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Mu Z, Zhang X, Liang D, Fang J, Chen G, Guo W, Sun D, Sun Y, Kai Z, Huang L, Liang J, Lin Y. Risk stratification for radioactive iodine refractoriness using molecular alterations in distant metastatic differentiated thyroid cancer. Chin J Cancer Res 2024; 36:25-35. [PMID: 38455372 PMCID: PMC10915639 DOI: 10.21147/j.issn.1000-9604.2024.01.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024] Open
Abstract
Objective Patients with radioactive iodine-refractory differentiated thyroid cancer (RAIR-DTC) are often diagnosed with delay and constrained to limited treatment options. The correlation between RAI refractoriness and the underlying genetic characteristics has not been extensively studied. Methods Adult patients with distant metastatic DTC were enrolled and assigned to undergo next-generation sequencing of a customized 26-gene panel (ThyroLead). Patients were classified into RAIR-DTC or non-RAIR groups to determine the differences in clinicopathological and molecular characteristics. Molecular risk stratification (MRS) was constructed based on the association between molecular alterations identified and RAI refractoriness, and the results were classified as high, intermediate or low MRS. Results A total of 220 patients with distant metastases were included, 63.2% of whom were identified as RAIR-DTC. Genetic alterations were identified in 90% of all the patients, with BRAF (59.7% vs. 17.3%), TERT promoter (43.9% vs. 7.4%), and TP53 mutations (11.5% vs. 3.7%) being more prevalent in the RAIR-DTC group than in the non-RAIR group, except for RET fusions (15.8% vs. 39.5%), which had the opposite pattern. BRAF and TERT promoter are independent predictors of RAIR-DTC, accounting for 67.6% of patients with RAIR-DTC. MRS was strongly associated with RAI refractoriness (P<0.001), with an odds ratio (OR) of high to low MRS of 7.52 [95% confidence interval (95% CI), 3.96-14.28; P<0.001] and an OR of intermediate to low MRS of 3.20 (95% CI, 1.01-10.14; P=0.041). Conclusions Molecular alterations were associated with RAI refractoriness, with BRAF and TERT promoter mutations being the predominant contributors, followed by TP53 and DICER1 mutations. MRS might serve as a valuable tool for both prognosticating clinical outcomes and directing precision-based therapeutic interventions.
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Affiliation(s)
- Zhuanzhuan Mu
- Department of Nuclear Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & PUMC, Beijing 100730, China
- Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine, Beijing 100730, China
| | - Xin Zhang
- Department of Nuclear Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & PUMC, Beijing 100730, China
- Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine, Beijing 100730, China
| | - Dongquan Liang
- Pepperdine University Graduate School of Education and Psychology, Los Angeles 90045, USA
| | - Jugao Fang
- Department of Head and Neck Surgery, Affiliated Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Ge Chen
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & PUMC, Beijing 100730, China
| | - Wenting Guo
- Central Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & PUMC, Beijing 100730, China
| | - Di Sun
- Department of Nuclear Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & PUMC, Beijing 100730, China
- Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine, Beijing 100730, China
| | - Yuqing Sun
- Department of Nuclear Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & PUMC, Beijing 100730, China
- Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine, Beijing 100730, China
| | - Zhentian Kai
- Department of Bioinformatics, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd, Shanghai 201321, China
| | - Lisha Huang
- Department of Medicine, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd, Shanghai 201321, China
| | - Jun Liang
- Department of Oncology, Peking University International Hospital, Beijing 102206, China
| | - Yansong Lin
- Department of Nuclear Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College (PUMC) Hospital, Chinese Academy of Medical Sciences & PUMC, Beijing 100730, China
- Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine, Beijing 100730, China
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Arancio W, Sciaraffa N, Coronnello C. MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome. Database (Oxford) 2023; 2023:7146264. [PMID: 37114805 PMCID: PMC10141451 DOI: 10.1093/database/baad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 04/29/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs) that play a role in many regulatory pathways in eukaryotes. They usually exert their functions by binding mature messenger RNAs. The prediction of the binding targets of the endogenous miRNAs is crucial to unravel the processes they are involved in. In this work, we performed an extensive miRNA binding sites (MBS) prediction over all the annotated transcript sequences and made them available through an UCSC track. MBS annotation track allows to study and visualize the human miRNA binding sites transcriptome-wide in a genome browser, together with any other available information the user is interested in. In the creation of the database that underlies the MBS track, three consolidated algorithms of miRNA binding prediction have been used: PITA, miRanda and TargetScan, and information about the binding sites predicted by all of them has been collected. MBS track displays high-confident miRNA binding sites for the whole length of each human transcript, both coding and non-coding ones. Each annotation can redirect to a web page with the details of the miRNA binding and the involved transcripts. MBS can be easily applied to retrieve specific information such as the effects of alternative splicing on miRNA binding or when a specific miRNA binds an exon-exon junction in the mature RNA. Overall, MBS will be of great help for studying and visualizing, in a user-friendly mode, the predicted miRNA binding sites on all the transcripts arising from a gene or a region of interest. Database URL https://datasharingada.fondazionerimed.com:8080/MBS.
