1
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Abu-Shahba N, Hegazy E, Khan FM, Elhefnawi M. In Silico Analysis of MicroRNA Expression Data in Liver Cancer. Cancer Inform 2023; 22:11769351231171743. [PMID: 37200943 PMCID: PMC10185868 DOI: 10.1177/11769351231171743] [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: 11/30/2022] [Accepted: 04/04/2023] [Indexed: 05/20/2023] Open
Abstract
Abnormal miRNA expression has been evidenced to be directly linked to HCC initiation and progression. This study was designed to detect possible prognostic, diagnostic, and/or therapeutic miRNAs for HCC using computational analysis of miRNAs expression. Methods: miRNA expression datasets meta-analysis was performed using the YM500v2 server to compare miRNA expression in normal and cancerous liver tissues. The most significant differentially regulated miRNAs in our study undergone target gene analysis using the mirWalk tool to obtain their validated and predicted targets. The combinatorial target prediction tool; miRror Suite was used to obtain the commonly regulated target genes. Functional enrichment analysis was performed on the resulting targets using the DAVID tool. A network was constructed based on interactions among microRNAs, their targets, and transcription factors. Hub nodes and gatekeepers were identified using network topological analysis. Further, we performed patient data survival analysis based on low and high expression of identified hubs and gatekeeper nodes, patients were stratified into low and high survival probability groups. Results: Using the meta-analysis option in the YM500v2 server, 34 miRNAs were found to be significantly differentially regulated (P-value ⩽ .05); 5 miRNAs were down-regulated while 29 were up-regulated. The validated and predicted target genes for each miRNA, as well as the combinatorially predicted targets, were obtained. DAVID enrichment analysis resulted in several important cellular functions that are directly related to the main cancer hallmarks. Among these functions are focal adhesion, cell cycle, PI3K-Akt signaling, insulin signaling, Ras and MAPK signaling pathways. Several hub genes and gatekeepers were found that could serve as potential drug targets for hepatocellular carcinoma. POU2F1 and PPARA showed a significant difference between low and high survival probabilities (P-value ⩽ .05) in HCC patients. Our study sheds light on important biomarker miRNAs for hepatocellular carcinoma along with their target genes and their regulated functions.
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Affiliation(s)
- Nourhan Abu-Shahba
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
- Stem Cell Research Group, Medical Research Center of Excellence, National Research Centre, Cairo, Egypt
| | - Elsayed Hegazy
- School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Faiz M. Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Mahmoud Elhefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Mahmoud Elhefnawi, Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, 33, elbohouth street, Cairo 11211, Egypt.
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2
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Hassani SF, Sayaf M, Danandeh SS, Nourollahzadeh Z, Shahmohammadi M, Akbari S, Shirvaliloo M, Sheervalilou R, Shams Z. Novel Insight Into the Association Between Obesity and Hepatocellular Carcinoma Occurrence and Recurrence: High-Throughput Microarray Data Set Analysis of Differentially Expressed Genes. JCO Clin Cancer Inform 2021; 5:1169-1180. [PMID: 34860577 DOI: 10.1200/cci.21.00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE This study aims to identify potential biomarkers of hepatocellular carcinoma (HCC) occurrence/recurrence and obesity, along with the molecular mechanisms that involve these biomarkers. METHODS Three microarray data sets, namely GSE18897, GSE25097, and GSE36376 (genetic suppressor elements associated with obesity, tumor, and recurrence, respectively), were downloaded from Gene Expression Omnibus database to be investigated for their expression as differentially expressed genes (DEGs) in HCC and obesity. The functional and pathway enrichment analysis of these DEGs were identified by the Database for Annotation Visualization and Integrated Discovery. The protein-protein interaction network analysis was performed with STRING online tool and Cytoscape software. RESULTS One hundred sixty common DEGs were screened. We found that these genes were associated with certain pathways such as metabolic pathways, terpenoid backbone biosynthesis, and adipocytokine signaling pathway. The involvements of 10 genes, including RPS16, RPS7, CCT3, HNRNPA2B1, EIF4G1, PSMC4, NHP2, EGR1, FDPS, and MCM4, were identified in the subnetwork. HNRNPA2B1 and RPS7 in the GSE18897 data set, RPS16, RPS7, CCT3, HNRNPA2B1, PSMC4, NHP2, FDPS, and MCM4 in the GSE25097 data set, and RPS16, RPS7, CCT3, HNRNPA2B1, EIF4G1, PSMC4, NHP2, FDPS, and MCM4 in the GSE36376 data set exhibited positive fold changes. CONCLUSION These DEGs and pathways could be of diagnostic value as potential biomarkers involved in the pathogenesis of HCC, pertaining to both obesity and HCC occurrence/recurrence.
