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Castanho EN, Aidos H, Madeira SC. Biclustering data analysis: a comprehensive survey. Brief Bioinform 2024; 25:bbae342. [PMID: 39007596 PMCID: PMC11247412 DOI: 10.1093/bib/bbae342] [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: 11/28/2023] [Revised: 05/16/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Biclustering, the simultaneous clustering of rows and columns of a data matrix, has proved its effectiveness in bioinformatics due to its capacity to produce local instead of global models, evolving from a key technique used in gene expression data analysis into one of the most used approaches for pattern discovery and identification of biological modules, used in both descriptive and predictive learning tasks. This survey presents a comprehensive overview of biclustering. It proposes an updated taxonomy for its fundamental components (bicluster, biclustering solution, biclustering algorithms, and evaluation measures) and applications. We unify scattered concepts in the literature with new definitions to accommodate the diversity of data types (such as tabular, network, and time series data) and the specificities of biological and biomedical data domains. We further propose a pipeline for biclustering data analysis and discuss practical aspects of incorporating biclustering in real-world applications. We highlight prominent application domains, particularly in bioinformatics, and identify typical biclusters to illustrate the analysis output. Moreover, we discuss important aspects to consider when choosing, applying, and evaluating a biclustering algorithm. We also relate biclustering with other data mining tasks (clustering, pattern mining, classification, triclustering, N-way clustering, and graph mining). Thus, it provides theoretical and practical guidance on biclustering data analysis, demonstrating its potential to uncover actionable insights from complex datasets.
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Affiliation(s)
- Eduardo N Castanho
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 16, P-1749-016 Lisbon, Portugal
| | - Helena Aidos
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 16, P-1749-016 Lisbon, Portugal
| | - Sara C Madeira
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Campo Grande 16, P-1749-016 Lisbon, Portugal
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2
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Liu F, Yang Y, Xu XS, Yuan M. MESBC: A novel mutually exclusive spectral biclustering method for cancer subtyping. Comput Biol Chem 2024; 109:108009. [PMID: 38219419 DOI: 10.1016/j.compbiolchem.2023.108009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/16/2024]
Abstract
Many soft biclustering algorithms have been developed and applied to various biological and biomedical data analyses. However, few mutually exclusive (hard) biclustering algorithms have been proposed, which could better identify disease or molecular subtypes with survival significance based on genomic or transcriptomic data. In this study, we developed a novel mutually exclusive spectral biclustering (MESBC) algorithm based on spectral method to detect mutually exclusive biclusters. MESBC simultaneously detects relevant features (genes) and corresponding conditions (patients) subgroups and, therefore, automatically uses the signature features for each subtype to perform the clustering. Extensive simulations revealed that MESBC provided superior accuracy in detecting pre-specified biclusters compared with the non-negative matrix factorization (NMF) and Dhillon's algorithm, particularly in very noisy data. Further analysis of the algorithm on real datasets obtained from the TCGA database showed that MESBC provided more accurate (i.e., smaller p-value) overall survival prediction in patients with lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) cancers when compared to the existing, gold-standard subtypes for lung cancers (integrative clustering). Furthermore, MESBC detected several genes with significant prognostic value in both LUAD and LUSC patients. External validation on an independent, unseen GEO dataset of LUAD showed that MESBC-derived clusters based on TCGA data still exhibited clear biclustering patterns and consistent, outstanding prognostic predictability, demonstrating robust generalizability of MESBC. Therefore, MESBC could potentially be used as a risk stratification tool to optimize the treatment for the patient, improve the selection of patients for clinical trials, and contribute to the development of novel therapeutic agents.
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Affiliation(s)
- Fengrong Liu
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | - Yaning Yang
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | | | - Min Yuan
- School of Public Health Administration, Anhui Medical University, Hefei 230032, China.
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Lu H, Zhou J, Li X, Han X, Ma S, Feng C. MiR-526b-3p enhances sensitivity of head and neck squamous cell carcinoma cells to radiotherapy via suppressing exosomal LAMP3-mediated autophagy. Autoimmunity 2023; 56:2259125. [PMID: 37740656 DOI: 10.1080/08916934.2023.2259125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/10/2023] [Indexed: 09/24/2023]
Abstract
Lysosomal associated membrane protein 3 (LAMP3) has been reported to be a tumour promoter in multiple cancer types by modulating tumour cell autophagy. However, the potential mechanism of LAMP3 in radio-resistance of head and neck squamous cell carcinoma (HNSCC) remains unknown. Therefore, our current study aims to detect the impacts of LAMP3 on the resistance of HNSCC cells to radiotherapy and meanwhile explore its functional mechanism. Through RT-Qpcr examination, LAMP3 expression was identified to be expressed at a significantly high level in irradiation-resistant HNSCC cell lines compared with irradiation-sensitive HNSCC cell lines. Functional assays including CCK-8, colony formation and Transwell assays demonstrated that LAMP3 enhanced the radio-resistance through inducing autophagy to promote HNSCC cell growth. Furthermore, irradiation-resistant HNSCC cells could transfer exosomal LAMP3 to elevate LAMP3 expression in irradiation-sensitive HNSCC cells. Mechanistically, microRNA (miRNA) miR-526b-3p could inhibit LAMP3 expression so as to strengthen sensitivity of HNSCC cells to radiotherapy. In a word, exosomal LAMP3 expression promoted radioresistance of HNSCC cells via inducing autophagy, while this effect could be suppressed by miR-526b-3p in a targeted manner.
