression Project and the Cancer Genome Atlas- Stomach Adenocarcinoma Profiles. Int J Gen Med 2021; 14:6035-6045. [PMID: 34588807 PMCID: PMC8475968 DOI: 10.2147/ijgm.s329064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/27/2021] [Indexed: 12/09/2022] Open
Abstract
Objective Alternative polyadenylation (APA) is a common mechanism that is present in most human genes and determines the length of the messenger ribonucleic acid (mRNA) three prime untranslated region (3ʹ-UTR), which can give rise to changes in mRNA stability and localization. However, little is known about the specific changes related to APA in stomach adenocarcinomas (STADs). Methods We integrated RNA sequencing data from The Cancer Genome Atlas and Genotype-Tissue Expression project to comprehensively analyze APA events in 289 cases of STAD. Results Our results showed that APA events were widespread in patients with STAD and were rich in genes related to known STAD pathways. The APA events result in the loss of tumor-suppressing micro-ribonucleic acid (miRNA) binding sites and increased heterogeneity in the length of the 3ʹ-UTR altered genes. Survival analysis revealed that specific subsets of 3ʹ-UTR-altered genes independently characterized a poor prognostic cohort among patients with STAD, thereby indicating the potential of APA as a new prognostic biomarker. Conclusion Our single-cancer analysis showed that by losing miRNA regulation, APA can become a driving factor for regulating the expression of oncogenic genes in STAD and promote its development. Our research revealed that APA events regulated STAD genes that were functionally related, thereby providing a new approach for gaining a better understanding of the progress of STADs and a means for identifying new drug targets as avenues of treatment.
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Affiliation(s)
- Jian Li
- Department of Gastrointestinal Surgery, Jiangxi Provincial People's Hospital Affiliated to Nanchang University, Nanchang, 330000, People's Republic of China
| | - Wen Chen
- Key Laboratory of Bioprocess Engineering of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, People's Republic of China
| | - Yi Cao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, People's Republic of China
| | - Zheng-Rong Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, People's Republic of China
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Wozniak M, Czyz M. The Functional Role of Long Non-Coding RNAs in Melanoma. Cancers (Basel) 2021; 13:cancers13194848. [PMID: 34638331 PMCID: PMC8508152 DOI: 10.3390/cancers13194848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/15/2022] Open
Abstract
Melanoma is the most lethal skin cancer, with increasing incidence worldwide. The molecular events that drive melanoma development and progression have been extensively studied, resulting in significant improvements in diagnostics and therapeutic approaches. However, a high drug resistance to targeted therapies and adverse effects of immunotherapies are still a major challenge in melanoma treatment. Therefore, the elucidation of molecular mechanisms of melanomagenesis and cancer response to treatment is of great importance. Recently, many studies have revealed the close association of long noncoding RNAs (lncRNAs) with the development of many cancers, including melanoma. These RNA molecules are able to regulate a plethora of crucial cellular processes including proliferation, differentiation, migration, invasion and apoptosis through diverse mechanisms, and even slight dysregulation of their expression may lead to tumorigenesis. lncRNAs are able to bind to protein complexes, DNA and RNAs, affecting their stability, activity, and localization. They can also regulate gene expression in the nucleus. Several functions of lncRNAs are context-dependent. This review summarizes current knowledge regarding the involvement of lncRNAs in melanoma. Their possible role as prognostic markers of melanoma response to treatment and in resistance to therapy is also discussed.
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11
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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12
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Antisense Oligonucleotide-Based Therapeutic against Menin for Triple-Negative Breast Cancer Treatment. Biomedicines 2021; 9:biomedicines9070795. [PMID: 34356858 PMCID: PMC8301388 DOI: 10.3390/biomedicines9070795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/20/2021] [Accepted: 06/30/2021] [Indexed: 01/01/2023] Open
Abstract
The tumor suppressor menin has dual functions, acting either as a tumor suppressor or as an oncogene/oncoprotein, depending on the oncological context. Triple-negative breast cancer (TNBC) is characterized by the lack of expression of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (ERBB2/HER2) and is often a basal-like breast cancer. TNBC is associated with a dismal prognosis and an insufficient response to chemotherapies. Previously, menin was shown to play a proliferative role in ER-positive breast cancer; however, the functions of menin in TNBC remain unknown. Here, we have demonstrated that menin is expressed in various TNBC subtypes with the strongest expression in the TNBC Hs 578T cells. The depletion of menin by an antisense oligonucleotide (ASO) inhibits cell proliferation, enhances apoptosis in Hs 578T cells, highlighting the oncogenic functions of menin in this TNBC model. ASO-based menin silencing also delays the tumor progression of TNBC xenografts. Analysis of the menin interactome suggests that menin could drive TNBC tumorigenesis through the regulation of MLL/KMT2A-driven transcriptional activity, mRNA 3′-end processing and apoptosis. The study provides a rationale behind the use of ASO-based therapy, targeting menin in monotherapy or in combination with chemo or PARP inhibitors for menin-positive TNBC treatments.
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13
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Xu D, Wang L, Pang S, Cao M, Wang W, Yu X, Xu Z, Xu J, Wang H, Lu J, Li K. The Functional Characterization of Epigenetically Related lncRNAs Involved in Dysregulated CeRNA-CeRNA Networks Across Eight Cancer Types. Front Cell Dev Biol 2021; 9:649755. [PMID: 34222227 PMCID: PMC8247484 DOI: 10.3389/fcell.2021.649755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Numerous studies have demonstrated that lncRNAs could compete with other RNAs to bind miRNAs, as competing endogenous RNAs (ceRNAs), to regulate each other. On the other hand, ceRNAs were found to be recurrently dysregulated in cancer status. However, limited studies considered the upstream epigenetic regulatory factors that disrupted the normal competing mechanism. In the present study, we constructed the lncRNA-associated dysregulated ceRNA networks across eight cancer types. lncRNAs in the individual dysregulated network and pan-cancer core dysregulated ceRNA subnetwork were found to play more important roles than mRNAs. Integrating lncRNA methylation profiles, we identified 49 epigenetically related (ER) lncRNAs involved in the dysregulated ceRNA networks, including 18 epigenetically activated (EA) lncRNAs, 18 epigenetically silenced (ES) lncRNAs, and 13 rewired ER lncRNAs across eight cancer types. Furthermore, we evaluated the epigenetic regulating patterns of these lncRNAs and screened nine pan-cancer ER lncRNAs (six EA and three ES lncRNAs). The nine lncRNAs were found to regulate the cancer hallmarks by competing with mRNAs. Moreover, we found that integrating the expression and methylation profiles of the nine lncRNAs could predict cancer incidence in eight cancer types robustly and the cancer outcome of several cancer types. These results provide an improved understanding of methylation regulation to ceRNA and offer novel potential molecular therapeutic targets for the diagnosis and prognosis across different cancer types.
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Affiliation(s)
- Dahua Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Liqiang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Sainan Pang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Meng Cao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenxiang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaorong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhizhou Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Jiankai Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
| | - Jianping Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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14
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Wang L, Lang GT, Xue MZ, Yang L, Chen L, Yao L, Li XG, Wang P, Hu X, Shao ZM. Dissecting the heterogeneity of the alternative polyadenylation profiles in triple-negative breast cancers. Am J Cancer Res 2020; 10:10531-10547. [PMID: 32929364 PMCID: PMC7482814 DOI: 10.7150/thno.40944] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is an aggressive malignancy with high heterogeneity. However, the alternative polyadenylation (APA) profiles of TNBC remain unknown. Here, we aimed to define the characteristics of the APA events at post-transcription level among TNBCs. Methods: Using transcriptome microarray data, we analyzed APA profiles of 165 TNBC samples and 33 paired normal tissues. A pooled short hairpin RNA screen targeting 23 core cleavage and polyadenylation (C/P) genes was used to identify key C/P factors. Results: We established an unconventional APA subtyping system composed of four stable subtypes: 1) luminal androgen receptor (LAR), 2) mesenchymal-like immune-activated (MLIA), 3) basal-like (BL), 4) suppressed (S) subtypes. Patients in the S subtype had the worst disease-free survival comparing to other patients (log-rank p = 0.021). Enriched clinically actionable pathways and putative therapeutic APA events were analyzed among each APA subtype. Furthermore, CPSF1 and PABPN1 were identified as the master C/P factors in regulating APA events and TNBC proliferation. The depletion of CPSF1 or PABPN1 weakened cell proliferation, enhanced apoptosis, resulted in cell cycle redistribution and a reversion of APA events of genes associated with tumorigenesis, proliferation, metastasis and chemosensitivity in breast cancer. Conclusions: Our findings advance the understanding of tumor heterogeneity regulation in APA and yield new insights into therapeutic target identification in TNBC.