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Affiliation(s)
- Walter Arancio
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), via Ugo la Malfa, 153, Palermo 90133, Italy
| | - Nicolina Sciaraffa
- Advanced Data Analysis Group, Ri.MED Foundation, via Bandiera, 11, Palermo 90133, Italy
| | - Claudia Coronnello
- Advanced Data Analysis Group, Ri.MED Foundation, via Bandiera, 11, Palermo 90133, Italy
- National Center for Gene Therapy and Drugs based on RNA Technology, via Bandiera, 11, Palermo 90133, Italy
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An extended catalogue of ncRNAs in Streptomyces coelicolor reporting abundant tmRNA, RNase-P RNA and RNA fragments derived from pre-ribosomal RNA leader sequences. Arch Microbiol 2022; 204:582. [PMID: 36042049 DOI: 10.1007/s00203-022-03203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
Streptomyces coelicolor is a model organism for studying streptomycetes. This genus possesses relevant medical and economical roles, because it produces many biologically active metabolites of pharmaceutical interest, including the majority of commercialized antibiotics. In this bioinformatic study, the transcriptome of S. coelicolor has been analyzed to identify novel RNA species and quantify the expression of both annotated and novel transcripts in solid and liquid growth medium cultures at different times. The major characteristics disclosed in this study are: (i) the diffuse antisense transcription; (ii) the great abundance of transfer-messenger RNAs (tmRNA); (iii) the abundance of rnpB transcripts, paramount for the RNase-P complex; and (iv) the presence of abundant fragments derived from pre-ribosomal RNA leader sequences of unknown biological function. Overall, this study extends the catalogue of ncRNAs in S. coelicolor and suggests an important role of non-coding transcription in the regulation of biologically active molecule production.
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Repetitive Sequence Transcription in Breast Cancer. Cells 2022; 11:cells11162522. [PMID: 36010599 PMCID: PMC9406339 DOI: 10.3390/cells11162522] [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: 07/20/2022] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Repetitive sequences represent about half of the human genome. They are actively transcribed and play a role during development and in epigenetic regulation. The altered activity of repetitive sequences can lead to genomic instability and they can contribute to the establishment or the progression of degenerative diseases and cancer transformation. In this work, we analyzed the expression profiles of DNA repetitive sequences in the breast cancer specimens of the HMUCC cohort. Satellite expression is generally upregulated in breast cancers, with specific families upregulated per histotype: in HER2-enriched cancers, they are the human satellite II (HSATII), in luminal A and B, they are part of the ALR family and in triple-negative, they are part of SAR and GSAT families, together with a perturbation in the transcription from endogenous retroviruses and their LTR sequences. We report that the background expression of repetitive sequences in healthy tissues of cancer patients differs from the tissues of non-cancerous controls. To conclude, peculiar patterns of expression of repetitive sequences are reported in each specimen, especially in the case of transcripts arising from satellite repeats.