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Affiliation(s)
- Huixiang Lu
- Heavy Ion Radiotherapy Department, Wuwei Cancer Hospital & Institute, Wuwei Academy of Medical Sciences, Wuwei, Gansu, China
| | - Junnian Zhou
- Head, Neck and Maxillofacial Surgery Department, Wuwei Cancer Hospital, Wuwei, Gansu, China
| | - Xiaojun Li
- Heavy Ion Radiotherapy Department, Wuwei Cancer Hospital & Institute, Wuwei Academy of Medical Sciences, Wuwei, Gansu, China
| | - Xiaoqin Han
- Head, Neck and Maxillofacial Surgery Department, Wuwei Cancer Hospital, Wuwei, Gansu, China
| | - Shuping Ma
- Heavy Ion Radiotherapy Department, Wuwei Cancer Hospital & Institute, Wuwei Academy of Medical Sciences, Wuwei, Gansu, China
| | - Chunlan Feng
- Heavy Ion Radiotherapy Department, Wuwei Cancer Hospital & Institute, Wuwei Academy of Medical Sciences, Wuwei, Gansu, China
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Moriondo G, Soccio P, Minoves M, Scioscia G, Tondo P, Foschino Barbaro MP, Pépin JL, Briançon-Marjollet A, Lacedonia D. Intermittent Hypoxia Mediates Cancer Development and Progression Through HIF-1 and miRNA Regulation. Arch Bronconeumol 2023; 59:629-637. [PMID: 37517933 DOI: 10.1016/j.arbres.2023.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023]
Abstract
INTRODUCTION There is still a debate for the link between obstructive sleep apnoea (OSA) and cancer. The mechanisms underlying this causality are poorly understood. Several miRNAs are involved in cancer development and progression with expression being influenced by hypoxia. The aims of this work were (i) to compare miRNAs expression in controls versus patients affected by OSA without or with cancer (ONCO-OSA) and (ii) in colorectal cancer cells exposed to intermittent hypoxia (IH), to evaluate miRNAs impact on tumor progression in vitro. METHODS We detected miRNAs by qRT-PCR in patients' sera and in CaCo2 cells exposed to 2-32h of IH with or without acriflavine (ACF), a HIF-1 inhibitor. Viability and transwell invasion test were applied to investigate the proliferation and migration of CaCo2 exposed to IH and treated with miRNA inhibitors or acriflavine. HIF-1α activity was evaluated in CaCo2 cells after IH. RESULTS The levels of miR-21, miR-26a and miR-210 increased in OSA and ONCO-OSA patients compared to controls. MiR-23b increased in ONCO-OSA patients, and miR-27b and miR-145 increased in OSA but not ONCO-OSA patients. MiR-21, miR-26a, miR-23b and miR-210 increased in cells after IH. IH stimulated cell proliferation and migration. This effect was reduced after either miRNA inhibition or acriflavine treatment. MiRNA inhibition reduces HIF-1α gene expression. Conversely, acriflavine reduced the expression of these miRNAs. CONCLUSIONS We identified a signature of miRNAs, induced by the IH environment. They could be implicated in cancer development and progression through a regulatory loop involving HIF-1.
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Affiliation(s)
- Giorgia Moriondo
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy.
| | - Piera Soccio
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Mélanie Minoves
- University Grenoble Alpes, INSERM U1300, CHU Grenoble Alpes, HP2 Laboratory, Grenoble, France
| | - Giulia Scioscia
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; Institute of Respiratory Diseases, Policlinico Riuniti of Foggia, 71122 Foggia, Italy
| | - Pasquale Tondo
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Maria Pia Foschino Barbaro
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; Institute of Respiratory Diseases, Policlinico Riuniti of Foggia, 71122 Foggia, Italy
| | - Jean-Louis Pépin
- University Grenoble Alpes, INSERM U1300, CHU Grenoble Alpes, HP2 Laboratory, Grenoble, France
| | - Anne Briançon-Marjollet
- University Grenoble Alpes, INSERM U1300, CHU Grenoble Alpes, HP2 Laboratory, Grenoble, France
| | - Donato Lacedonia
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; Institute of Respiratory Diseases, Policlinico Riuniti of Foggia, 71122 Foggia, Italy
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Chen J, Han G, Xu A, Akutsu T, Cai H. Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:421-431. [PMID: 35320104 DOI: 10.1109/tcbb.2022.3161635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Identifying regulatory modules between miRNAs and genes is crucial in cancer research. It promotes a comprehensive understanding of the molecular mechanisms of cancer. The genomic data collected from subjects usually relate to different cancer statuses, such as different TNM Classifications of Malignant Tumors (TNM) or histological subtypes. Simple integrated analyses generally identify the core of the tumorigenesis (common modules) but miss the subtype-specific regulatory mechanisms (specific modules). In contrast, separate analyses can only report the differences and ignore important common modules. Therefore, there is an urgent need to develop a novel method to jointly analyze miRNA and gene data of different cancer statuses to identify common and specific modules. To that end, we developed a High-Order Graph Matching model to identify Common and Specific modules (HOGMCS) between miRNA and gene data of different cancer statuses. We first demonstrate the superiority of HOGMCS through a comparison with four state-of-the-art techniques using a set of simulated data. Then, we apply HOGMCS on stomach adenocarcinoma data with four TNM stages and two histological types, and breast invasive carcinoma data with four PAM50 subtypes. The experimental results demonstrate that HOGMCS can accurately extract common and subtype-specific miRNA-gene regulatory modules, where many identified miRNA-gene interactions have been confirmed in several public databases.
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Arshinchi Bonab R, Asfa S, Kontou P, Karakülah G, Pavlopoulou A. Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach. PeerJ 2022; 10:e14149. [PMID: 36213495 PMCID: PMC9536303 DOI: 10.7717/peerj.14149] [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: 04/28/2022] [Accepted: 09/07/2022] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
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Affiliation(s)
- Reza Arshinchi Bonab
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Seyedehsadaf Asfa
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Panagiota Kontou
- Department of Mathematics, University of Thessaly, Lamia, Greece
| | - Gökhan Karakülah
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey,Izmir Biomedicine and Genome Center, Izmir, Turkey
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Zhu F, Li J, Liu J, Min W. Network-based cancer genomic data integration for pattern discovery. BMC Genom Data 2021; 22:54. [PMID: 34886811 PMCID: PMC8662848 DOI: 10.1186/s12863-021-01004-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Since genes involved in the same biological modules usually present correlated expression profiles, lots of computational methods have been proposed to identify gene functional modules based on the expression profiles data. Recently, Sparse Singular Value Decomposition (SSVD) method has been proposed to bicluster gene expression data to identify gene modules. However, this model can only handle the gene expression data where no gene interaction information is integrated. Ignoring the prior gene interaction information may produce the identified gene modules hard to be biologically interpreted. RESULTS In this paper, we develop a Sparse Network-regularized SVD (SNSVD) method that integrates a prior gene interaction network from a protein protein interaction network and gene expression data to identify underlying gene functional modules. The results on a set of simulated data show that SNSVD is more effective than the traditional SVD-based methods. The further experiment results on real cancer genomic data show that most co-expressed modules are not only significantly enriched on GO/KEGG pathways, but also correspond to dense sub-networks in the prior gene interaction network. Besides, we also use our method to identify ten differentially co-expressed miRNA-gene modules by integrating matched miRNA and mRNA expression data of breast cancer from The Cancer Genome Atlas (TCGA). Several important breast cancer related miRNA-gene modules are discovered. CONCLUSIONS All the results demonstrate that SNSVD can overcome the drawbacks of SSVD and capture more biologically relevant functional modules by incorporating a prior gene interaction network. These identified functional modules may provide a new perspective to understand the diagnostics, occurrence and progression of cancer.