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15
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Ala U. Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story. Cells 2020; 9:E1574. [PMID: 32605220 PMCID: PMC7407898 DOI: 10.3390/cells9071574] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNA molecules, are responsible for RNA silencing and post-transcriptional regulation of gene expression. They can mediate a fine-tuned crosstalk among coding and non-coding RNA molecules sharing miRNA response elements (MREs). In a suitable environment, both coding and non-coding RNA molecules can be targeted by the same miRNAs and can indirectly regulate each other by competing for them. These RNAs, otherwise known as competing endogenous RNAs (ceRNAs), lead to an additional post-transcriptional regulatory layer, where non-coding RNAs can find new significance. The miRNA-mediated interplay among different types of RNA molecules has been observed in many different contexts. The analyses of ceRNA networks in cancer and other pathologies, as well as in other physiological conditions, provide new opportunities for interpreting omics data for the field of personalized medicine. The development of novel computational tools, providing putative predictions of ceRNA interactions, is a rapidly growing field of interest. In this review, I discuss and present the current knowledge of the ceRNA mechanism and its implications in a broad spectrum of different pathologies, such as cardiovascular or autoimmune diseases, cancers and neurodegenerative disorders.
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Affiliation(s)
- Ugo Ala
- Department of Veterinary Sciences, University of Turin, 10124 Turin, Italy
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16
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Yang C, Wang L, Sun J, Zhou JH, Tan YL, Wang YF, You H, Wang QX, Kang CS. Identification of long non-coding RNA HERC2P2 as a tumor suppressor in glioma. Carcinogenesis 2020; 40:956-964. [PMID: 30809632 DOI: 10.1093/carcin/bgz043] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 01/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been reported to play important roles in glioma; however, most of them promote glioma progression. We constructed a competing endogenous (ceRNA) network based on the Chinese Glioma Genome Atlas dataset, and lncRNA hect domain and RLD 2 pseudogene 2 (HERC2P2) is the core of this network. Highly connected genes in the ceRNA network classified the glioma patients into three clusters with significantly different survival rates. The expression of HERC2P2 is positively correlated with survival and negatively correlated with clinical grade. Cell colony formation, Transwell and cell scratch tests were performed to evaluate the role of HERC2P2 in glioblastoma growth. Furthermore, we overexpressed HERC2P2 in U87 cells and established a mouse intracranial glioma model to examine the function of HERC2P2 in vivo. In conclusion, we identified a lncRNA with tumor suppressor functions in glioma that could be a potential biomarker for glioma patients.
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Affiliation(s)
- Chao Yang
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.,Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Lin Wang
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.,Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Jia Sun
- ProteinT Biotechnology Ltd. Co. Tianjin Airport Free Trade Zone, Tianjin, China
| | - Jun-Hu Zhou
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.,Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yan-Li Tan
- College of Fundamental Medicine, Hebei University, Baoding, China
| | - Yun-Fei Wang
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.,Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Hua You
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Qi-Xue Wang
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.,Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chun-Sheng Kang
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.,Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
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17
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Venkat S, Tisdale AA, Schwarz JR, Alahmari AA, Maurer HC, Olive KP, Eng KH, Feigin ME. Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma. Genome Res 2020; 30:347-360. [PMID: 32029502 PMCID: PMC7111527 DOI: 10.1101/gr.257550.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/04/2020] [Indexed: 01/08/2023]
Abstract
Alternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3'-UTR length, resulting in changes in mRNA stability and localization. APA is frequently disrupted in cancer and promotes tumorigenesis through altered expression of oncogenes and tumor suppressors. Pan-cancer analyses have revealed common APA events across the tumor landscape; however, little is known about tumor type-specific alterations that may uncover novel events and vulnerabilities. Here, we integrate RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Atlas (TCGA) to comprehensively analyze APA events in 148 pancreatic ductal adenocarcinomas (PDACs). We report widespread, recurrent, and functionally relevant 3'-UTR alterations associated with gene expression changes of known and newly identified PDAC growth-promoting genes and experimentally validate the effects of these APA events on protein expression. We find enrichment for APA events in genes associated with known PDAC pathways, loss of tumor-suppressive miRNA binding sites, and increased heterogeneity in 3'-UTR forms of metabolic genes. Survival analyses reveal a subset of 3'-UTR alterations that independently characterize a poor prognostic cohort among PDAC patients. Finally, we identify and validate the casein kinase CSNK1A1 (also known as CK1alpha or CK1a) as an APA-regulated therapeutic target in PDAC. Knockdown or pharmacological inhibition of CSNK1A1 attenuates PDAC cell proliferation and clonogenic growth. Our single-cancer analysis reveals APA as an underappreciated driver of protumorigenic gene expression in PDAC via the loss of miRNA regulation.
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Affiliation(s)
- Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Johann R Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - H Carlo Maurer
- Klinikum rechts der Isar, II. Medizinische Klinik, Technische Universität München, 81675 Munich, Germany
| | - Kenneth P Olive
- Herbert Irving Comprehensive Cancer Center, Department of Medicine, Division of Digestive and Liver Diseases, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
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18
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The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium. Cells 2019; 8:cells8121634. [PMID: 31847302 PMCID: PMC6953095 DOI: 10.3390/cells8121634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
: Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have on cancer development.
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19
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Zhou RS, Zhang EX, Sun QF, Ye ZJ, Liu JW, Zhou DH, Tang Y. Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue. BMC Cancer 2019; 19:779. [PMID: 31391008 PMCID: PMC6686570 DOI: 10.1186/s12885-019-5983-8] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/26/2019] [Indexed: 12/19/2022] Open
Abstract
Background Numerous studies have highlighted that long non-coding RNAs (lncRNAs) can bind to microRNA (miRNA) sites as competing endogenous RNAs (ceRNAs), thereby affecting and regulating the expression of mRNAs and target genes. These lncRNA-associated ceRNAs have been theorized to play a significant role in cancer initiation and progression. However, the roles and functions of the lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of the tongue (SCCT) are still unclear. Methods The miRNA, mRNA and lncRNA expression profiles from 138 patients with SCCT were downloaded from The Cancer Genome Atlas database. We identified the differential expression of miRNAs, mRNAs, and lncRNAs using the limma package of R software. We used the clusterProfiler package for GO and KEGG pathway annotations. The survival package was used to estimate survival analysis according to the Kaplan-Meier curve. Finally, the GDCRNATools package was used to construct the lncRNA-miRNA-mRNA ceRNA network. Results In total, 1943 SCCT-specific mRNAs, 107 lncRNAs and 100 miRNAs were explored. Ten mRNAs (CSRP2, CKS2, ADGRG6, MB21D1, GMNN, RIPOR3, RAD51, PCLAF, ORC1, NAGS), 9 lncRNAs (LINC02560, HOXC13 − AS, FOXD2 − AS1, AC105277.1, AC099850.3, STARD4 − AS1, SLC16A1 − AS1, MIR503HG, MIR100HG) and 8 miRNAs (miR − 654, miR − 503, miR − 450a, miR − 379, miR − 369, miR − 190a, miR − 101, and let−7c) were found to be significantly associated with overall survival (log-rank p < 0.05). Based on the analysis of the lncRNA-miRNA-mRNA ceRNA network, one differentially expressed (DE) lncRNA, five DEmiRNAs, and three DEmRNAs were demonstrated to be related to the pathogenesis of SCCT. Conclusions In this study, we described the gene regulation by the lncRNA-miRNA-mRNA ceRNA network in the progression of SCCT. We propose a new lncRNA-associated ceRNA that could help in the diagnosis and treatment of SCCT. Electronic supplementary material The online version of this article (10.1186/s12885-019-5983-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rui-Sheng Zhou
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - En-Xin Zhang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qin-Feng Sun
- Stomatological Hospital of Shandong University, Shandong, China
| | - Zeng-Jie Ye
- Guangzhou University of Chinese Medicine, Guangzhou, China
| | | | - Dai-Han Zhou
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Tang
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China. .,Guangzhou University of Chinese Medicine, Guangzhou, China. .,Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China.