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5
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Ergun S, Gunes S, Hekim N, Esteves SC. In silico analysis of microRNA genes in azoospermia factor Y-chromosome microdeletions. Int Urol Nephrol 2022; 54:773-780. [DOI: 10.1007/s11255-022-03133-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 12/01/2022]
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Abstract
Viral RNAs can perturb the miRNA regulatory network, competing with host RNAs as part of their infective process. An in silico competing endogenous RNA (ceRNA) analysis has been carried on SARS-CoV-2. The results suggest that, in humans, the decrease of microRNA activity caused by viral RNAs can lead to a perturbation of vesicle trafficking and the inflammatory response, in particular by enhancing KLF10 activity. The results suggest also that, during the study of the mechanics of viral infections, it could be of general interest to investigate the competition of viral RNA with cellular transcripts for shared microRNAs.
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Affiliation(s)
- Walter Arancio
- University of Palermo, Viale delle Scienze, 90127, Palermo, Italy. .,Scuola "Borgese XXVII Maggio", Piazza Contardo Ferrini, 13, 90146, Palermo, Italy. .,Advanced data analysis group, Fondazione Ri.MED, Via Bandiera 11, 90133, Palermo, Italy.
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Yan L, Li K, Feng Z, Zhang Y, Han R, Ma J, Zhang J, Wu X, Liu H, Jiang Y, Zhang Y, Zhu Y. lncRNA CERS6-AS1 as ceRNA promote cell proliferation of breast cancer by sponging miR-125a-5p to upregulate BAP1 expression. Mol Carcinog 2020; 59:1199-1208. [PMID: 32808708 DOI: 10.1002/mc.23249] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 12/21/2022]
Abstract
Long noncoding RNAs (lncRNAs) can act as oncogene and tumor suppressor genes in many types of cancers including breast cancer (BC). Our previous study has indicated microRNA (miR)-125a-5p was downregulated and function as a tumor suppressor in BC. However, its upstream regulation mechanism is still unclear. In this study, we used bioinformatics algorithms, RNA pulldown assay, and dual-luciferase reports assay to predict and confirm lncRNA CERS6-AS1 interacted with miR-125a-5p. Then we found CERS6-AS1 was upregulated in BC tissues. Experimental results of tumor growth in nude mice show that CERS6-AS1 promotes tumor growth. Furthermore, CERS6-AS1 regulated BC susceptibility gene 1-associated protein 1 (BAP1) expression via sponging miR-125a-5p via Western blot analysis and quantitative polymerase chain reaction arrays. Finally, we showed that miR-125a-5p had opposing effects to those of CERS6-AS1 on BC cells, demonstrating that CERS6-AS1 may promote cell proliferation and inhibit cell apoptosis via sponging miR-125a-5p. Our results indicated CERS6-AS1 promote BC cell proliferation and inhibit cell apoptosis via sponging miR-125a-5p to upregulate BAP1 expression.