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Affiliation(s)
- Fangfang Zhu
- State Key Laboratory of Nuclear Resources and Environment and School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, 330013, China
- State Key Laboratory of Nuclear Resources and Environment and School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China
| | - Jiang Li
- State Key Laboratory of Nuclear Resources and Environment and School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China.
| | - Juan Liu
- School of Computer Science, Wuhan University, Wuhan, 430072, China.
| | - Wenwen Min
- School of Mathematics and Computer Science, Jiangxi Science and Technology Normal University, Nanchang, 330038, China.
- Information School, Yunnan University, Kunming, 650091, China.
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Shommo G, Apolloni B. A holistic miRNA-mRNA module discovery. Noncoding RNA Res 2021; 6:159-166. [PMID: 34703956 PMCID: PMC8521321 DOI: 10.1016/j.ncrna.2021.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
The regulatory role of the Micro-RNAs (miRNAs) in the messenger RNAs (mRNAs) gene expression is well understood by the biologists since some decades, even though the delving into specific aspects is in progress. In this paper we will focus on miRNA-mRNA modules, where regulation jointly occurs in miRNA-mRNA pairs. Namely, we propose a holistic procedure to identify miRNA-mRNA modules within a population of candidate pairs. Since current methods still leave open issues, we adopt the strategy of postponing any decision on the value of the module ingredients exactly at the end, i.e. at the moment of biologically exploiting the results. This diverts chains of statistical tests into sequences of specially-devised-evolving metrics on the possible solutions. This strategy is rather expensive under a computational perspective, so needing implementations on HPC. The reward stands in the discovery of new modules, possibly hosting non differentially expressed miRNAs and mRNAs and pairs containing genes that currently are considered not targeted. In the paper we implement the procedure on a Multiple Myeloma dataset publicly available on GEO platform, as a template of a cancer instance analysis, and hazard some biological issues. These results, jointly with the normal manageability of the computations, suggest that the discovery procedure may be profitably extended to a wide spectrum of diseases where miRNA-mRNA interactions play a relevant role.
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Affiliation(s)
- Ghada Shommo
- Sudan University of Science and Technology, Department of Information Technology and Computer Science, Sudan
| | - Bruno Apolloni
- Department of Computer Science, Via Comelico 39/41, 20135, Milano, Italy
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Jia C, Gao J, Wang L, Li Z, Dong Z, Yao L, Yao X. miR-877 inhibits the proliferation, migration, and invasion of osteosarcoma cells by targeting gamma-glutamylcyclotransferase. Endocr J 2021; 68:1109-1116. [PMID: 34121038 DOI: 10.1507/endocrj.ej20-0752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gamma-glutamylcyclotransferase (GGCT) can promote the progression of osteosarcoma (OS). MicroRNAs also play significant roles in regulating the progression of OS. This study was designed to investigate whether miR-877 exerts its function in OS by targeting GGCT. The proliferation of OS cells (Saos-2 and U2OS) was detected by MTT and colony formation assays. The migration and invasion of OS cells were detected by transwell assays. The expressions of miRNAs and GGCT were detected by quantitative real-time PCR and Western blot. The luciferase reporter assay was performed to assess whether miR-877 could target GGCT. miR-877 was down-regulated both in OS tissues and OS cell lines (Saos-2 and U2OS). The overexpression of miR-877 inhibited the proliferation, migration, and invasion of OS cell lines, while the knockdown of miR-877 could negate effects. The expression of GGCT was increased in Saos-2 and U2OS cells. miR-877 could target GGCT, and the mRNA level of GGCT in Saos-2 and U2OS cells was decreased by the overexpression of miR-877. miR-877 overexpression inhibited the migration and invasion and suppressed the proliferation of Saos-2 and U2OS cells, and the overexpression of GGCT reversed this effects. The knockdown of miR-877 promoted the migration and invasion and facilitated the proliferation of Saos-2 and U2OS cells, and the silence of GGCT abolished this effects. Our findings suggested that miR-877 could inhibit the proliferation, migration, and invasion of OS cells by targeting GGCT.
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Affiliation(s)
- Chenguang Jia
- Department of Orthopedics, the Chest Hospital of Hebei Province, Shijiazhuang 050041, China
| | - Jianguo Gao
- Department of Orthopedics, the Chest Hospital of Hebei Province, Shijiazhuang 050041, China
| | - Lianbo Wang
- Department of Orthopedics, the Chest Hospital of Hebei Province, Shijiazhuang 050041, China
| | - Zhuo Li
- Department of Orthopedics, the Chest Hospital of Hebei Province, Shijiazhuang 050041, China
| | - Zhaoliang Dong
- Department of Orthopedics, the Chest Hospital of Hebei Province, Shijiazhuang 050041, China
| | - Liming Yao
- Department of Orthopedics, the Chest Hospital of Hebei Province, Shijiazhuang 050041, China
| | - Xiaowei Yao
- Department of Orthopedics, the Chest Hospital of Hebei Province, Shijiazhuang 050041, China
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TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers. PLoS Comput Biol 2021; 17:e1009044. [PMID: 34061840 PMCID: PMC8195367 DOI: 10.1371/journal.pcbi.1009044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 06/11/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022] Open
Abstract
Existing studies have demonstrated that dysregulation of microRNAs (miRNAs or miRs) is involved in the initiation and progression of cancer. Many efforts have been devoted to identify microRNAs as potential biomarkers for cancer diagnosis, prognosis and therapeutic targets. With the rapid development of miRNA sequencing technology, a vast amount of miRNA expression data for multiple cancers has been collected. These invaluable data repositories provide new paradigms to explore the relationship between miRNAs and cancer. Thus, there is an urgent need to explore the complex cancer-related miRNA-gene patterns by integrating multi-omics data in a pan-cancer paradigm. In this study, we present a tensor sparse canonical correlation analysis (TSCCA) method for identifying cancer-related miRNA-gene modules across multiple cancers. TSCCA is able to overcome the drawbacks of existing solutions and capture both the cancer-shared and specific miRNA-gene co-expressed modules with better biological interpretations. We comprehensively evaluate the performance of TSCCA using a set of simulated data and matched miRNA/gene expression data across 33 cancer types from the TCGA database. We uncover several dysfunctional miRNA-gene modules with important biological functions and statistical significance. These modules can advance our understanding of miRNA regulatory mechanisms of cancer and provide insights into miRNA-based treatments for cancer. MicroRNAs (miRNAs) are a class of small non-coding RNAs. Previous studies have revealed that miRNA-gene regulatory modules play key roles in the occurrence and development of cancer. However, little has been done to discover miRNA-gene regulatory modules from a pan-cancer view. Thus, it is urgently needed to develop new methods to explore the complex cancer-related miRNA-gene patterns by integrating multi-omics data of multi-cancers. To build the connections between miRNA-gene regulatory modules across different cancer types, we propose a tensor sparse canonical correlation analysis (TSCCA) method. Our specific contributions are two-fold: (1) We propose a sparse statistical learning model TSCCA and an efficient block-coordinate descent algorithm to solve it. (2) We apply TSCCA to a multi-omics data set of 33 cancer types from TCGA and identify some cancer-related miRNA-gene modules with important biological functions and statistical significance.