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20
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Chen Y, Lin Y, Bai Y, Cheng D, Bi Z. A Long Noncoding RNA (lncRNA)-Associated Competing Endogenous RNA (ceRNA) Network Identifies Eight lncRNA Biomarkers in Patients with Osteoarthritis of the Knee. Med Sci Monit 2019; 25:2058-2065. [PMID: 30890688 PMCID: PMC6437717 DOI: 10.12659/msm.915555] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Osteoarthritis (OA) of the knee is a common disease that is associated with chronic pain. This study aimed to identify and investigate the functional role of biomarkers associated with long noncoding RNA (lncRNA) in the progression of OA of the knee by lncRNA-associated competing endogenous RNA (ceRNA) integrated network analysis. Material/Methods High-quality microRNA (miRNA)-lncRNA and miRNA-mRNA interactions and lncRNA and mRNA expression profiles for patients with OA of the knee with mild and severe pain were obtained from the Gene Expression Omnibus (GEO) database (GSE99662). A three-step computational method was used to construct the lncRNA-associated ceRNA interaction network in OA by integrating miRNA-lncRNA/mRNA interactions and lncRNA/mRNA expression profiles in patients with OA with mild and severe pain. Results A total of 1,870 dysregulated lncRNA-mRNA interactions were obtained in the lncRNA-associated ceRNA network in OA, including 476 gain and 1,394 loss interactions, covering 131 lncRNAs and 1,251 mRNAs. Characterization of the lncRNA-associated ceRNA network in OA indicated that lncRNAs had roles in the network. Further differential expression analysis identified eight lncRNA biomarkers, which could distinguish between patients with OA with mild pain and severe pain. These lncRNA-associated interactions showed significantly different co-expression patterns in samples from patients with OA of the knee associated with mild pain. Conclusions Integrated network analysis of lncRNA-associated ceRNA identified eight lncRNA molecular biomarkers associated with the progression of OA of the knee.
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Affiliation(s)
- Yuxi Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
| | - Yu Lin
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
| | - Ye Bai
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland).,Department of Orthopedics, The People's Liberation Army (PLA) 211 Hospital, Harbin, Heilongjiang, China (mainland)
| | - Daolin Cheng
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
| | - Zhenggang Bi
- Department of Orthopedic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China (mainland)
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21
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Grozdanov PN, Masoumzadeh E, Latham MP, MacDonald CC. The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity. Nucleic Acids Res 2018; 46:12022-12039. [PMID: 30257008 PMCID: PMC6294498 DOI: 10.1093/nar/gky862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/31/2018] [Accepted: 09/12/2018] [Indexed: 01/14/2023] Open
Abstract
Cleavage and polyadenylation (C/P) of mRNA is an important cellular process that promotes increased diversity of mRNA isoforms and could change their stability in different cell types. The cleavage stimulation factor (CstF) complex, part of the C/P machinery, binds to U- and GU-rich sequences located downstream from the cleavage site through its RNA-binding subunit, CstF-64. Less is known about the function of the other two subunits of CstF, CstF-77 and CstF-50. Here, we show that the carboxy-terminus of CstF-77 plays a previously unrecognized role in enhancing C/P by altering how the RNA recognition motif (RRM) of CstF-64 binds RNA. In support of this finding, we also show that CstF-64 relies on CstF-77 to be transported to the nucleus; excess CstF-64 localizes to the cytoplasm, possibly via interaction with cytoplasmic RNAs. Reverse genetics and nuclear magnetic resonance studies of recombinant CstF-64 (RRM-Hinge) and CstF-77 (monkeytail-carboxy-terminal domain) indicate that the last 30 amino acids of CstF-77 increases the stability of the RRM, thus altering the affinity of the complex for RNA. These results provide new insights into the mechanism by which CstF regulates the location of the RNA cleavage site during C/P.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Elahe Masoumzadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Michael P Latham
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
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22
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Fan Z, Gao S, Chen Y, Xu B, Yu C, Yue M, Tan X. Integrative analysis of competing endogenous RNA networks reveals the functional lncRNAs in heart failure. J Cell Mol Med 2018; 22:4818-4829. [PMID: 30019841 PMCID: PMC6156393 DOI: 10.1111/jcmm.13739] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 05/20/2018] [Indexed: 02/05/2023] Open
Abstract
Heart failure has become one of the top causes of death worldwide. It is increasing evidence that lncRNAs play important roles in the pathology processes of multiple cardiovascular diseases. Additionally, lncRNAs can function as ceRNAs by sponging miRNAs to affect the expression level of mRNAs, implicating in numerous biological processes. However, the functional roles and regulatory mechanisms of lncRNAs in heart failure are still unclear. In our study, we constructed a heart failure-related lncRNA-mRNA network by integrating probe re-annotation pipeline and miRNA-target interactions. Firstly, some lncRNAs that had the central topological features were found in the heart failure-related lncRNA-mRNA network. Then, the lncRNA-associated functional modules were identified from the network, using bidirectional hierarchical clustering. Some lncRNAs that involved in modules were demonstrated to be enriched in many heart failure-related pathways. To investigate the role of lncRNA-associated ceRNA crosstalks in certain disease or physiological status, we further identified the lncRNA-associated dysregulated ceRNA interactions. And we also performed a random walk algorithm to identify more heart failure-related lncRNAs. All these lncRNAs were verified to show a strong diagnosis power for heart failure. These results will help us to understand the mechanism of lncRNAs in heart failure and provide novel lncRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
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Affiliation(s)
- Zhimin Fan
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
| | - Shanshan Gao
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
| | - Yequn Chen
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
| | - Bayi Xu
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
| | - Chengzhi Yu
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
| | - Minghui Yue
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
| | - Xuerui Tan
- Department of CardiologyThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
- Shantou University Medical CollegeShantouGuangdongChina
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23
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LncRNA-NR_033515 promotes proliferation, fibrogenesis and epithelial-to-mesenchymal transition by targeting miR-743b-5p in diabetic nephropathy. Biomed Pharmacother 2018; 106:543-552. [DOI: 10.1016/j.biopha.2018.06.104] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 01/10/2023] Open
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24
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Wang Q, Cai J, Fang C, Yang C, Zhou J, Tan Y, Wang Y, Li Y, Meng X, Zhao K, Yi K, Zhang S, Zhang J, Jiang C, Zhang J, Kang C. Mesenchymal glioblastoma constitutes a major ceRNA signature in the TGF-β pathway. Theranostics 2018; 8:4733-4749. [PMID: 30279734 PMCID: PMC6160778 DOI: 10.7150/thno.26550] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 08/15/2018] [Indexed: 12/27/2022] Open
Abstract
Rationale: Competitive endogenous RNA (ceRNA) networks play important roles in posttranscriptional regulation. Their dysregulation is common in cancer. However, ceRNA signatures have been poorly examined in the invasive and aggressive phenotypes of mesenchymal glioblastoma (GBM). This study aims to characterize mesenchymal glioblastoma at the mRNA-miRNA level and identify the mRNAs in ceRNA networks (micNET) markers and their mechanisms in tumorigenesis. Methods: The mRNAs in ceRNA networks (micNETs) of glioblastoma were investigated by constructing a GBM ceRNA network followed by integration with a STRING protein interaction network. The prognostic micNET markers of mesenchymal GBM were identified and validated across multiple datasets. ceRNA interactions were identified between micNETs and miR181 family members. LY2109761, an inhibitor of TGFBR2, demonstrated tumor-suppressive effects on both primary cultured cells and a patient-derived xenograft intracranial model. Results: We characterized mesenchymal glioblastoma at the mRNA-miRNA level and reported a ceRNA network that could separate the mesenchymal subtype from other subtypes. Six genes (TGFBR2, RUNX1, PPARG, ACSL1, GIT2 and RAP1B) that interacted with each other in both a ceRNA-related manner and in terms of their protein functions were identified as markers of the mesenchymal subtype. The coding sequence (CDS) and 3'-untranslated region (UTR) of TGFBR2 upregulated the expression of these genes, whereas TGFBR2 inhibition by siRNA or miR-181a/d suppressed their expression levels. Furthermore, mesenchymal subtype-related genes and the invasion phenotype could be reversed by suppressing the six mesenchymal marker genes. Conclusions: This study suggests that the micNETs may have translational significance in the diagnosis of mesenchymal GBM and may be novel therapeutic targets.