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Affiliation(s)
- Liang Yan
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Kai Li
- Department of Clinical Diagnostics, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui, China
| | - Zunyong Feng
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yizongheng Zhang
- Department of Clinical Medicine, The First College of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Renrui Han
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Jinzhu Ma
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Jieling Zhang
- Department of Clinical Diagnostics, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui, China
| | - Xu Wu
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Haijun Liu
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yuxin Jiang
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yao Zhang
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yiping Zhu
- Department of Clinical Diagnostics, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui, China
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Seyed Abutorabi E, Irani S, Yaghmaie M, Ghaffari SH. Abemaciclib (CDK4/6 Inhibitor) Blockade Induces Cytotoxicity in Human Anaplastic Thyroid Carcinoma Cells. Rep Biochem Mol Biol 2020; 8:438-445. [PMID: 32582803 PMCID: PMC7275834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 08/09/2019] [Indexed: 06/11/2023]
Abstract
BACKGROUND Thyroid cancer is the most prevalent endocrine malignancies globally. Anaplastic thyroid carcinoma (ATC) accounts for 1-3% of all Thyroid cancer. The evidence showed that ATC is a highly invasive solid tumor with poor prognosis. Despite conventional chemotherapy treatments, a considerable number of patients show developing resistance to therapeutic agents and tumor relapse. The aim of this study was the investigation anti-tumor effect of Abemaciclib (novel targeted cancer therapy drug) on Anaplastic Thyroid carcinoma SW1736 and C643 cell lines. METHODS SW1736 and C643 cell lines were treated by desire concentrations of Abemaciclib (0, 1, 2.5, 5, 10, and 20 μM) and cell viability was measured by MTT assay. Also, Anoikis resistance assay was conducted for non-adherent the cells in the exposure of Abemaciclib. The gene expression of apoptotic and anti-apoptotic genes was conducted by quantitative Real-time PCR. RESULTS Abemaciclib at the concentration of 10 and 20 μM effectively reduced cell proliferation and growth of the ATC cells compared to the control (p=0.000). Furthermore, we showed that 10 and 20 μM doses of the Abemaciclib inhibited the non-adherent ATC cells which were resistant to Anoikis death significantly (p=0.001). Moreover, we demonstrated this targeted therapy significantly reduced anti-apoptotic gene expression levels (BCL2 and CMYC) (p<0.05) and increased apoptotic gene expressions such as P21 and BAX (p<0.05). CONCLUSION Our data suggested that Abemaciclib can be utilized as a novel therapeutic agent in ATC cancer. Further in vivo and in vitro investigations are needed to evaluate molecular and clinical mechanisms of Abemaciclib.
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Affiliation(s)
- Elaheh Seyed Abutorabi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Marjan Yaghmaie
- Hematology/Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Seyed Hamid Ghaffari
- Hematology/Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Zhao Y, Wang H, Wu C, Yan M, Wu H, Wang J, Yang X, Shao Q. Construction and investigation of lncRNA-associated ceRNA regulatory network in papillary thyroid cancer. Oncol Rep 2018; 39:1197-1206. [PMID: 29328463 PMCID: PMC5802034 DOI: 10.3892/or.2018.6207] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/20/2017] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence has experimentally proved the competitive endogenous RNA (ceRNA) hypothesis that long non-coding RNA (lncRNA) can affect the expression of RNA targets by competitively combining microRNA (miRNA) via miRNA response elements. However, an extensive ceRNA network of thyroid carcinoma in a large cohort has not been evaluated. We analyzed the RNAseq and miRNAseq data of 348 cases of primary papillary thyroid cancer (PTC) patients with clinical information downloaded from The Cancer Genome Atlas (TCGA) project to search for potential biomarkers or therapeutic targets. A computational approach was applied to build an lncRNA-miRNA-mRNA regulatory network of PTC. In total, 780 lncRNAs were detected as collectively dysregulated lncRNAs in all 3 PTC variants compared with normal tissues (fold change >2 and false discovery rate <0.05). The interactions among 45 lncRNAs, 13 miRNAs and 86 mRNAs constituted a ceRNA network of PTC. Nine out of the 45 aberrantly expressed lncRNAs were related to the clinical features of PTC patients. However, the expression levels of 3 lncRNAs (LINC00284, RBMS3-AS1 and ZFX-AS1) were identified to be tightly correlated with the patients overall survival (log-rank, P<0.05). The present study identified a list of specific lncRNAs associated with PTC progression and prognosis. This complex ceRNA interaction network in PTC may provide guidance for better understanding the molecular mechanisms underlying PTC.