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Bai Y, Baker S, Exoo K, Dai X, Ding L, Khattak NA, Li H, Liu H, Liu X. MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network. BMC Bioinformatics 2020; 21:247. [PMID: 32631332 PMCID: PMC7336395 DOI: 10.1186/s12859-020-3436-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/02/2020] [Indexed: 11/22/2022] Open
Abstract
Background Although there are many studies on the characteristics of miRNA-mRNA interactions using miRNA and mRNA sequencing data, the complexity of the change of the correlation coefficients and expression values of the miRNA-mRNA pairs between tumor and normal samples is still not resolved, and this hinders the potential clinical applications. There is an urgent need to develop innovative methodologies and tools that can characterize and visualize functional consequences of cancer risk gene and miRNA pairs while analyzing the tumor and normal samples simultaneously. Results We developed an innovative bioinformatics tool for visualizing functional annotation of miRNA-mRNA pairs in a network, known as MMiRNA-Viewer2. The tool takes mRNA and miRNA interaction pairs and visualizes mRNA and miRNA regulation network. Moreover, our MMiRNA-Viewer2 web server integrates and displays the mRNA and miRNA gene annotation information, signaling cascade pathways and direct cancer association between miRNAs and mRNAs. Functional annotation and gene regulatory information can be directly retrieved from our web server, which can help users quickly identify significant interaction sub-network and report possible disease or cancer association. The tool can identify pivotal miRNAs or mRNAs that contribute to the complexity of cancer, while engaging modern next-generation sequencing technology to analyze the tumor and normal samples concurrently. We compared our tools with other visualization tools. Conclusion Our MMiRNA-Viewer2 serves as a multitasking platform in which users can identify significant interaction clusters and retrieve functional and cancer-associated information for miRNA-mRNA pairs between tumor and normal samples. Our tool is applicable across a range of diseases and cancers and has advantages over existing tools.
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Xie J, Ma A, Fennell A, Ma Q, Zhao J. It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. Brief Bioinform 2020; 20:1449-1464. [PMID: 29490019 DOI: 10.1093/bib/bby014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. These algorithms and tools have been applied to a wide variety of data types, including but not limited to, genomes, transcriptomes, exomes, epigenomes, phenomes and pharmacogenomes. However, there is still a considerable gap between biclustering methodology development and comprehensive data interpretation, mainly because of the lack of knowledge for the selection of appropriate biclustering tools and further supporting computational techniques in specific studies. Here, we first deliver a brief introduction to the existing biclustering algorithms and tools in public domain, and then systematically summarize the basic applications of biclustering for biological data and more advanced applications of biclustering for biomedical data. This review will assist researchers to effectively analyze their big data and generate valuable biological knowledge and novel insights with higher efficiency.
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13
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Zhang L, Wu H, Zhao M, Chang C, Lu Q. Clinical significance of miRNAs in autoimmunity. J Autoimmun 2020; 109:102438. [PMID: 32184036 DOI: 10.1016/j.jaut.2020.102438] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) are evolutionally conserved, single-stranded RNAs that regulate gene expression at the posttranscriptional level by disrupting translation. MiRNAs are key players in variety of biological processes that regulate the differentiation, development and activation of immune cells in both innate and adaptive immunity. The disruption and dysfunction of miRNAs can perturb the immune response, stimulate the release of inflammatory cytokines and initiate the production of autoantibodies, and contribute to the pathogenesis of autoimmune diseases, including systemic lupus erythmatosus (SLE), rheumatoid arthritis (RA), primary biliary cholangitis (PBC), and multiple sclerosis (MS). Accumulating studies demonstrate that miRNAs, which can be collected by noninvasive methods, have the potential to be developed as diagnostic and therapeutic biomarkers, the discovery and validation of which is essential for the improvement of disease diagnosis and clinical monitoring. Recently, with the development of detection tools, such as microarrays and NGS (Next Generation Sequencing), large amounts of miRNAs have been identified and suggest a critical role in the pathogenesis of autoimmune diseases. Several miRNAs associated diagnostic biomarkers have been developed and applied clinically, though the pharmaceutical industry is still facing challenges in commercialization and drug delivery. The development of miRNAs is less advanced for autoimmune diseases compared with cancer. However, drugs that target miRNAs have been introduced as candidates and adopted in clinical trials. This review comprehensively summarizes the differentially expressed miRNAs in several types of autoimmune diseases and discusses the role and the significance of miRNAs in clinical management. The study of miRNAs in autoimmunity promises to provide novel and broad diagnostic and therapeutic strategies for a clinical market that is still in its infancy.
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Affiliation(s)
- Lian Zhang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China
| | - Haijing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China
| | - Christopher Chang
- Division of Rheumatology, Allergy and Clinical, Immunology, University of California at Davis School of Medicine, Davis, CA, 95616, USA
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China.
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14
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Wang Y, Yang J, Chen P, Song Y, An W, Zhang H, Butegeleqi B, Yan J. MicroRNA-320a inhibits invasion and metastasis in osteosarcoma by targeting cytoplasmic polyadenylation element-binding protein 1. Cancer Med 2020; 9:2833-2845. [PMID: 32064777 PMCID: PMC7163091 DOI: 10.1002/cam4.2919] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/07/2020] [Accepted: 01/26/2020] [Indexed: 02/06/2023] Open
Abstract
Osteosarcoma is a primary malignant bone tumor, which affects children, adolescents, and young adults commonly. MicroRNAs (miRNAs) have been proved to be dysregulated in different cancers, including osteosarcoma. Although miR‐320a has been implicated in many types of malignancies, little is known about the role of miR‐320a in osteosarcoma. In this study, we show that the overexpression of miR‐320a or knockdown of cytoplasmic polyadenylation element‐binding protein 1 (CPEB1) inhibited osteosarcoma cell migration and invasion. miR‐320a downregulates CPEB1 expression by directly targeting the CPEB1 3′‐UTR. Furthermore, CPEB1 reintroduction reversed the antiproliferation, antimigration, and antiinvasion roles of miR‐320a, indicating that miR‐320a might function as a tumor suppressor in osteosarcoma through CPEB1. In conclusion, our study demonstrates that miR‐320a plays a critical role in osteosarcoma progression and may provide a potential therapeutic target for osteosarcoma.