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Affiliation(s)
- Qixue Wang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Jinquan Cai
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Chuan Fang
- Department of Neurosurgery, Hebei University Affiliated Hospital, Baoding 071000, China
| | - Chao Yang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Junhu Zhou
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Yanli Tan
- Department of Pathology, Medical College of Hebei University, Baoding, Hebei 071000, China
| | - Yunfei Wang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Yansheng Li
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Xiangqi Meng
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Kai Zhao
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Kaikai Yi
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Sijing Zhang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Jianning Zhang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Chuanlu Jiang
- Department of Neurosurgery, the Second Affiliated Hospital of Harbin Medical University, Neuroscience Institute, Heilongjiang Academy of Medical Sciences, Harbin 150086, China
| | - Jing Zhang
- Institute for Cancer Genetics, Columbia University Medical Center, Columbia University, New York, New York 10032, USA
| | - Chunsheng Kang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
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25
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Wang L, Hu X, Wang P, Shao ZM. Integrative 3' Untranslated Region-Based Model to Identify Patients with Low Risk of Axillary Lymph Node Metastasis in Operable Triple-Negative Breast Cancer. Oncologist 2018; 24:22-30. [PMID: 30082491 DOI: 10.1634/theoncologist.2017-0609] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/09/2018] [Accepted: 05/16/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sentinel lymph node biopsy is the standard surgical staging approach for operable triple-negative breast cancer (TNBC) with clinically negative axillae. In this study, we sought to develop a model to predict TNBC patients with negative nodal involvement, who would benefit from the exemption of the axillary staging surgery. MATERIALS AND METHODS We evaluated 3' untranslated region (3'UTR) profiles using microarray data of TNBC from two Gene Expression Omnibus datasets. Samples from GSE31519 were divided into training set (n = 164) and validation set (n = 163), and GSE76275 was used to construct testing set (n = 164). We built a six-member 3'UTR panel (ADD2, COL1A1, APOL2, IL21R, PKP2, and EIF4G3) using an elastic net model to estimate the risk of lymph node metastasis (LNM). Receiver operating characteristic and logistic analyses were used to assess the association between the panel and LNM status. RESULTS The six-member 3'UTR-panel showed a high distinguishing power with an area under the curve of 0.712, 0.729, and 0.708 in the training, validation, and testing sets, respectively. After adjustment by tumor size, the 3'UTR panel retained significant predictive power in the training, validation, and testing sets (odds ratio = 4.93, 4.58, and 3.59, respectively; p < .05 for all). A combinatorial analysis of the 3'UTR panel and tumor size yielded an accuracy of 97.2%, 100%, and 100% in training, validation, and testing set, respectively. CONCLUSION This study established an integrative 3'UTR-based model as a promising predictor for nodal negativity in operable TNBC. Although a prospective study is needed to validate the model, our results may permit a no axillary surgery option for selected patients. IMPLICATIONS FOR PRACTICE Currently, sentinel lymph node biopsy is the standard approach for surgical staging in breast cancer patients with negative axillae. Prediction estimation for lymph node metastasis of breast cancer relies on clinicopathological characteristics, which is unreliable, especially in triple-negative breast cancer (TNBC)-a highly heterogeneous disease. The authors developed and validated an effective prediction model for the lymph node status of patients with TNBC, which integrates 3'UTR markers and tumor size. This is the first 3'UTR-based model that will help identify TNBC patients with low risk of nodal involvement who are most likely to benefit from exemption axillary surgery.
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Affiliation(s)
- Lei Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xin Hu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Peng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
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26
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Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L, Su J, Chen K, Masamha CP, Baillat D, Fontes-Garfias CR, Shyu AB, Neilson JR, Wagner EJ, Li W. 3' UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk. Nat Genet 2018; 50:783-789. [PMID: 29785014 DOI: 10.1038/s41588-018-0118-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 03/22/2018] [Indexed: 01/27/2023]
Abstract
Widespread mRNA 3' UTR shortening through alternative polyadenylation 1 promotes tumor growth in vivo 2 . A prevailing hypothesis is that it induces proto-oncogene expression in cis through escaping microRNA-mediated repression. Here we report a surprising enrichment of 3'UTR shortening among transcripts that are predicted to act as competing-endogenous RNAs (ceRNAs) for tumor-suppressor genes. Our model-based analysis of the trans effect of 3' UTR shortening (MAT3UTR) reveals a significant role in altering ceRNA expression. MAT3UTR predicts many trans-targets of 3' UTR shortening, including PTEN, a crucial tumor-suppressor gene 3 involved in ceRNA crosstalk 4 with nine 3'UTR-shortening genes, including EPS15 and NFIA. Knockdown of NUDT21, a master 3' UTR-shortening regulator 2 , represses tumor-suppressor genes such as PHF6 and LARP1 in trans in a miRNA-dependent manner. Together, the results of our analysis suggest a major role of 3' UTR shortening in repressing tumor-suppressor genes in trans by disrupting ceRNA crosstalk, rather than inducing proto-oncogenes in cis.
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Affiliation(s)
- Hyun Jung Park
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ping Ji
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Soyeon Kim
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zheng Xia
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin Rodriguez
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lei Li
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jianzhong Su
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kaifu Chen
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Chioniso P Masamha
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN, USA
| | - David Baillat
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Camila R Fontes-Garfias
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, University of Texas, McGovern Medical School, Houston, TX, USA
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J Wagner
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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27
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Swain AC, Mallick B. miRNA-mediated 'tug-of-war' model reveals ceRNA propensity of genes in cancers. Mol Oncol 2018; 12:855-868. [PMID: 29603582 PMCID: PMC5983123 DOI: 10.1002/1878-0261.12198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/15/2018] [Accepted: 03/19/2018] [Indexed: 12/11/2022] Open
Abstract
Competing endogenous RNA (ceRNA) are transcripts that cross‐regulate each other at the post‐transcriptional level by competing for shared microRNA response elements (MREs). These have been implicated in various biological processes impacting cell‐fate decisions and diseases including cancer. There are several studies that predict possible ceRNA pairs by adopting various machine‐learning and mathematical approaches; however, there is no method that enables us to gauge as well as compare the propensity of the ceRNA of a gene and precisely envisages which among a pair exerts a stronger pull on the shared miRNA pool. In this study, we developed a method that uses the ‘tug of war of genes’ concept to predict and quantify ceRNA potential of a gene for the shared miRNA pool in cancers based on a score represented by SoCeR (score of competing endogenous RNA). The method was executed on the RNA‐Seq transcriptional profiles of genes and miRNA available at TCGA along with CLIP‐supported miRNA‐target sites to predict ceRNA in 32 cancer types which were validated with already reported cases. The proposed method can be used to determine the sequestering capability of the gene of interest as well as in ranking the probable ceRNA candidates of a gene. Finally, we developed standalone applications (SoCeR tool) to aid researchers in easier implementation of the method in analysing different data sets or diseases.
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Affiliation(s)
- Arpit Chandan Swain
- Department of Mathematics, National Institute of Technology, Rourkela, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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28
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MicroRNA Regulation of Telomerase Reverse Transcriptase (TERT): Micro Machines Pull Strings of Papier-Mâché Puppets. Int J Mol Sci 2018; 19:ijms19041051. [PMID: 29614790 PMCID: PMC5979469 DOI: 10.3390/ijms19041051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/12/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022] Open
Abstract
Substantial fraction of high-quality information is continuously being added into the existing pool of knowledge related to the biology of telomeres. Based on the insights gleaned from decades of research, it is clear that chromosomal stability needs a highly controlled and dynamic balance of DNA gain and loss in each terminal tract of telomeric repeats. Telomeres are formed by tandem repeats of TTAGGG sequences, which are gradually lost with each round of division of the cells. Targeted inhibition of telomerase to effectively induce apoptosis in cancer cells has attracted tremendous attention and overwhelmingly increasingly list of telomerase inhibitors truthfully advocates pharmacological significance of telomerase. Telomerase reverse transcriptase (TERT) is a multi-talented and catalytically active component of the telomerase-associated protein machinery. Different proteins of telomerase-associated machinery work in a synchronized and orchestrated manner to ensure proper maintenance of telomeric length of chromosomes. Rapidly emerging scientific findings about regulation of TERT by microRNAs has revolutionized our understanding related to the biology of telomeres and telomerase. In this review, we have comprehensively discussed how different miRNAs regulate TERT in different cancers. Use of miRNA-based therapeutics against TERT in different cancers needs detailed research in preclinical models for effective translation of laboratory findings to clinically effective therapeutics.