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Affiliation(s)
| | - Masoud Sayaf
- Central Tehran Branch, Faculty of Science, Department of Biology, Tehran, Iran
| | | | - Zahra Nourollahzadeh
- Department of Biological Science, Ahar Branch, Islamic Azad University, Ahar, Iran
| | | | | | - Milad Shirvaliloo
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Zinat Shams
- Department of Biological Science, Kharazmi University, Tehran, Iran
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3
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Dogan H, Hakguder Z, Madadjim R, Scott S, Pierobon M, Cui J. Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning. Brief Bioinform 2021; 22:6346341. [PMID: 34373890 DOI: 10.1093/bib/bbab270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Empowered by advanced genomics discovery tools, recent biomedical research has produced a massive amount of genomic data on (post-)transcriptional regulations related to transcription factors, microRNAs, long non-coding RNAs, epigenetic modifications and genetic variations. Computational modeling, as an essential research method, has generated promising testable quantitative models that represent complex interplay among different gene regulatory mechanisms based on these data in many biological systems. However, given the dynamic changes of interactome in chaotic systems such as cancers, and the dramatic growth of heterogeneous data on this topic, such promise has encountered unprecedented challenges in terms of model complexity and scalability. In this study, we introduce a new integrative machine learning approach that can infer multifaceted gene regulations in cancers with a particular focus on microRNA regulation. In addition to new strategies for data integration and graphical model fusion, a supervised deep learning model was integrated to identify conditional microRNA-mRNA interactions across different cancer stages. RESULTS In a case study of human breast cancer, we have identified distinct gene regulatory networks associated with four progressive stages. The subsequent functional analysis focusing on microRNA-mediated dysregulation across stages has revealed significant changes in major cancer hallmarks, as well as novel pathological signaling and metabolic processes, which shed light on microRNAs' regulatory roles in breast cancer progression. We believe this integrative model can be a robust and effective discovery tool to understand key regulatory characteristics in complex biological systems. AVAILABILITY http://sbbi-panda.unl.edu/pin/.
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Affiliation(s)
- Haluk Dogan
- Department of Computer Science and Engineering (CSE) at the University of Nebraska- Lincoln (UNL), Lincoln, NE 68588-0115, USA
| | | | | | | | | | - Juan Cui
- CSE department at UNL, Lincoln, NE 68588-0115, USA
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4
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Yerukala Sathipati S, Ho SY. Novel miRNA signature for predicting the stage of hepatocellular carcinoma. Sci Rep 2020; 10:14452. [PMID: 32879391 PMCID: PMC7467934 DOI: 10.1038/s41598-020-71324-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer deaths worldwide. Recently, microRNAs (miRNAs) are reported to be altered and act as potential biomarkers in various cancers. However, miRNA biomarkers for predicting the stage of HCC are limitedly discovered. Hence, we sought to identify a novel miRNA signature associated with cancer stage in HCC. We proposed a support vector machine (SVM)-based cancer stage prediction method, SVM-HCC, which uses an inheritable bi-objective combinatorial genetic algorithm for selecting a minimal set of miRNA biomarkers while maximizing the accuracy of predicting the early and advanced stages of HCC. SVM-HCC identified a 23-miRNA signature that is associated with cancer stages in patients with HCC and achieved a 10-fold cross-validation accuracy, sensitivity, specificity, Matthews correlation coefficient, and area under the receiver operating characteristic curve (AUC) of 92.59%, 0.98, 0.74, 0.80, and 0.86, respectively; and test accuracy and test AUC of 74.28% and 0.73, respectively. We prioritized the miRNAs in the signature based on their contributions to predictive performance, and validated the prognostic power of the prioritized miRNAs using Kaplan–Meier survival curves. The results showed that seven miRNAs were significantly associated with prognosis in HCC patients. Correlation analysis of the miRNA signature and its co-expressed miRNAs revealed that hsa-let-7i and its 13 co-expressed miRNAs are significantly involved in the hepatitis B pathway. In clinical practice, a prediction model using the identified 23-miRNA signature could be valuable for early-stage detection, and could also help to develop miRNA-based therapeutic strategies for HCC.
