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Variation in the co-expression profile highlights a loss of miRNA-mRNA regulation in multiple cancer types. Noncoding RNA Res 2022; 7:98-105. [PMID: 35387279 PMCID: PMC8958468 DOI: 10.1016/j.ncrna.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/01/2023] Open
Abstract
Recent research provides insight into the ability of miRNA to regulate various pathways in several cancer types. Despite their involvement in the regulation of the mRNA via targeting the 3′UTR, there are relatively few studies examining the changes in these regulatory mechanisms specific to single cancer types or shared between different cancer types. We analyzed samples where both miRNA and mRNA expression had been measured and performed a thorough correlation analysis on 7494 experimentally validated human miRNA-mRNA target-gene pairs in both healthy and tumoral samples. We show how more than 90% of these miRNA-mRNA interactions show a loss of regulation in the tumoral samples compared with their healthy counterparts. As expected, we found shared miRNA-mRNA dysregulated pairs among different tumors of the same tissue. However, anatomically different cancers also share multiple dysregulated interactions, suggesting that some cancer-related mechanisms are not tumor-specific. 2865 unique miRNA-mRNA pairs were identified across 13 cancer types, ≈ 40% of these pairs showed a loss of correlation in the tumoral samples in at least 2 out of the 13 analyzed cancers. Specifically, miR-200 family, miR-155 and miR-1 were identified, based on the computational analysis described below, as the miRNAs that potentially lose the highest number of interactions across different samples (only literature-based interactions were used for this analysis). Moreover, the miR-34a/ALDH2 and miR-9/MTHFD2 pairs show a switch in their correlation between healthy and tumor kidney samples suggesting a possible change in the regulation exerted by the miRNAs. Interestingly, the expression of these mRNAs is also associated with the overall survival. The disruption of miRNA regulation on its target, therefore, suggests the possible involvement of these pairs in cell malignant functions. The analysis reported here shows how the regulation of miRNA-mRNA interactions strongly differs between healthy and tumoral cells, based on the strong correlation variation between miRNA and its target that we obtained by analyzing the expression data of healthy and tumor tissue in highly reliable miRNA-target pairs. Finally, a go term enrichment analysis shows that the critical pairs identified are involved in cellular adhesion, proliferation, and migration.
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Xiao Q, Luo J, Liang C, Li G, Cai J, Ding P, Liu Y. Identifying lncRNA and mRNA Co-Expression Modules from Matched Expression Data in Ovarian Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:623-634. [PMID: 30106686 DOI: 10.1109/tcbb.2018.2864129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been shown to be involved in multiple biological processes and play critical roles in tumorigenesis. Numerous lncRNAs have been discovered in diverse species, but the functions of most lncRNAs still remain unclear. Meanwhile, their expression patterns and regulation mechanisms are also far from being fully understood. With the advances of high-throughput technologies, the increasing availability of genomic data creates opportunities for deciphering the molecular mechanism and underlying pathogenesis of human diseases. Here, we develop an integrative framework called JONMF to identify lncRNA-mRNA co-expression modules based on the sample-matched lncRNA and mRNA expression profiles. We formulate the module detection task as an optimization problem with joint orthogonal non-negative matrix factorization that could effectively prevent multicollinearity and produce a good modularity interpretation. The constructed lncRNA-mRNA co-expression network and the gene-gene interaction network are used as the network-regularized constraints to improve the module accuracy, while the sparsity constraints are simultaneously utilized to achieve modular sparse solutions. We applied JONMF to human ovarian cancer dataset and the experiment results demonstrate that the proposed method can effectively discover biologically functional co-expression modules, which may provide insights into the function of lncRNAs and molecular mechanism of human diseases.