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29
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The 3'UTR signature defines a highly metastatic subgroup of triple-negative breast cancer. Oncotarget 2018; 7:59834-59844. [PMID: 27494850 PMCID: PMC5312352 DOI: 10.18632/oncotarget.10975] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 07/18/2016] [Indexed: 01/13/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly heterogeneous disease with an aggressive clinical course. Prognostic models are needed to chart potential patient outcomes. To address this, we used alternative 3′UTR patterns to improve postoperative risk stratification. We collected 327 publicly available microarrays and generated the 3′UTR landscape based on expression ratios of alternative 3′UTR. After initial feature filtering, we built a 17-3′UTR-based classifier using an elastic net model. Time-dependent ROC comparisons and Kaplan–Meier analyses confirmed an outstanding discriminating power of our prognostic model for TNBC patients. In the training cohort, 5-year event-free survival (EFS) was 78.6% (95% CI 71.2–86.0) for the low-risk group, and 16.3% (95% CI 2.3–30.4) for the high-risk group (log-rank p<0.0001; hazard ratio [HR] 8.29, 95% CI 4.78–14.4), In the validation set, 5-year EFS was 75.6% (95% CI 68.0–83.2) for the low-risk group, and 33.2% (95% CI 17.1–49.3) for the high-risk group (log-rank p<0.0001; HR 3.17, 95% CI 1.66–5.42). In conclusion, the 17-3′UTR-based classifier provides a superior prognostic performance for estimating disease recurrence and metastasis in TNBC patients and it may permit personalized management strategies.
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30
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Szkop KJ, Nobeli I. Untranslated Parts of Genes Interpreted: Making Heads or Tails of High-Throughput Transcriptomic Data via Computational Methods: Computational methods to discover and quantify isoforms with alternative untranslated regions. Bioessays 2017; 39. [PMID: 29052251 DOI: 10.1002/bies.201700090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 09/12/2017] [Indexed: 01/07/2023]
Abstract
In this review we highlight the importance of defining the untranslated parts of transcripts, and present a number of computational approaches for the discovery and quantification of alternative transcription start and poly-adenylation events in high-throughput transcriptomic data. The fate of eukaryotic transcripts is closely linked to their untranslated regions, which are determined by the position at which transcription starts and ends at a genomic locus. Although the extent of alternative transcription starts and alternative poly-adenylation sites has been revealed by sequencing methods focused on the ends of transcripts, the application of these methods is not yet widely adopted by the community. We suggest that computational methods applied to standard high-throughput technologies are a useful, albeit less accurate, alternative to the expertise-demanding 5' and 3' sequencing and they are the only option for analysing legacy transcriptomic data. We review these methods here, focusing on technical challenges and arguing for the need to include better normalization of the data and more appropriate statistical models of the expected variation in the signal.
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Affiliation(s)
- Krzysztof J Szkop
- Institute of Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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31
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Li MJ, Zhang J, Liang Q, Xuan C, Wu J, Jiang P, Li W, Zhu Y, Wang P, Fernandez D, Shen Y, Chen Y, Kocher JPA, Yu Y, Sham PC, Wang J, Liu JS, Liu XS. Exploring genetic associations with ceRNA regulation in the human genome. Nucleic Acids Res 2017; 45:5653-5665. [PMID: 28472449 PMCID: PMC5449616 DOI: 10.1093/nar/gkx331] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/26/2017] [Indexed: 01/01/2023] Open
Abstract
Competing endogenous RNAs (ceRNAs) are RNA molecules that sequester shared microRNAs (miRNAs) thereby affecting the expression of other targets of the miRNAs. Whether genetic variants in ceRNA can affect its biological function and disease development is still an open question. Here we identified a large number of genetic variants that are associated with ceRNA's function using Geuvaids RNA-seq data for 462 individuals from the 1000 Genomes Project. We call these loci competing endogenous RNA expression quantitative trait loci or 'cerQTL', and found that a large number of them were unexplored in conventional eQTL mapping. We identified many cerQTLs that have undergone recent positive selection in different human populations, and showed that single nucleotide polymorphisms in gene 3΄UTRs at the miRNA seed binding regions can simultaneously regulate gene expression changes in both cis and trans by the ceRNA mechanism. We also discovered that cerQTLs are significantly enriched in traits/diseases associated variants reported from genome-wide association studies in the miRNA binding sites, suggesting that disease susceptibilities could be attributed to ceRNA regulation. Further in vitro functional experiments demonstrated that a cerQTL rs11540855 can regulate ceRNA function. These results provide a comprehensive catalog of functional non-coding regulatory variants that may be responsible for ceRNA crosstalk at the post-transcriptional level.
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Affiliation(s)
- Mulin Jun Li
- Department of pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Statistics, Harvard University, Cambridge, MA 02138, USA.,Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jian Zhang
- Department of pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qian Liang
- Department of pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chenghao Xuan
- Department of pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jiexing Wu
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Peng Jiang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA 02215, USA
| | - Wei Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA 02215, USA
| | - Yun Zhu
- Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China.,School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Panwen Wang
- Department of Health Sciences Research & Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Daniel Fernandez
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Yujun Shen
- Department of pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jean-Pierre A Kocher
- Department of Health Sciences Research & Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Ying Yu
- Department of pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Pak Chung Sham
- Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China.,Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Junwen Wang
- Department of Health Sciences Research & Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA.,Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA 02215, USA
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32
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Turner RE, Pattison AD, Beilharz TH. Alternative polyadenylation in the regulation and dysregulation of gene expression. Semin Cell Dev Biol 2017; 75:61-69. [PMID: 28867199 DOI: 10.1016/j.semcdb.2017.08.056] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/30/2017] [Accepted: 08/30/2017] [Indexed: 01/08/2023]
Abstract
Transcriptional control shapes a cell's transcriptome composition, but it is RNA processing that refines its expression. The untranslated regions (UTRs) of mRNA are hotspots for regulatory control. Features in these can impact mRNA stability, localisation and translation. Here we describe how alternative cleavage and polyadenylation can change mRNA fate by changing the length of its 3'UTR.
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Affiliation(s)
- Rachael Emily Turner
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia
| | - Andrew David Pattison
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia
| | - Traude Helene Beilharz
- Development and stem cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia.
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33
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Song C, Zhang J, Qi H, Feng C, Chen Y, Cao Y, Ba L, Ai B, Wang Q, Huang W, Li C, Sun H. The global view of mRNA-related ceRNA cross-talks across cardiovascular diseases. Sci Rep 2017; 7:10185. [PMID: 28860540 PMCID: PMC5579186 DOI: 10.1038/s41598-017-10547-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/10/2017] [Indexed: 12/14/2022] Open
Abstract
Competing endogenous RNA (ceRNA) have received wide attention because they are a novel way to regulate genes through sharing microRNAs (miRNAs) that are crucial for complex processes in many diseases. However, no systematic analysis of ceRNA mechanism in cardiovascular disease (CVD) is known. To gain insights into the global properties of ceRNAs in multi-CVDs, we constructed the global view of mRNA-related ceRNA cross-talk in eight major CVDs from ~2,800 samples. We found common features that could be used to uncover similarities among different CVDs and highlighted a common core ceRNA network across CVDs. Comparative analysis of hub ceRNAs in each network revealed three types of hubs, which might play key roles in diverse biological processes. Importantly, by combining CVD-related pathway genes with ceRNA-ceRNA interactions, common modules that might exert functions in specific mechanisms were identified. In addition, our study investigated a potential mechanistic linkage between pathway cross-talk and ceRNA cross-talk. In summary, this study uncovered and systematically characterized global properties of mRNA-related ceRNA cross-talks across CVDs, which may provide a new layer for exploring biological mechanisms and shed new light on cardiology.
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Affiliation(s)
- Chao Song
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Jian Zhang
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Hanping Qi
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Chenchen Feng
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Yunping Chen
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Yonggang Cao
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Lina Ba
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Bo Ai
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Qiuyu Wang
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Wei Huang
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, 163319, China
| | - Chunquan Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, 163319, China.
| | - Hongli Sun
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, 163319, China.
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34
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Wu Q, Yan H, Tao SQ, Wang XN, Mou L, Chen P, Cheng XW, Wu WY, Wu ZS. XIAP 3'-untranslated region as a ceRNA promotes FSCN1 function in inducing the progression of breast cancer by binding endogenous miR-29a-5p. Oncotarget 2017; 8:16784-16800. [PMID: 28186968 PMCID: PMC5370001 DOI: 10.18632/oncotarget.15159] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 01/23/2017] [Indexed: 12/23/2022] Open
Abstract
The non-coding 3′-untranslated region (UTR) of genes play an important role in the regulation of microRNA (miRNA) functions, since it can bind and inactivate multiple miRNAs. Herein, we report that ectopic expression of XIAP 3′UTR increased human breast cancer cells proliferation, colony formation, migration, invasion and xenograft tumor growth and suppressed tumor cell death. To investigate this process, we further correlated the genome-wide transcriptional profiling with the gene expression alterations after transfecting XIAP 3′UTR in MCF-7 cells. We identified a robust, genome-wide mechanism of cell migration, motility and epithelial to mesenchymal transition by which mediated by a previously described cellular component movement factor FSCN1. Expression of XIAP and FSCN1 were up-regulated synergistically after transfecting XIAP 3′UTR in vitro and in vivo. Interactions between XIAP and FSCN1 appear to be a key determinant of these processes. Co-transfection with Dicer siRNA reversed the XIAP 3′UTR-mediated oncogenicity, suggesting the miRNAs might be involved in that process. Furthermore, we demonstrated that one miRNA, miR-29a-5p, can bind to both the XIAP and FSCN1 3′UTRs and play an important role in that interactions. We showed that the 3′UTR of XIAP was able to antagonize miR-29a-5p, and resulted in the increased translation of XIAP and FSCN1. Thus, our findings reveal important new insights into how XIAP 3′UTR works, suggesting that the non-coding XIAP 3′UTR serves as a competitor for miRNA binding and subsequently inactivates miRNA functions, by which XIAP 3′UTR frees the target mRNAs from being repressed.