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Affiliation(s)
- Srinivasulu Yerukala Sathipati
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan. .,Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan.
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5
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Cui J, Shu J. Circulating microRNA trafficking and regulation: computational principles and practice. Brief Bioinform 2020; 21:1313-1326. [PMID: 31504144 PMCID: PMC7412956 DOI: 10.1093/bib/bbz079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 01/18/2023] Open
Abstract
Rapid advances in genomics discovery tools and a growing realization of microRNA's implication in intercellular communication have led to a proliferation of studies of circulating microRNA sorting and regulation across cells and different species. Although sometimes, reaching controversial scientific discoveries and conclusions, these studies have yielded new insights in the functional roles of circulating microRNA and a plethora of analytical methods and tools. Here, we consider this body of work in light of key computational principles underpinning discovery of circulating microRNAs in terms of their sorting and targeting, with the goal of providing practical guidance for applications that is focused on the design and analysis of circulating microRNAs and their context-dependent regulation. We survey a broad range of informatics methods and tools that are available to the researcher, discuss their key features, applications and various unsolved problems and close this review with prospects and broader implication of this field.
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Affiliation(s)
- Juan Cui
- Systems Biology and Biomedical Informatics Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jiang Shu
- Systems Biology and Biomedical Informatics Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
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6
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Bao F, Deng Y, Du M, Ren Z, Wan S, Liang KY, Liu S, Wang B, Xin J, Chen F, Christiani DC, Wang M, Dai Q. Explaining the Genetic Causality for Complex Phenotype via Deep Association Kernel Learning. PATTERNS 2020; 1:100057. [PMID: 33205126 PMCID: PMC7660384 DOI: 10.1016/j.patter.2020.100057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
The genetic effect explains the causality from genetic mutations to the development of complex diseases. Existing genome-wide association study (GWAS) approaches are always built under a linear assumption, restricting their generalization in dissecting complicated causality such as the recessive genetic effect. Therefore, a sophisticated and general GWAS model that can work with different types of genetic effects is highly desired. Here, we introduce a deep association kernel learning (DAK) model to enable automatic causal genotype encoding for GWAS at pathway level. DAK can detect both common and rare variants with complicated genetic effects where existing approaches fail. When applied to four real-world GWAS datasets including cancers and schizophrenia, our DAK discovered potential casual pathways, including the association between dilated cardiomyopathy pathway and schizophrenia.
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Affiliation(s)
- Feng Bao
- Department of Automation, Tsinghua University, Beijing 100084, China.,Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China
| | - Yue Deng
- School of Astronautics, Beihang University, Beijing 100191, China.,Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing 100191, China
| | - Mulong Du
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhiquan Ren
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Sen Wan
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Kenny Ye Liang
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shaohua Liu
- School of Astronautics, Beihang University, Beijing 100191, China
| | - Bo Wang
- School of Astronautics, Beihang University, Beijing 100191, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China.,Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China
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7
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Mohamed RH, Abu-Shahba N, Mahmoud M, Abdelfattah AMH, Zakaria W, ElHefnawi M. Co-regulatory Network of Oncosuppressor miRNAs and Transcription Factors for Pathology of Human Hepatic Cancer Stem Cells (HCSC). Sci Rep 2019; 9:5564. [PMID: 30944375 PMCID: PMC6447552 DOI: 10.1038/s41598-019-41978-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/21/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatic cancer stem cells (HCSCs) are considered as main players for the hepatocellular carcinoma (HCC) initiation, metastasis, drug resistance and recurrence. There is a growing evidence supporting the down-regulated miRNAs in HCSCs as key suppressors for the stemness traits, but still more details are vague about how these miRNAs modulate the HCC development. To uncover some of these miRNA regulatory aspects in HCSC, we compiled 15 down-regulated miRNA and their validated and predicted up-regulated targets in HCSC. The targets were enriched for several cancer cell stemness hallmarks and CSC pre-metastatic niche, which support these miRNAs role in suppression of HCSCs neoplastic transformation. Further, we constructed miRNA-Transcription factor (TF) regulatory networks, which provided new insights on the role of the proposed miRNA-TF co-regulation in the cancer stemness axis and its cross talk with the surrounding microenvironment. Our analysis revealed HCSC important hubs as candidate regulators for targeting hepatic cancer stemness such as, miR-148a, miR-214, E2F family, MYC and SLC7A5. Finally, we proposed a possible model for miRNA and TF co-regulation of HCSC signaling pathways. Our study identified an HCSC signature and set bridges between the reported results to give guide for future validation of HCC therapeutic strategies avoiding drug resistance.