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Affiliation(s)
- Yangjing Zhao
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Hui Wang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Chengjiang Wu
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Meina Yan
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Haojie Wu
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Jingzhe Wang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Xinxin Yang
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Qixiang Shao
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
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Johnson TS, Li S, Kho JR, Huang K, Zhang Y. Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2018; 23:536-547. [PMID: 29218912 PMCID: PMC5744670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pseudogenes are fossil relatives of genes. Pseudogenes have long been thought of as "junk DNAs", since they do not code proteins in normal tissues. Although most of the human pseudogenes do not have noticeable functions, ∼20% of them exhibit transcriptional activity. There has been evidence showing that some pseudogenes adopted functions as lncRNAs and work as regulators of gene expression. Furthermore, pseudogenes can even be "reactivated" in some conditions, such as cancer initiation. Some pseudogenes are transcribed in specific cancer types, and some are even translated into proteins as observed in several cancer cell lines. All the above have shown that pseudogenes could have functional roles or potentials in the genome. Evaluating the relationships between pseudogenes and their gene counterparts could help us reveal the evolutionary path of pseudogenes and associate pseudogenes with functional potentials. It also provides an insight into the regulatory networks involving pseudogenes with transcriptional and even translational activities.In this study, we develop a novel approach integrating graph analysis, sequence alignment and functional analysis to evaluate pseudogene-gene relationships, and apply it to human gene homologs and pseudogenes. We generated a comprehensive set of 445 pseudogene-gene (PGG) families from the original 3,281 gene families (13.56%). Of these 438 (98.4% PGG, 13.3% total) were non-trivial (containing more than one pseudogene). Each PGG family contains multiple genes and pseudogenes with high sequence similarity. For each family, we generate a sequence alignment network and phylogenetic trees recapitulating the evolutionary paths. We find evidence supporting the evolution history of olfactory family (both genes and pseudogenes) in human, which also supports the validity of our analysis method. Next, we evaluate these networks in respect to the gene ontology from which we identify functions enriched in these pseudogene-gene families and infer functional impact of pseudogenes involved in the networks. This demonstrates the application of our PGG network database in the study of pseudogene function in disease context.
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Affiliation(s)
- Travis S Johnson
- Dept. Biomedical Informatics, Ohio State University, 5000 HITS, 410 W. 10th St. Indianapolis, Indiana, 46202, USA,
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11
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Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach. Sci Rep 2017; 7:7755. [PMID: 28798471 PMCID: PMC5552881 DOI: 10.1038/s41598-017-08209-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022] Open
Abstract
Regulation by microRNAs (miRNAs) and modulation of miRNA activity are critical components of diverse cellular processes. Recent research has shown that miRNA-based regulation of the tumor suppressor gene PTEN can be modulated by the expression of other miRNA targets acting as competing endogenous RNAs (ceRNAs). However, the key sequence-based features enabling a transcript to act as an effective ceRNA are not well understood and a quantitative model associating statistical significance to such features is currently lacking. To identify and assess features characterizing target recognition by PTEN-regulating miRNAs, we analyze multiple datasets from PAR-CLIP experiments in conjunction with RNA-Seq data. We consider a set of miRNAs known to regulate PTEN and identify high-confidence binding sites for these miRNAs on the 3′ UTR of protein coding genes. Based on the number and spatial distribution of these binding sites, we calculate a set of probabilistic features that are used to make predictions for novel ceRNAs of PTEN. Using a series of experiments in human prostate cancer cell lines, we validate the highest ranking prediction (TNRC6B) as a ceRNA of PTEN. The approach developed can be applied to map ceRNA networks of critical cellular regulators and to develop novel insights into crosstalk between different pathways involved in cancer.
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Abstract
MicroRNA (miRNA) are negative regulators of gene expression and subsequent protein production. This method of action translates into regulatory control over cellular processes, including development, signaling, metabolism, and apoptosis. A broad range of miRNA are shown to have abnormal expressions in thyroid cancers which could explain the pathology of tumor oncogenesis and disease progression. A review is conducted of the current research on miRNA dysregulation in thyroid cancers, including papillary thyroid carcinoma (PTC), follicular thyroid carcinoma (FTC), anaplastic thyroid cancer (ATC), and medullary thyroid carcinoma (MTC). Dysregulated miRNA and their associated regulatory pathways are identified and their oncogenic and pathological significance are discussed.