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Affiliation(s)
- Qiang Wu
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Hong Yan
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Pathology, Anhui Provincial Cancer Hospital, Hefei, Anhui, China
| | - Si-Qi Tao
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Xiao-Nan Wang
- Laboratory of Pathogenic Microbiology and Immunology, Anhui Medical University, Hefei, Anhui, China
| | - Lang Mou
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Ping Chen
- Department of Pathology, Anhui Medical University, Hefei, Anhui, China
| | - Xing-Wang Cheng
- Department of Emergency, The First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
| | - Wen-Yong Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zheng-Sheng Wu
- Department of Pathology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of Pathology, Anhui Medical University, Hefei, Anhui, China
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35
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Sweet TJ, Ting AH. WOMEN IN CANCER THEMATIC REVIEW: Diverse functions of DNA methylation: implications for prostate cancer and beyond. Endocr Relat Cancer 2016; 23:T169-T178. [PMID: 27605446 DOI: 10.1530/erc-16-0306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 12/31/2022]
Abstract
Prostate cancer is one of the most common malignancies in men worldwide. Current clinical screening ensures that most prostate cancers are diagnosed while still organ confined, but disease outcome is highly variable. Thus, a better understanding of the molecular features contributing to prostate cancer aggressiveness is being sought. For many cancers, aberrant genome-wide patterns of cytosine DNA methylation in CpG dinucleotides distinguish tumor from normal tissue and contribute to disease progression by altering the transcriptome. In prostate cancer, recent genomic studies identified cancer and high grade-specific differential DNA methylation in gene promoters, gene bodies, gene 3' ends and at distal regulatory elements. Using examples from developmental and disease systems, we will discuss how DNA methylation in each of these genomic contexts can contribute to transcriptome diversity by modulating transcription initiation, alternative transcription start site selection, alternative pre-mRNA splicing and alternative polyadenylation. Alternative transcripts from the same gene often exhibit altered protein-coding potential, translatability, stability and/or localization. All of these can have functional consequences in cells. In future work, it will be important to determine if DNA methylation abnormalities in prostate cancer modify the transcriptome through some or all of these mechanisms and if these DNA methylation-mediated transcriptome alterations impact prostate tumorigenesis and aggressiveness.
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Affiliation(s)
- Thomas J Sweet
- Genomic Medicine InstituteLerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Angela H Ting
- Genomic Medicine InstituteLerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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36
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Oncogenic p95HER2 regulates Na+-HCO3- cotransporter NBCn1 mRNA stability in breast cancer cells via 3'UTR-dependent processes. Biochem J 2016; 473:4027-4044. [PMID: 27609814 DOI: 10.1042/bcj20160054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/08/2016] [Indexed: 02/08/2023]
Abstract
The Na+-HCO3- cotransporter NBCn1 (SLC4A7) is up-regulated in breast cancer, important for tumor growth, and a single nucleotide polymorphism (SNP), rs4973768, in its 3' untranslated region (3'UTR) correlates with increased breast cancer risk. We previously demonstrated that NBCn1 expression and promoter activity are strongly increased in breast cancer cells expressing a constitutively active oncogenic human epidermal growth factor receptor 2 (HER2) (p95HER2). Here, we address the roles of p95HER2 in regulating NBCn1 expression via post-transcriptional mechanisms. p95HER2 expression in MCF-7 cells reduced the rate of NBCn1 mRNA degradation. The NBCn1 3'UTR down-regulated luciferase reporter expression in control cells, and this was reversed by p95HER2, suggesting that p95HER2 counteracts 3'UTR-mediated suppression of NBCn1 expression. Truncation analyses identified three NBCn1 3'UTR regions of regulatory importance. Mutation of putative miRNA-binding sites (miR-374a/b, miR-200b/c, miR-29a/b/c, miR-488) in these regions did not have significant impact on 3'UTR activity. The NBCn1 3'UTR interacted directly with the RNA-binding protein human antigen R (HuR), and HuR knockdown reduced NBCn1 expression. Conversely, ablation of a distal AU-rich element increased 3'UTR-driven reporter activity, suggesting complex regulatory roles of these sites. The cancer-associated SNP variant decreased reporter expression in T-47D breast cancer cells, yet not in MCF-7, MDA-MB-231 and SK-BR-3 cells, arguing against a general role in regulating NBCn1 expression. Finally, p95HER2 expression increased total and plasma membrane NBCn1 protein levels and decreased the rate of NBCn1 protein degradation. Collectively, this is the first work to demonstrate 3'UTR-mediated NBCn1 regulation, shows that p95HER2 regulates NBCn1 expression at multiple levels, and substantiates the central position of p95HER2-NBCn1 signaling in breast cancer.
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37
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The long non-coding RNA, SNHG6-003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma. Oncogene 2016; 36:1112-1122. [PMID: 27530352 DOI: 10.1038/onc.2016.278] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/25/2016] [Accepted: 07/01/2016] [Indexed: 01/17/2023]
Abstract
The expression of long non-coding RNAs (lncRNAs) is dysregulated in hepatocellular carcinoma (HCC). However, the functions and contributions of lncRNAs remain largely unknown. Here, we identified a critical role of SNHG6-003 in HCC. We found that five SNHG6 transcripts were differentially expressed in HCC tissues while only the SNHG6-003 had an oncogenic function. Ectopic expression of SNHG6-003 in HCC cells promoted cell proliferation and induced drug resistance, whereas SNHG6-003 knockdown promoted apoptosis. Moreover, SNHG6-003 functioned as a competitive endogenous RNA (ceRNA), effectively becoming sponge for miR-26a/b and thereby modulating the expression of transforming growth factor-β-activated kinase 1 (TAK1). Importantly, expression analysis revealed that both SNHG6-003 and TAK1 were upregulated in human cancers, exhibiting a co-expression pattern. In HCC patients, high expression of SNHG6-003 closely correlated with tumor progression and shorter survival. Thus, targeting the ceRNA network involving SNHG6-003 may be used as a treatment strategy against HCC.
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38
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Wan M, Zhang FM, Li ZL, Kang PC, Jiang PM, Wang YM, Wang ZD, Zhong XY, Li CL, Wang H, Zhao SY, Cui YF. Identifying survival-associated ceRNA clusters in cholangiocarcinoma. Oncol Rep 2016; 36:1542-50. [PMID: 27432084 DOI: 10.3892/or.2016.4934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 03/17/2016] [Indexed: 11/06/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) represent a novel layer regulations of long non-coding RNAs (lncRNAs) and genes that play important roles in cancer pathogenesis by binding microRNAs (miRNAs). However, the competition mechanism of ceRNAs in cholangiocarcinoma (CHOL) is not fully understood. In this study, we constructed a dysregulated ceRNA competitive network (CCEN) to globally characterize the competing difference between CHOL and normal tissues. Then, we integrated affinity propagation and Kaplan‑Meier (K-M) methods to identify functional clusters associated with survival. A total of 7 key ceRNA clusters were identified. Further functional annotation analyses found that Cluster23 and Cluster32 involved cell based functions, and the loss of ceRNA competitive relations in clusters may contribute to CHOL, by disturbing important biological processes, such as 'Pathway in cancer', MAPK and Neurotrophin signaling pathway. This study provides further insights into understanding the competitive mechanism of ceRNAs in CHOL.