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Affiliation(s)
- Rania Hassan Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nourhan Abu-Shahba
- Stem Cell Research Group, Centre of Excellence for Advanced Sciences, Department of Medical Molecular Genetics, National Research Centre, Cairo, Egypt
| | - Marwa Mahmoud
- Stem Cell Research Group, Centre of Excellence for Advanced Sciences, Department of Medical Molecular Genetics, National Research Centre, Cairo, Egypt
| | - Ahmed M H Abdelfattah
- Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, Egypt.,VAP, CS Department, SUNY, Oswego, NY, USA
| | - Wael Zakaria
- Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mahmoud ElHefnawi
- Biomedical informatics and Chemoinformatics group, Centre of Excellence for Advanced Sciences, Informatics and Systems Department, National Research Centre, Cairo, Egypt. .,Informatics and systems Department, Division of Engineering research, National Research Centre, Cairo, Egypt.
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8
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Augello C, Colombo F, Terrasi A, Trombetta E, Maggioni M, Porretti L, Rossi G, Guerneri S, Silipigni R, Bosari S, Vaira V. Expression of C19MC miRNAs in HCC associates with stem-cell features and the cancer-testis genes signature. Dig Liver Dis 2018; 50:583-593. [PMID: 29673952 DOI: 10.1016/j.dld.2018.03.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Intratumor heterogeneity of hepatocellular carcinoma (HCC) and, among HCC cell subsets, the cancer stem cell population (hCSC), is responsible for therapeutic resistance and disease relapse. AIMS To characterize hCSC-enriched HCCs at the molecular level. METHODS Side population (SP) was used to identify the hCSCs in multiple tumor sampling from different patients and primary HCCs cultures. FACS was used to immunoprofile cultures. miRNAs were profiled in samples and correlated to SP. The Cancer Genome Atlas (TCGA) HCC dataset was analyzed to search for signatures associated with C19MC miRNAs expression. Results were confirmed by immunohistochemistry. RESULTS The miRNA cluster on chromosome 19 (C19MC) was enriched in SP and in HCCs with a high SP fraction. At the molecular level, an elevated C19MC was correlated with expression of precursor transcripts. In TCGA-HCC series, high C19MC expression identified a subset of patients with poorer prognosis, advanced disease and overexpression of the cancer-testis (CT) antigens. These data were confirmed in an independent cohort of HCCs and at the protein level. CONCLUSION C19MC miRNAs and CT antigens overexpression represents a novel oncogenic pathway in a subset of hCSC-enriched HCCs with dismal prognosis. CT antigens are promising immunotherapy targets. Therefore, these molecular signatures could identify HCCs who could benefit from immunotherapy.