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Xiao Q, Luo J, Dai J. Computational Prediction of Human Disease- Associated circRNAs Based on Manifold Regularization Learning Framework. IEEE J Biomed Health Inform 2019; 23:2661-2669. [DOI: 10.1109/jbhi.2019.2891779] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Defoort J, Van de Peer Y, Vermeirssen V. Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. Nucleic Acids Res 2019; 46:6480-6503. [PMID: 29873777 PMCID: PMC6061849 DOI: 10.1093/nar/gky468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/14/2018] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein–protein, genetic and homologous interactions, and directed protein–DNA, regulatory and miRNA–mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similar modules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.
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Affiliation(s)
- Jonas Defoort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Vanessa Vermeirssen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
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Xiao Q, Luo J, Liang C, Cai J, Li G, Cao B. CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer. BMC Bioinformatics 2019; 20:67. [PMID: 30732558 PMCID: PMC6367773 DOI: 10.1186/s12859-019-2654-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/24/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Non-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs (miRNAs) and indirectly regulate miRNA targets through competing interactions. Therefore, uncovering the competing endogenous RNA (ceRNA) regulatory mechanism of lncRNAs, miRNAs and mRNAs in post-transcriptional level will aid in deciphering the underlying pathogenesis of human polygenic diseases and may unveil new diagnostic and therapeutic opportunities. However, the functional roles of vast majority of cancer specific ncRNAs and their combinational regulation patterns are still insufficiently understood. RESULTS Here we develop an integrative framework called CeModule to discover lncRNA, miRNA and mRNA-associated regulatory modules. We fully utilize the matched expression profiles of lncRNAs, miRNAs and mRNAs and establish a model based on joint orthogonality non-negative matrix factorization for identifying modules. Meanwhile, we impose the experimentally verified miRNA-lncRNA interactions, the validated miRNA-mRNA interactions and the weighted gene-gene network into this framework to improve the module accuracy through the network-based penalties. The sparse regularizations are also used to help this model obtain modular sparse solutions. Finally, an iterative multiplicative updating algorithm is adopted to solve the optimization problem. CONCLUSIONS We applied CeModule to two cancer datasets including ovarian cancer (OV) and uterine corpus endometrial carcinoma (UCEC) obtained from TCGA. The modular analysis indicated that the identified modules involving lncRNAs, miRNAs and mRNAs are significantly associated and functionally enriched in cancer-related biological processes and pathways, which may provide new insights into the complex regulatory mechanism of human diseases at the system level.
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Affiliation(s)
- Qiu Xiao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, Hunan Normal University, Changsha, 410081, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
| | - Cheng Liang
- College of Information Science and Engineering, Shandong Normal University, Jinan, 250000, China
| | - Jie Cai
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Guanghui Li
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Buwen Cao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
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Li X, Yu X, He Y, Meng Y, Liang J, Huang L, Du H, Wang X, Liu W. Integrated Analysis of MicroRNA (miRNA) and mRNA Profiles Reveals Reduced Correlation between MicroRNA and Target Gene in Cancer. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1972606. [PMID: 30627543 PMCID: PMC6304515 DOI: 10.1155/2018/1972606] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/10/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Accumulating evidences demonstrated that microRNA-target gene pairs were closely related to tumorigenesis and development. However, the correlation between miRNA and target gene was insufficiently understood, especially its changes between tumor and normal tissues. OBJECTIVES The aim of this study was to evaluate the changes of correlation of miRNAs-target pairs between normal and tumor. MATERIALS AND METHODS 5680 mRNA and 5740 miRNA expression profiles of 11 major human cancers were downloaded from the Cancer Genome Atlas (TCGA). The 11 cancer types were bladder urothelial carcinoma, breast invasive carcinoma, head and neck squamous cell carcinoma, kidney chromophobe, kidney renal clear cell carcinoma, kidney renal papillary cell carcinoma, liver hepatocellular carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, stomach adenocarcinoma, and thyroid carcinoma. For each cancer type, we firstly obtained differentially expressed miRNAs (DEMs) and genes (DEGs) in tumor and then acquired critical miRNA-target gene pairs by combining DEMs, DEGs and two experimentally validated miRNA-target interaction databases, miRTarBase and miRecords. We collected samples with both miRNA and mRNA expression values and performed a correlation analysis by Pearson method for miRNA-target pairs in normal and tumor, respectively. RESULTS We totally got 4743 critical miRNA-target pairs across 11 cancer types, and 4572 of them showed weaker correlation in tumor than in normal. The average correlation coefficients of miRNA-target pairs were different greatly between normal (-0.38 ~ -0.61) and tumor (-0.04 ~ -0.26) for 11 cancer type. The pan-cancer network, which consisted of 108 edges connecting 35 miRNAs and 89 target genes, showed the interactions of pairs appeared in multicancers. CONCLUSIONS This comprehensive analysis revealed that correlation between miRNAs and target genes was greatly reduced in tumor and these critical pairs we got were involved in cellular adhesion, proliferation, and migration. Our research could provide opportunities for investigating cancer molecular regulatory mechanism and seeking therapeutic targets.