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Affiliation(s)
- Yanlong Wang
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Jiyu Yang
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Pangtao Chen
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Yu Song
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Weizheng An
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Haoran Zhang
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Butegeleqi Butegeleqi
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
| | - Jinglong Yan
- Departments of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, P.R. China
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15
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Oliveira AC, Bovolenta LA, Alves L, Figueiredo L, Ribeiro AO, Campos VF, Lemke N, Pinhal D. Understanding the Modus Operandi of MicroRNA Regulatory Clusters. Cells 2019; 8:cells8091103. [PMID: 31540501 PMCID: PMC6770051 DOI: 10.3390/cells8091103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that regulate a wide range of biological pathways by post-transcriptionally modulating gene expression levels. Given that even a single miRNA may simultaneously control several genes enrolled in multiple biological functions, one would expect that these tiny RNAs have the ability to properly sort among distinctive cellular processes to drive protein production. To test this hypothesis, we scrutinized previously published microarray datasets and clustered protein-coding gene expression profiles according to the intensity of fold-change levels caused by the exogenous transfection of 10 miRNAs (miR-1, miR-7, miR-9, miR-124, miR-128a, miR-132, miR-133a, miR-142, miR-148b, miR-181a) in a human cell line. Through an in silico functional enrichment analysis, we discovered non-randomic regulatory patterns, proper of each cluster identified. We demonstrated that miRNAs are capable of equivalently modulate the expression signatures of target genes in regulatory clusters according to the biological function they are assigned to. Moreover, target prediction analysis applied to ten vertebrate species, suggest that such miRNA regulatory modus operandi is evolutionarily conserved within vertebrates. Overall, we discovered a complex regulatory cluster-module strategy driven by miRNAs, which relies on the controlled intensity of the repression over distinct targets under specific biological contexts. Our discovery helps to clarify the mechanisms underlying the functional activity of miRNAs and makes it easier to take the fastest and most accurate path in the search for the functions of miRNAs in any distinct biological process of interest.
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Affiliation(s)
- Arthur C Oliveira
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Luiz A Bovolenta
- Department of Physics and Biophysics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Lucas Alves
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Lucas Figueiredo
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Amanda O Ribeiro
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Vinicius F Campos
- Laboratory of Structural Genomics (GenEstrut), Technology Developmental Center, Graduate Program of Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul 96010-610, Brazil.
| | - Ney Lemke
- Department of Physics and Biophysics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Danillo Pinhal
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
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16
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Ding L, Feng Z, Bai Y. Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms. BMC Med Genomics 2019; 12:117. [PMID: 31382962 PMCID: PMC6683425 DOI: 10.1186/s12920-019-0562-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
Background microRNA (miRNA) is a short RNA (~ 22 nt) that regulates gene expression at the posttranscriptional level. Aberration of miRNA expressions could affect their targeting mRNAs involved in cancer-related signaling pathways. We conduct clustering analysis of miRNA and mRNA using expression data from the Cancer Genome Atlas (TCGA). We combine the Hungarian algorithm and blossom algorithm in graph theory. Data analysis is done using programming language R and Python. Methods We first quantify edge-weights of the miRNA-mRNA pairs by combining their expression correlation coefficient in tumor (T_CC) and correlation coefficient in normal (N_CC). We thereby introduce a bipartite graph partition procedure to identify cluster candidates. Specifically, we propose six weight formulas to quantify the change of miRNA-mRNA expression T_CC relative to N_CC, and apply the traditional hierarchical clustering to subjectively evaluate the different weight formulas of miRNA-mRNA pairs. Among these six different weight formulas, we choose the optimal one, which we define as the integrated mean value weights, to represent the connections between miRNA and mRNAs. Then the Hungarian algorithm and the blossom algorithm are employed on the miRNA-mRNA bipartite graph to passively determine the clusters. The combination of Hungarian and the blossom algorithms is dubbed maximum weighted merger method (MWMM). Results MWMM identifies clusters of different sizes that meet the mathematical criterion that internal connections inside a cluster are relatively denser than external connections outside the cluster and biological criterion that the intra-cluster Gene Ontology (GO) term similarities are larger than the inter-cluster GO term similarities. MWMM is developed using breast invasive carcinoma (BRCA) as training data set, but can also applies to other cancer type data sets. MWMM shows advantage in GO term similarity in most cancer types, when compared to other algorithms. Conclusions miRNAs and mRNAs that are likely to be affected by common underlying causal factors in cancer can be clustered by MWMM approach and potentially be used as candidate biomarkers for different cancer types and provide clues for targets of precision medicine in cancer treatment. Electronic supplementary material The online version of this article (10.1186/s12920-019-0562-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lizhong Ding
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA
| | - Zheyun Feng
- Department of Mathematics and Computer Science, Indiana State University, Terre Haute, IN, 47809, USA
| | - Yongsheng Bai
- Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA. .,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48105, USA.
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17
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Integrating microRNA and mRNA expression in rapamycin-treated T-cell acute lymphoblastic leukemia. Pathol Res Pract 2019; 215:152494. [PMID: 31229277 DOI: 10.1016/j.prp.2019.152494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/24/2019] [Accepted: 06/08/2019] [Indexed: 12/16/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) has a relatively improved remission rate, but the poor outcomes are primarily due to resistance and relapse. Moreover, organs infiltration trends to occur during remission. Rapamycin was applied to treat malignancies for decades. In this investigation, we aimed to explore the molecular mechanisms and pathway changes during the T-ALL therapeutic process. T-ALL cell line Molt-4 cells were treated with rapamycin and performed microarray analysis to identify the deregulated miRNAs and mRNAs (log2 fold change>2 or <-2). To obtain regulatory miRNA/mRNA network, miRNA target prediction softwares and Cytoscape were used to plot and modularize the rapamycin treatment-related network. Surprisingly, the enriched pathways were not involved in mediating either cell death or apoptosis but were responsible for angiogenesis, cell survival, and anti-apoptosis, which is consistent with the Gene Ontology analysis and PPI network based on all deregulated mRNAs, indicating that these elements likely play a role in promoting Molt-4 cell survival or escaping from rapamycin. The expression of 3 miRNAs (miR-149-3p, miR-361-3p, and miR-944) and their putative targets, which play central roles in their module, were validated by qRT-PCR. These results provide novel insight into potentially relevant biological pathways for T-ALL cells escaping from chemotherapy or developing central nervous system infiltration.