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Affiliation(s)
- Ming Wan
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Fu-Min Zhang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Zheng-Long Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Peng-Cheng Kang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Ping-Ming Jiang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Yi-Min Wang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Zhi-Dong Wang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Xiang-Yu Zhong
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Chun-Long Li
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Hao Wang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Shi-Yong Zhao
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Yun-Fu Cui
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
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39
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Rhodes LV, Martin EC, Segar HC, Miller DFB, Buechlein A, Rusch DB, Nephew KP, Burow ME, Collins-Burow BM. Dual regulation by microRNA-200b-3p and microRNA-200b-5p in the inhibition of epithelial-to-mesenchymal transition in triple-negative breast cancer. Oncotarget 2016; 6:16638-52. [PMID: 26062653 PMCID: PMC4599295 DOI: 10.18632/oncotarget.3184] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/23/2015] [Indexed: 12/31/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) involves loss of an epithelial phenotype and activation of a mesenchymal one. Enhanced expression of genes associated with a mesenchymal transition includes ZEB1/2, TWIST, and FOXC1. miRNAs are known regulators of gene expression and altered miRNA expression is known to enhance EMT in breast cancer. Here we demonstrate that the tumor suppressive miRNA family, miR-200, is not expressed in triple negative breast cancer (TNBC) cell lines and that miR-200b-3p over-expression represses EMT, which is evident through decreased migration and increased CDH1 expression. Despite the loss of migratory capacity following re-expression of miR-200b-3p, no subsequent loss of the conventional miR-200 family targets and EMT markers ZEB1/2 was observed. Next generation RNA-sequencing analysis showed that enhanced expression of pri-miR-200b lead to ectopic expression of both miR-200b-3p and miR-200b-5p with multiple isomiRs expressed for each of these miRNAs. Furthermore, miR-200b-5p was expressed in the receptor positive, epithelial breast cancer cell lines but not in the TNBC (mesenchymal) cell lines. In addition, a compensatory mechanism for miR-200b-3p/200b-5p targeting, where both miRNAs target the RHOGDI pathway leading to non-canonical repression of EMT, was demonstrated. Collectively, these data are the first to demonstrate dual targeting by miR-200b-3p and miR-200b-5p and a previously undescribed role for microRNA processing and strand expression in EMT and TNBC, the most aggressive breast cancer subtype.
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Affiliation(s)
- Lyndsay V Rhodes
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Elizabeth C Martin
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA
| | - H Chris Segar
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA
| | - David F B Miller
- Medical Sciences and Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Bloomington, IN, USA
| | - Aaron Buechlein
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, USA
| | - Douglas B Rusch
- Indiana University Center for Genomics and Bioinformatics, Bloomington, IN, USA
| | - Kenneth P Nephew
- Medical Sciences and Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Bloomington, IN, USA
| | - Matthew E Burow
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA.,Department of Pharmacology, Tulane University, New Orleans, LA, USA
| | - Bridgette M Collins-Burow
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University, New Orleans, LA, USA
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40
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Abstract
The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.
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Affiliation(s)
- Daniel W Thomson
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
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41
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Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression. Int J Genomics 2015; 2015:269127. [PMID: 26114098 PMCID: PMC4465843 DOI: 10.1155/2015/269127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/11/2015] [Indexed: 11/24/2022] Open
Abstract
There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript) length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5′ and 3′ UTRs) between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.
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42
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Sanchez-Mejias A, Tay Y. Competing endogenous RNA networks: tying the essential knots for cancer biology and therapeutics. J Hematol Oncol 2015; 8:30. [PMID: 25888444 PMCID: PMC4381443 DOI: 10.1186/s13045-015-0129-1] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
A recently discovered dimension of post-transcriptional gene regulation involves co-regulatory crosstalk between RNA transcripts, which compete for common pools of microRNA (miRNA) molecules. These competing endogenous RNAs (ceRNAs), or natural miRNA sponges, have an active role in regulating miRNA availability within the cell and form intertwined regulatory networks. Recent reports have implicated diverse RNA species including protein-coding messenger RNAs and non-coding RNAs as ceRNAs in human development and diseases including human cancer. In this review, we discuss the most recent discoveries that implicate natural miRNA decoys in human cancer biology, as well as exciting advances in the study of ceRNA networks and dynamics. The structure and topology of intricate genome-scale ceRNA networks can be predicted computationally, and their dynamic response to fluctuations in ceRNA and miRNA levels can be studied via mathematical modeling. Additionally, the development of new methods to quantitatively determine absolute expression levels of miRNA and ceRNA molecules have expanded the capacity to accurately study the efficiency of ceRNA crosstalk in diverse biological models. These major milestones are of critical importance to identify key components of ceRNA regulatory networks that could aid the development of new approaches to cancer diagnostics and oligonucleotide-based therapeutics.
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Affiliation(s)
- Avencia Sanchez-Mejias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
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43
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Ergun S, Oztuzcu S. Oncocers: ceRNA-mediated cross-talk by sponging miRNAs in oncogenic pathways. Tumour Biol 2015; 36:3129-36. [PMID: 25809705 DOI: 10.1007/s13277-015-3346-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/15/2015] [Indexed: 12/12/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) are RNA transcripts which can communicate with each other by decreasing targeting concentration of micro-RNA (miRNA) with the derepression of other messenger RNAs (mRNAs) having the common miRNA response elements (MREs). Oncocers are ceRNAs taking crucial roles in oncogenic pathways processed in many types of cancer, and this study analyzes oncocer-mediated cross-talk by sponging microRNAs (miRNAs) in these pathways. While doing this, breast, liver, colon, prostate, gastric, lung, endometrium, thyroid and epithelial cancers and melanoma, rhabdomyosarcoma, glioblastoma, acute promyelocytic leukemia, retinoblastoma, and neuroblastoma were analyzed with respect to ceRNA-based carcinogenesis. This study defines, firstly, oncocers in the literature and contains all oncocer-related findings found up to now. Therefore, it will help to increase our comprehension about oncocer-mediated mechanisms. Via this study, a novel perspective would be produced to make clear cancer mechanisms and suggest novel approaches to regulate ceRNA networks via miRNA competition for cancer therapeutics. Graphical Abstract Multiple RNA transcripts have common MREs for the similar miRNA in their 3'-untranslated regions (3'-UTRs). Upregulation of ceRNAs rises the abundance of specific MREs and shifts the miRNA pool distribution, as a result, leading to the increased expression of target mRNA. The depot of genomic mutations and epigenetic alterations changing gene function and expression causes cancers. Herewith, genome-based somatic base-pair mutations, DNA copy number alterations, chromosomal translocation, also transcript fusions, alternative splicing are usually seen in cancer situations. Consequently, such cases causing changed UTR expression in transcripts influence the levels of MRE or present new MREs into the cells. Alterations in MREs of ceRNAs affect the capability of a specific mRNA transcript to attach or titrate miRNAs. As a result, the disturbed ceRNA network can lead to diseases and cancers. As a new term in RNA world, oncocers-the name for ceRNAs taking crucial roles in oncogenic pathways-are processed in many types of cancer, and oncocer-mediated cross-talk are analyzed by sponging miRNAs in these pathways.
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Affiliation(s)
- Sercan Ergun
- Ulubey Vocational Higher School, Ordu University, Ordu, Turkey,
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44
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The 3'UTR of the pseudogene CYP4Z2P promotes tumor angiogenesis in breast cancer by acting as a ceRNA for CYP4Z1. Breast Cancer Res Treat 2015; 150:105-18. [PMID: 25701119 DOI: 10.1007/s10549-015-3298-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/03/2015] [Indexed: 12/31/2022]
Abstract
Pseudogenes are now known to regulate their protein-coding counterparts. Additionally, disturbances of 3'UTRs could increase the risk of cancer susceptibility by acting as modulators of gene expression. The aim of this study was to investigate the roles of the pseudogene CYP4Z2P-3'UTR and functional gene CYP4Z1-3'UTR in breast cancer angiogenesis process. The levels of CYP4Z2P- and CYP4Z1-3'UTR and miRNA of interests were measured in 22 cancerous tissues paired with non-cancerous samples by qRT-PCR. The effects of CYP4Z2P- and CYP4Z1-3'UTR were studied by overexpression and RNA interference approaches in vitro and ex vivo. Insights of the mechanism of competitive endogenous RNAs were gained from bioinformatic analysis, luciferase assays, and western blot. The positive CYP4Z2P/CYP4Z1 interaction and negative interaction between predicted miRNAs and CYP4Z2P or CYP4Z1 were identified via qRT-PCR assay and bivariate correlation analysis. CYP4Z2P- and CYP4Z1-3'UTR share several miRNA-binding sites, including miR-211, miR-125a-3p, miR-197, miR-1226, and miR-204. The CYP4Z2P- and CYP4Z1-3'UTRs arrest the interference caused by of these miRNAs, resulting in increased translation of CYP4Z1. Moreover, ectopic expression of the CYP4Z2P- and CYP4Z1-3'UTRs exhibit tumor angiogenesis-promoting properties in breast cancer collectively by inducing the phosphorylation of ERK1/2 and PI3K/Akt. Co-transfection with Dicer siRNA reversed the CYP4Z2P 3'UTR-mediated changes. Additionally, PI3K or ERK inhibitors reversed CYP4Z2P- and CYP4Z1-3'UTR-mediated changes in VEGF-A expression. Increased CYP4Z2P- and CYP4Z1-3'UTR expression promotes tumor angiogenesis in breast cancer partly via miRNA-dependent activation of PI3K/Akt and ERK1/2. The CYP4Z2P- and CYP4Z1-3'UTRs could thus be used as combinatorial miRNA inhibitors.