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MESH Headings
- Adenocarcinoma, Follicular/genetics
- Adenocarcinoma, Follicular/pathology
- Animals
- Carcinoma, Neuroendocrine/genetics
- Carcinoma, Neuroendocrine/pathology
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/pathology
- Gene Expression Regulation, Neoplastic
- Humans
- MicroRNAs/genetics
- Thyroid Cancer, Papillary
- Thyroid Carcinoma, Anaplastic/genetics
- Thyroid Carcinoma, Anaplastic/pathology
- Thyroid Gland/metabolism
- Thyroid Gland/pathology
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/pathology
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Affiliation(s)
- Gaohong Zhu
- Department of Nuclear Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China.
| | - Lijun Xie
- Department of Nuclear Medicine, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Daniel Miller
- School of Computing, University of South Alabama, Mobile, AL, 36688, USA
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Xu J, Feng L, Han Z, Li Y, Wu A, Shao T, Ding N, Li L, Deng W, Di X, Wang J, Zhang L, Li X, Zhang K, Cheng S. Extensive ceRNA-ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues. Nucleic Acids Res 2016; 44:9438-9451. [PMID: 27365046 PMCID: PMC5100587 DOI: 10.1093/nar/gkw587] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/19/2016] [Indexed: 12/14/2022] Open
Abstract
Crosstalk between RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in development. In this study, we analyzed time series expression data for coding genes and long non-coding RNAs (lncRNAs) to identify thousands of interactions among competitive endogenous RNAs (ceRNAs) in four rhesus tissues. The ceRNAs exhibited dynamic expression and regulatory patterns during each tissue development process, which suggests that ceRNAs might work synergistically during different developmental stages or tissues to control specific functions. In addition, lncRNAs exhibit higher specificity as ceRNAs than coding-genes and their functions were predicted based on their competitive coding-gene partners to discover their important developmental roles. In addition to the specificity of tissue development, functional analyses demonstrated that the combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in multiple tissues, especially transcription-related functions where competitive interactions. Moreover, ceRNA interactions could sequentially and/or synergistically mediate the crosstalk among different signaling pathways during brain development. Analyzing ceRNA interactions during the development of multiple tissues will provideinsights in the regulation of normal development and the dysregulation of key mechanisms during pathogenesis.
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Affiliation(s)
- Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Zujing Han
- BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Aiwei Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Tingting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Lili Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Wei Deng
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 10021, China
| | - Xuebing Di
- State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jian Wang
- BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Lianfeng Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 10021, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Shujun Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin 150081, China .,State Key Laboratory of Molecular Oncology, Department of Aetiology and Carcinogenesis, Cancer Hospital, Peking UnionMedical College and Chinese Academy of Medical Sciences, Beijing 100021, China
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A ceRNA approach may unveil unexpected contributors to deletion syndromes, the model of 5q- syndrome. Oncoscience 2015; 2:872-9. [PMID: 26682279 PMCID: PMC4671954 DOI: 10.18632/oncoscience.261] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/09/2015] [Indexed: 02/06/2023] Open
Abstract
In genomic deletions, gene haploinsufficiency might directly configure a specific disease phenotype. Nevertheless, in some cases no functional association can be identified between haploinsufficient genes and the deletion-associated phenotype. Transcripts can act as microRNA sponges. The reduction of transcripts from the hemizygous region may increase the availability of specific microRNAs, which in turn may exert in-trans regulation of target genes outside the deleted region, eventually contributing to the phenotype. Here we prospect a competing endogenous RNA (ceRNA) approach for the identification of candidate genes target of epigenetic regulation in deletion syndromes. As a model, we analyzed the 5q- myelodysplastic syndrome. Genes in haploinsufficiency within the common 5q deleted region in CD34+ blasts were identified in silico. Using the miRWalk 2.0 platform, we predicted microRNAs whose availability, and thus activity, could be enhanced by the deletion, and performed a genomewide analysis of the genes outside the 5q deleted region that could be targeted by the predicted miRNAs. The analysis pointed to two genes with altered expression in 5q- transcriptome, which have never been related with 5q- before. The prospected approach allows investigating the global transcriptional effect of genomic deletions, possibly prompting discovery of unsuspected contributors in the deletion-associated phenotype. Moreover, it may help in functionally characterizing previously reported unexpected interactions.
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