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18
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Mura M, Jaksik R, Lalik A, Biernacki K, Kimmel M, Rzeszowska-Wolny J, Fujarewicz K. A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes. BMC Genomics 2019; 20:114. [PMID: 30727966 PMCID: PMC6366035 DOI: 10.1186/s12864-019-5464-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023] Open
Abstract
Background Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation, since the amounts of miRNAs in cells also vary upon irradiation. To address this possibility, we designed experiments using cancer-derived cell lines transfected with luciferase reporter gene containing sequences targeted by different miRNA species in its 3′- untranslated region. We focus on the early time-course response (1 h past irradiation) to eliminate secondary mRNA expression waves. Results Experiments revealed that the irradiation-induced changes in the mRNA expression depend on the miRNAs which interact with mRNA. To identify the strongest interactions, we propose a mathematical model which predicts the mRNA fold expression changes, caused by perturbation of microRNA-mRNA interactions. Model was applied to experimental data including various cell lines, irradiation doses and observation times, both ours and literature-based. Comparison of modelled and experimental mRNA expression levels given miRNA level changes allows estimating how many and which miRNAs play a significant role in transcriptome response to stress conditions in different cell types. As an example, in the human melanoma cell line the comparison suggests that, globally, a major part of the irradiation-induced changes of mRNA expression can be explained by perturbed miRNA-mRNA interactions. A subset of about 30 out of a few hundred miRNAs expressed in these cells appears to account for the changes. These miRNAs play crucial roles in regulatory mechanisms observed after irradiation. In addition, these miRNAs have a higher average content of GC and a higher number of targeted transcripts, and many have been reported to play a role in the development of cancer. Conclusions Our proposed mathematical modeling approach may be used to identify miRNAs which participate in responses of cells to ionizing radiation, and other stress factors such as extremes of temperature, exposure to toxins, and drugs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5464-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marzena Mura
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland. .,, Ardigen S.A., ul. Bobrzyńskiego 14, 30-348, Cracow, Poland.
| | - Roman Jaksik
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland
| | - Anna Lalik
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland
| | - Krzysztof Biernacki
- Department of Medical and Molecular Biology, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, USA
| | - Marek Kimmel
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Departments of Statistics and Bioengineering, Rice University, MS 138, 6100 Main, Houston, TX, 77005, USA
| | - Joanna Rzeszowska-Wolny
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland. .,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland.
| | - Krzysztof Fujarewicz
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland
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19
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Motieghader H, Kouhsar M, Najafi A, Sadeghi B, Masoudi-Nejad A. mRNA-miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation. MOLECULAR BIOSYSTEMS 2018; 13:2168-2180. [PMID: 28861579 DOI: 10.1039/c7mb00400a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biomarker detection is one of the most important and challenging problems in cancer studies. Recently, non-coding RNA based biomarkers such as miRNA expression levels have been used for early diagnosis of many cancer types. In this study, a systems biology approach was used to detect novel miRNA based biomarkers for CRC diagnosis in early stages. The mRNA expression data from three CRC stages (Low-grade Intraepithelial Neoplasia (LIN), High-grade Intraepithelial Neoplasia (HIN) and Adenocarcinoma) were used to reconstruct co-expression networks. The networks were clustered to extract co-expression modules and detected low preserved modules among CRC stages. Then, the experimentally validated mRNA-miRNA interaction data were applied to reconstruct three mRNA-miRNA bipartite networks. Twenty miRNAs with the highest degree (hub miRNAs) were selected in each bipartite network to reconstruct three bipartite subnetworks for further analysis. The analysis of these hub miRNAs in the bipartite subnetworks revealed 30 distinct important miRNAs as prognostic markers in CRC stages. There are two novel CRC related miRNAs (hsa-miR-190a-3p and hsa-miR-1277-5p) in these 30 hub miRNAs that have not been previously reported in CRC. Furthermore, a drug-gene interaction network was reconstructed to detect potential candidate drugs for CRC treatment. Our analysis shows that the hub miRNAs in the mRNA-miRNA bipartite network are very essential in CRC progression and should be investigated precisely in future studies. In addition, there are many important target genes in the results that may be critical in CRC progression and can be analyzed as therapeutic targets in future research.
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Affiliation(s)
- Habib Motieghader
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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20
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Surveying computational algorithms for identification of miRNA–mRNA regulatory modules. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0208-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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21
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22
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Olsen LC, O'Reilly KC, Liabakk NB, Witter MP, Sætrom P. MicroRNAs contribute to postnatal development of laminar differences and neuronal subtypes in the rat medial entorhinal cortex. Brain Struct Funct 2017; 222:3107-3126. [PMID: 28260163 PMCID: PMC5585308 DOI: 10.1007/s00429-017-1389-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/13/2017] [Indexed: 01/23/2023]
Abstract
The medial entorhinal cortex (MEC) is important in spatial navigation and memory formation and its layers have distinct neuronal subtypes, connectivity, spatial properties, and disease susceptibility. As little is known about the molecular basis for the development of these laminar differences, we analyzed microRNA (miRNA) and messenger RNA (mRNA) expression differences between rat MEC layer II and layers III–VI during postnatal development. We identified layer and age-specific regulation of gene expression by miRNAs, which included processes related to neuron specialization and locomotor behavior. Further analyses by retrograde labeling and expression profiling of layer II stellate neurons and in situ hybridization revealed that the miRNA most up-regulated in layer II, miR-143, was enriched in stellate neurons, whereas the miRNA most up-regulated in deep layers, miR-219-5p, was expressed in ependymal cells, oligodendrocytes and glia. Bioinformatics analyses of predicted mRNA targets with negatively correlated expression patterns to miR-143 found that miR-143 likely regulates the Lmo4 gene, which is known to influence hippocampal-based spatial learning.
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Affiliation(s)
- Lene C Olsen
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kally C O'Reilly
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University for Science and Technology, Trondheim, Norway
| | - Nina B Liabakk
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University for Science and Technology, Trondheim, Norway
| | - Pål Sætrom
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway. .,Department of Computer and Information Science, Norwegian University for Science and Technology, Trondheim, Norway. .,Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, Trondheim, Norway.
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23
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Wake C, Labadorf A, Dumitriu A, Hoss AG, Bregu J, Albrecht KH, DeStefano AL, Myers RH. Novel microRNA discovery using small RNA sequencing in post-mortem human brain. BMC Genomics 2016; 17:776. [PMID: 27716130 PMCID: PMC5050850 DOI: 10.1186/s12864-016-3114-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/23/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. METHODS We used high-throughput small RNA sequencing to discover novel miRNAs in 93 human post-mortem prefrontal cortex samples from individuals with Huntington's disease (n = 28) or Parkinson's disease (n = 29) and controls without neurological impairment (n = 36). A custom miRNA identification analysis pipeline was built, which utilizes miRDeep* miRNA identification and result filtering based on false positive rate estimates. RESULTS Ninety-nine novel miRNA candidates with a false positive rate of less than 5 % were identified. Thirty-four of the candidate miRNAs show sequence similarity with known mature miRNA sequences and may be novel members of known miRNA families, while the remaining 65 may constitute previously undiscovered families of miRNAs. Nineteen of the 99 candidate miRNAs were replicated using independent, publicly-available human brain RNA-sequencing samples, and seven were experimentally validated using qPCR. CONCLUSIONS We have used small RNA sequencing to identify 99 putative novel miRNAs that are present in human brain samples.