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Affiliation(s)
- Xingsong Li
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Xiaokang Yu
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Yuting He
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Yuhuan Meng
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Jinsheng Liang
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Hongli Du
- School of Biology and Biological Engineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Xueping Wang
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanli Liu
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
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Chen J, Zhang K, Song H, Wang R, Chu X, Chen L. Long noncoding RNA CCAT1 acts as an oncogene and promotes chemoresistance in docetaxel-resistant lung adenocarcinoma cells. Oncotarget 2018; 7:62474-62489. [PMID: 27566568 PMCID: PMC5308740 DOI: 10.18632/oncotarget.11518] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 08/11/2016] [Indexed: 01/17/2023] Open
Abstract
Chemoresistance remains one of the major obstacles in clinical treatment of lung adenocarcinoma (LAD). Indeed, docetaxel-resistant LAD cells present chemoresistance and epithelial-to-mesenchymal transition phenotypes. Long non-coding RNAs (lncRNAs) are known to promote tumorigenesis in many cancer types. Here, we showed that the lncRNA colon cancer-associated transcript-1 (CCAT1) was upregulated in docetaxel-resistant LAD cells. Furthermore, downregulation of CCAT1 decreased chemoresistance, inhibited proliferation, enhanced apoptosis and reversed the epithelial-to-mesenchymal transition phenotype of docetaxel-resistant LAD cells. We also found that the oncogenic function of CCAT1 in docetaxel-resistant LAD cells depended on the sponging of let-7c. In turn, the sponging of let-7c by CCAT1 released Bcl-xl (a let-7c target), thereby promoting the acquisition of chemoresistance and epithelial-to-mesenchymal transition phenotypes in docetaxel-resistant LAD cells. Our data reveal a novel pathway underlying chemoresistance and the epithelial-to-mesenchymal transition in docetaxel-resistant LAD cells.
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Affiliation(s)
- Jing Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Kai Zhang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Haizhu Song
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Rui Wang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
| | - Longbang Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu, China
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MicroRNAs as regulators and mediators of forkhead box transcription factors function in human cancers. Oncotarget 2017; 8:12433-12450. [PMID: 27999212 PMCID: PMC5355356 DOI: 10.18632/oncotarget.14015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/07/2016] [Indexed: 02/07/2023] Open
Abstract
Evidence has shown that microRNAs are widely implicated as indispensable components of tumor suppressive and oncogenic pathways in human cancers. Thus, identification of microRNA targets and their relevant pathways will contribute to the development of microRNA-based therapeutics. The forkhead box transcription factors regulate numerous processes including cell cycle progression, metabolism, metastasis and angiogenesis, thereby facilitating tumor initiation and progression. A complex network of protein and non-coding RNAs mediates the expression and activity of forkhead box transcription factors. In this review, we summarize the current knowledge and concepts concerning the involvement of microRNAs and forkhead box transcription factors and describe the roles of microRNAs-forkhead box axis in various disease states including tumor initiation and progression. Additionally, we describe some of the technical challenges in the use of the microRNA-forkhead box signaling pathway in cancer treatment.
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