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45
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Poliseno L, Pandolfi PP. PTEN ceRNA networks in human cancer. Methods 2015; 77-78:41-50. [PMID: 25644446 DOI: 10.1016/j.ymeth.2015.01.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/19/2015] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
In multiple human cancer types, a close link exists between the expression levels of Phosphatase and Tensin Homolog deleted on chromosome 10 (PTEN) and its oncosuppressive activities. Therefore, an in depth understanding of the molecular mechanisms by which PTEN expression is modulated is crucial in order to achieve a comprehensive knowledge of its biological roles. In recent years, the competition between PTEN mRNA and other RNAs for shared microRNA molecules has emerged as one such mechanism and has brought into focus the coding-independent activities of PTEN and other mRNAs. In this review article, we examine the competing endogenous RNA (ceRNA) partners of PTEN that have been identified so far. We also discuss how PTEN-centered ceRNA networks can contribute to a deeper understanding of PTEN function and tumorigenesis.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori, Pisa, Italy; Institute of Clinical Physiology, CNR, Pisa, Italy.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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46
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Zheng W, Sai W, Yao M, Gu H, Yao Y, Qian Q, Yao D. Silencing clusterin gene transcription on effects of multidrug resistance reversing of human hepatoma HepG2/ADM cells. Tumour Biol 2015. [PMID: 25600802 DOI: 10.1007/s13277-015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abnormal clusterin (CLU) expression is associated with multidrug resistance (MDR) of hepatocellular carcinoma (HCC). In the present study, the CLU expression was analyzed in human hepatoma cells and chemoresistant counterpart HepG2/ADM cells. Compared with L02 cells, the overexpression of cellular CLU was identified in HepG2, HepG2/ADM, SMMC7721, Hep3B ,and PLC cells and relatively lower expression in Bel-7404, SNU-739, and MHCC97H cells. Specific short hairpin RNAs (shRNAs) to silence CLU gene transcription were designed, and the most effective sequences were screened. After the HepG2/ADM cells transfected with shRNA-1, the inhibition of CLU expression was 73.68 % at messenger RNA (mRNA) level by real-time quantitative RT-PCR with obvious enhancement in cell chemosensitivity, increasing apoptosis induced by doxorubicin using fluorescence kit, and Rh-123 retention qualified with flow cytometry. Knockdown CLU also significantly decreased the drug efflux pump activity through the depression of MDR1/P-glycoprotein (q = 11.739, P < 0.001). Moreover, silencing CLU led to downregulation of β-catenin (q = 13.544, P = 0.001), suggesting that downregulation of CLU might be a key point to reverse multidrug resistance of HepG2/ADM cells.
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Affiliation(s)
- Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 West Temple Road, Nantong, 226001, Jiangsu Province, China
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47
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Mione M, Bosserhoff A. MicroRNAs in melanocyte and melanoma biology. Pigment Cell Melanoma Res 2015; 28:340-54. [PMID: 25515738 DOI: 10.1111/pcmr.12346] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/15/2014] [Indexed: 12/18/2022]
Abstract
The importance of microRNAs as key molecular components of cellular processes is now being recognized. Recent reports have shown that microRNAs regulate processes as diverse as protein expression and nuclear functions inside cells and are able to signal extracellularly, delivered via exosomes, to influence cell fate at a distance. The versatility of microRNAs as molecular tools inspires the design of novel strategies to control gene expression, protein stability, DNA repair and chromatin accessibility that may prove very useful for therapeutic approaches due to the extensive manageability of these small molecules. However, we still lack a comprehensive understanding of the microRNA network and its interactions with the other layers of regulatory elements in cellular and extracellular functions. This knowledge may be necessary before we exploit microRNA versatility in therapeutic settings. To identify rules of interactions between microRNAs and other regulatory systems, we begin by reviewing microRNA activities in a single cell type: the melanocyte, from development to disease.
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Affiliation(s)
- Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggestein-Leopoldshafen, Germany
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Shao T, Wu A, Chen J, Chen H, Lu J, Bai J, Li Y, Xu J, Li X. Identification of module biomarkers from the dysregulated ceRNA–ceRNA interaction network in lung adenocarcinoma. MOLECULAR BIOSYSTEMS 2015; 11:3048-58. [DOI: 10.1039/c5mb00364d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The dysregulated ceRNA–ceRNA interaction network in lung adenocarcinoma.
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Affiliation(s)
- Tingting Shao
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Aiwei Wu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Juan Chen
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Hong Chen
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Jianping Lu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Jing Bai
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Juan Xu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Xia Li
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
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Zheng L, Li X, Gu Y, Ma Y, Xi T. Pseudogene CYP4Z2P 3'UTR promotes angiogenesis in breast cancer. Biochem Biophys Res Commun 2014; 453:545-51. [PMID: 25281903 DOI: 10.1016/j.bbrc.2014.09.112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 09/26/2014] [Indexed: 01/22/2023]
Abstract
Pseudogenes have long been marked as "false" genes, which are similar with real genes but have no apparent function. The 3'UTR is well-known to regulate gene expression post-transcriptionally. Our recent evidence, however, indicates novel functional roles of pseudogene CYP4Z2P 3'UTR (Z2P-UTR). We found that ectopic expression of Z2P-UTR in breast cancer cells significantly increased the expression of VEGF-A without affecting cell proliferation in vitro. Meanwhile, conditioned medium (CM) from Z2P-UTR overexpression cells enhanced proliferation, migration and tube formation of HUVEC, and promoted angiogenesis in ex vivo models. Also, CM increased the expression of VEGFR2 in HUVEC. Our data suggest that Z2P-UTR can promote breast cancer angiogenesis partly via paracrine pathway of VEGF-A/VEGFR2.
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Affiliation(s)
- Lufeng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiaoman Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yi Gu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yihua Ma
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, People's Republic of China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
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50
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Xia T, Liao Q, Jiang X, Shao Y, Xiao B, Xi Y, Guo J. Long noncoding RNA associated-competing endogenous RNAs in gastric cancer. Sci Rep 2014; 4:6088. [PMID: 25124853 PMCID: PMC4133709 DOI: 10.1038/srep06088] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/30/2014] [Indexed: 12/14/2022] Open
Abstract
Some long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNAs (ceRNAs). However, the roles of lncRNA associated-ceRNAs in oncogenesis are not fully understood. Here, based on lncRNA microarray data of gastric cancer, bioinformatic algorithm miRcode and microRNA (miRNA) targets database TarBase, we first constructed an lncRNA-miRNA-mRNA network. Then, we confirmed it by data of six types of other cancer including head and neck squamous cell carcinoma, prostate cancer, papillary thyroid carcinoma, pituitary gonadotrope tumors, ovarian cancer, and chronic lymphocytic leukemia. The results showed a clear cancer-associated ceRNA network. Eight lncRNAs (AC009499.1, GACAT1, GACAT3, H19, LINC00152, AP000288.2, FER1L4, and RP4-620F22.3) and nine miRNAs (miR-18a-5p, miR-18b-5p, miR-19a-3p, miR-20b-5p, miR-106a-5p, miR-106b-5p, miR-31-5p, miR-139-5p, and miR-195-5p) were involved. For instance, through its miRNA response elements (MREs) to compete for miR-106a-5p, lncRNA-FER1L4 regulates the expression of PTEN, RB1, RUNX1, VEGFA, CDKN1A, E2F1, HIPK3, IL-10, and PAK7. Furthermore, cellular experimental results indicated that FER1L4-small interfering RNA (siRNA) simultaneously suppressed FER1L4 and RB1 mRNA level. These results suggest that lncRNAs harbor MREs and play important roles in post-transcriptional regulation in cancer.
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Affiliation(s)
- Tian Xia
- 1] Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China [2]
| | - Qi Liao
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Xiaoming Jiang
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Yongfu Shao
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Bingxiu Xiao
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Yang Xi
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
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