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Affiliation(s)
- Christian Wake
- Department of Neurology, Boston University School of Medicine, Boston, USA. .,Bioinformatics Program, Boston University, Boston, USA.
| | - Adam Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Bioinformatics Program, Boston University, Boston, USA
| | - Alexandra Dumitriu
- Department of Neurology, Boston University School of Medicine, Boston, USA
| | - Andrew G Hoss
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, USA
| | - Joli Bregu
- Department of Neurology, Boston University School of Medicine, Boston, USA
| | - Kenneth H Albrecht
- Genome Science Institute, Boston University School of Medicine, Boston, USA.,Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, USA
| | - Anita L DeStefano
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Genome Science Institute, Boston University School of Medicine, Boston, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, USA.,Bioinformatics Program, Boston University, Boston, USA.,Graduate Program in Genetics and Genomics, Boston University School of Medicine, Boston, USA.,Genome Science Institute, Boston University School of Medicine, Boston, USA.,Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, USA
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24
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A Two-Stage Method to Identify Joint Modules From Matched MicroRNA and mRNA Expression Data. IEEE Trans Nanobioscience 2016. [DOI: 10.1109/tnb.2016.2556744] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Di Martino MT, Arbitrio M, Guzzi PH, Cannataro M, Tagliaferri P, Tassone P. Experimental treatment of multiple myeloma in the era of precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1142356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of Potential RNAi (miRNA and siRNA) Molecules for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Gene Silencing by Computational Method. Interdiscip Sci 2015. [PMID: 26223545 PMCID: PMC7090891 DOI: 10.1007/s12539-015-0266-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF1ab replicase polyprotein may be used as a suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence-specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In the current study, four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, at genomic level.
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Affiliation(s)
- Suza Mohammad Nur
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Md Anayet Hasan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh.
| | - Mohammad Al Amin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Mehjabeen Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Tahmina Sharmin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
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Bradesi S, Karagiannides I, Bakirtzi K, Joshi SM, Koukos G, Iliopoulos D, Pothoulakis C, Mayer EA. Identification of Spinal Cord MicroRNA and Gene Signatures in a Model of Chronic Stress-Induced Visceral Hyperalgesia in Rat. PLoS One 2015. [PMID: 26222740 PMCID: PMC4519289 DOI: 10.1371/journal.pone.0130938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Introduction Animal studies have shown that stress could induce epigenetic and transcriptomic alterations essential in determining the balance between adaptive or maladaptive responses to stress. We tested the hypothesis that chronic stress in rats deregulates coding and non-coding gene expression in the spinal cord, which may underline neuroinflammation and nociceptive changes previously observed in this model. Methods Male Wistar rats were exposed to daily stress or handled, for 10 days. At day 11, lumbar spinal segments were collected and processed for mRNA/miRNA isolation followed by expression profiling using Agilent SurePrint Rat Exon and Rat miRNA Microarray platforms. Differentially expressed gene lists were generated using the dChip program. Microarrays were analyzed using the Ingenuity Pathways Analysis (IPA) tool from Ingenuity Systems. Multiple methods were used for the analysis of miRNA-mRNA functional modules. Quantitative real time RT-PCR for Interleukin 6 signal transducer (gp130), the Signal Transducer And Activator Of Transcription 3 (STAT3), glial fibrillary acidic protein and mir-17-5p were performed to confirm levels of expression. Results Gene network analysis revealed that stress deregulated different inflammatory (IL-6, JAK/STAT, TNF) and metabolic (PI3K/AKT) signaling pathways. MicroRNA array analysis revealed a signature of 39 deregulated microRNAs in stressed rats. MicroRNA-gene network analysis showed that microRNAs are regulators of two gene networks relevant to inflammatory processes. Specifically, our analysis of miRNA-mRNA functional modules identified miR-17-5p as an important regulator in our model. We verified miR-17-5p increased expression in stress using qPCR and in situ hybridization. In addition, we observed changes in the expression of gp130 and STAT3 (involved in intracellular signaling cascades in response to gp130 activation), both predicted targets for miR-17-5p. A modulatory role of spinal mir17-5p in the modulation of visceral sensitivity was confirmed in vivo. Conclusion Using an integrative high throughput approach, our findings suggest a link between miR-17-5p increased expression and gp130/STAT3 activation providing new insight into the possible mechanisms mediating the effect of chronic stress on neuroinflammation in the spinal cord.
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Affiliation(s)
- Sylvie Bradesi
- Oppenheimer Family Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- CURE Center, Veterans Administration, Greater Los Angeles, California, United States of America
- * E-mail:
| | - Iordanes Karagiannides
- Oppenheimer Family Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Inflammatory Bowel Disease Center, and Neuroendocrine Assay Core, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Kyriaki Bakirtzi
- Inflammatory Bowel Disease Center, and Neuroendocrine Assay Core, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Swapna Mahurkar Joshi
- Oppenheimer Family Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Georgios Koukos
- Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Dimitrios Iliopoulos
- Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Charalabos Pothoulakis
- Oppenheimer Family Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Center for Systems Biomedicine, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Emeran A. Mayer
- Oppenheimer Family Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
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Identification of subtype specific miRNA-mRNA functional regulatory modules in matched miRNA-mRNA expression data: multiple myeloma as a case. BIOMED RESEARCH INTERNATIONAL 2015; 2015:501262. [PMID: 25874214 PMCID: PMC4385567 DOI: 10.1155/2015/501262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/19/2014] [Accepted: 10/27/2014] [Indexed: 12/30/2022]
Abstract
Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it is important to identify subtype specific miRNA-mRNA modules. In this study, we integrated the Ping-Pong algorithm and multiobjective genetic algorithm to identify subtype specific miRNA-mRNA functional regulatory modules (MFRMs) through integrative analysis of three biological data sets: GO biological processes, miRNA target information, and matched miRNA and mRNA expression data. We applied our method on a heterogeneous disease, multiple myeloma (MM), to identify MM subtype specific MFRMs. The constructed miRNA-mRNA regulatory networks provide modular outlook at subtype specific miRNA-mRNA interactions. Furthermore, clustering analysis demonstrated that heterogeneous MFRMs were able to separate corresponding MM subtypes. These subtype specific MFRMs may aid in the further elucidation of the pathogenesis of each subtype and may serve to guide MM subtype diagnosis and treatment.
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Ding J, Li X, Hu H. MicroRNA modules prefer to bind weak and unconventional target sites. ACTA ACUST UNITED AC 2014; 31:1366-74. [PMID: 25527098 PMCID: PMC4410656 DOI: 10.1093/bioinformatics/btu833] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/13/2014] [Indexed: 11/13/2022]
Abstract
Motivation: MicroRNAs (miRNAs) play critical roles in gene regulation. Although it is well known that multiple miRNAs may work as miRNA modules to synergistically regulate common target mRNAs, the understanding of miRNA modules is still in its infancy. Results: We employed the recently generated high throughput experimental data to study miRNA modules. We predicted 181 miRNA modules and 306 potential miRNA modules. We observed that the target sites of these predicted modules were in general weaker compared with those not bound by miRNA modules. We also discovered that miRNAs in predicted modules preferred to bind unconventional target sites rather than canonical sites. Surprisingly, contrary to a previous study, we found that most adjacent miRNA target sites from the same miRNA modules were not within the range of 10–130 nucleotides. Interestingly, the distance of target sites bound by miRNAs in the same modules was shorter when miRNA modules bound unconventional instead of canonical sites. Our study shed new light on miRNA binding and miRNA target sites, which will likely advance our understanding of miRNA regulation. Availability and implementation: The software miRModule can be freely downloaded at http://hulab.ucf.edu/research/projects/miRNA/miRModule. Supplementary information:Supplementary data are available at Bioinformatics online. Contact:haihu@cs.ucf.edu or xiaoman@mail.ucf.edu.
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Affiliation(s)
- Jun Ding
- Department of Electrical Engineering and Computer Science and Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Xiaoman Li
- Department of Electrical Engineering and Computer Science and Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Haiyan Hu
- Department of Electrical Engineering and Computer Science and Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of potential RNAi (miRNA and siRNA) molecules for Middle East respiratory syndrome coronavirus (MERS-CoV) gene silencing by computational method. Interdiscip Sci 2014. [PMID: 25373633 DOI: 10.1007/s12539-014-0208-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/17/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, at genomic level.
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Affiliation(s)
- Suza Mohammad Nur
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
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Nur SM, Hasan MA, Amin MA, Hossain M, Sharmin T. Design of potential RNAi (miRNA and siRNA) molecules for Middle East respiratory syndrome coronavirus (MERS-CoV) gene silencing by computational method. Interdiscip Sci 2014. [PMID: 25519155 DOI: 10.1007/s12539-014-0233-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/17/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) is a virus that manifests itself in viral infection with fever, cough, shortness of breath, renal failure and severe acute pneumonia, which often result in a fatal outcome. MERS-CoV has been shown to spread between people who are in close contact. Transmission from infected patients to healthcare personnel has also been observed and is irredeemable with present technology. Genetic studies on MERS-CoV have shown that ORF 1ab encodes replicase polyproteins and play a foremost role in viral infection. Therefore, ORF 1ab replicase polyprotein may be used as suitable target for disease control. Viral activity can be controlled by RNA interference (RNAi) technology, a leading method for post transcriptional gene silencing in a sequence specific manner. However, there is a genetic inconsistency in different viral isolates; it is a great challenge to design potential RNAi (miRNA and siRNA) molecules which can silence the respective target genes rather than any other viral gene simultaneously. In current study four effective miRNA and five siRNA molecules for silencing of nine different strains of MERS-CoV were rationally designed and corroborated using computational methods, which might lead to knockdown the activity of virus. siRNA and miRNA molecules were predicted against ORF1ab gene of different strains of MERS-CoV as effective candidate using computational methods. Thus, this method may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of MERS-CoV, at genomic level.
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Affiliation(s)
- Suza Mohammad Nur
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
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Transcriptional expression changes of glucose metabolism genes after exercise in thoroughbred horses. Gene 2014; 547:152-8. [DOI: 10.1016/j.gene.2014.06.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/15/2014] [Accepted: 06/23/2014] [Indexed: 11/22/2022]
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Wu C, Bardes EE, Jegga AG, Aronow BJ. ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. Nucleic Acids Res 2014; 42:W107-13. [PMID: 24829448 PMCID: PMC4086116 DOI: 10.1093/nar/gku409] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 12/14/2022] Open
Abstract
Identifying functionally significant microRNAs (miRs) and their correspondingly most important messenger RNA targets (mRNAs) in specific biological contexts is a critical task to improve our understanding of molecular mechanisms underlying organismal development, physiology and disease. However, current miR-mRNA target prediction platforms rank miR targets based on estimated strength of physical interactions and lack the ability to rank interactants as a function of their potential to impact a given biological system. To address this, we have developed ToppMiR (http://toppmir.cchmc.org), a web-based analytical workbench that allows miRs and mRNAs to be co-analyzed via biologically centered approaches in which gene function associated annotations are used to train a machine learning-based analysis engine. ToppMiR learns about biological contexts based on gene associated information from expression data or from a user-specified set of genes that relate to context-relevant knowledge or hypotheses. Within the biological framework established by the genes in the training set, its associated information content is then used to calculate a features association matrix composed of biological functions, protein interactions and other features. This scoring matrix is then used to jointly rank both the test/candidate miRs and mRNAs. Results of these analyses are provided as downloadable tables or network file formats usable in Cytoscape.
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Affiliation(s)
- Chao Wu
- Department of Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Eric E Bardes
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Anil G Jegga
- Department of Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Bruce J Aronow
- Department of Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA
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Biswas A, Brown CM. Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3' untranslated regions (3' UTRs) of mRNAs. BMC Bioinformatics 2014; 15:174. [PMID: 24909639 PMCID: PMC4067372 DOI: 10.1186/1471-2105-15-174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/16/2014] [Indexed: 11/21/2022] Open
Abstract
Background Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly the 3′UTRs. Results Scan for Motifs (SFM) simplifies the process of identifying a wide range of regulatory elements on alignments of vertebrate 3′UTRs. SFM includes identification of both RNA Binding Protein (RBP) sites and targets of miRNAs. In addition to searching pre-computed alignments, the tool provides users the flexibility to search their own sequences or alignments. The regulatory elements may be filtered by expected value cutoffs and are cross-referenced back to their respective sources and literature. The output is an interactive graphical representation, highlighting potential regulatory elements and overlaps between them. The output also provides simple statistics and links to related resources for complementary analyses. The overall process is intuitive and fast. As SFM is a free web-application, the user does not need to install any software or databases. Conclusions Visualisation of the binding sites of different classes of effectors that bind to 3′UTRs will facilitate the study of regulatory elements in 3′ UTRs.
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Affiliation(s)
| | - Chris M Brown
- Department of Biochemistry, Genetics Otago, University of Otago, Dunedin, New Zealand.
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