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Affiliation(s)
- Claudia Augello
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Divisions of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Federico Colombo
- Clinical Chemistry and Microbiology Laboratory, Flow Cytometry and Experimental Hepatology Service, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Terrasi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Divisions of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elena Trombetta
- Clinical Chemistry and Microbiology Laboratory, Flow Cytometry and Experimental Hepatology Service, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marco Maggioni
- Divisions of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Porretti
- Clinical Chemistry and Microbiology Laboratory, Flow Cytometry and Experimental Hepatology Service, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giorgio Rossi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; General Surgery and Liver Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvana Guerneri
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Silvano Bosari
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Divisions of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Valentina Vaira
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Divisions of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
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9
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Li C, Dinu V. miR2Pathway: A novel analytical method to discover MicroRNA-mediated dysregulated pathways involved in hepatocellular carcinoma. J Biomed Inform 2018; 81:31-40. [PMID: 29578099 DOI: 10.1016/j.jbi.2018.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 02/10/2018] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs involved in the regulation of gene expression at a post-transcriptional level. Recent studies have shown miRNAs as key regulators of a variety of biological processes, such as proliferation, differentiation, apoptosis, metabolism, etc. Aberrantly expressed miRNAs influence individual gene expression level, but rewired miRNA-mRNA connections can influence the activity of biological pathways. Here, we define rewired miRNA-mRNA connections as the differential (rewiring) effects on the activity of biological pathways between hepatocellular carcinoma (HCC) and normal phenotypes. Our work presented here uses a PageRank-based approach to measure the degree of miRNA-mediated dysregulation of biological pathways between HCC and normal samples based on rewired miRNA-mRNA connections. In our study, we regard the degree of miRNA-mediated dysregulation of biological pathways as disease risk of biological pathways. Therefore, we propose a new method, miR2Pathway, to measure and rank the degree of miRNA-mediated dysregulation of biological pathways by measuring the total differential influence of miRNAs on the activity of pathways between HCC and normal states. miR2Pathway proposed here systematically shows the first evidence for a mechanism of biological pathways being dysregulated by rewired miRNA-mRNA connections, and provides new insight into exploring mechanisms behind HCC. Thus, miR2Pathway is a novel method to identify and rank miRNA-dysregulated pathways in HCC.
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Affiliation(s)
- Chaoxing Li
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Valentin Dinu
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85255, USA.
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10
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Zhang L, Zhang Y, Wong SH, Law PTY, Zhao S, Yu J, Chan MTV, Wu WKK. Common Deregulation of Seven Biological Processes by MicroRNAs in Gastrointestinal Cancers. Sci Rep 2018; 8:3287. [PMID: 29459716 PMCID: PMC5818544 DOI: 10.1038/s41598-018-21573-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/07/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are frequently dysregulated in human neoplasms, including gastrointestinal cancers. Nevertheless, the global influence of microRNA dysregulation on cellular signaling is still unknown. Here we sought to elucidate cellular signaling dysregulation by microRNAs in gastrointestinal cancers at the systems biology level followed by experimental validation. Signature dysregulated microRNAs in gastric, colorectal and liver cancers were defined based on our previous studies. Targets of signature dysregulated miRNAs were predicted using multiple computer algorithms followed by gene enrichment analysis to identify biological processes perturbed by dysregulated microRNAs. Effects of microRNAs on endocytosis were measured by epidermal growth factor (EGF) internalization assay. Our analysis revealed that, aside from well-established cancer-related signaling pathways, several novel pathways, including axon guidance, neurotrophin/nerve growth factor signaling, and endocytosis, were found to be involved in the pathogenesis of gastrointestinal cancers. The regulation of EGF receptor (EGFR) endocytosis by two predicted miRNAs, namely miR-17 and miR-145, was confirmed experimentally. Functionally, miR-145, which blocked EGFR endocytosis, prolonged EGFR membrane signaling and altered responsiveness of colon cancer cells to EGFR-targeting drugs. In conclusion, our analysis depicts a comprehensive picture of cellular signaling dysregulation, including endocytosis, by microRNAs in gastrointestinal cancers.
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Affiliation(s)
- Lin Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuchen Zhang
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Priscilla T Y Law
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shan Zhao
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China. .,Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, LKS Institute of Health Sciences and Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.
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11
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Lu S, Ma S, Wang Y, Huang T, Zhu Z, Zhao G. Mus musculus-microRNA-449a ameliorates neuropathic pain by decreasing the level of KCNMA1 and TRPA1, and increasing the level of TPTE. Mol Med Rep 2017; 16:353-360. [DOI: 10.3892/mmr.2017.6559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/13/2017] [Indexed: 11/06/2022] Open
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12
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Mou T, Zhu D, Wei X, Li T, Zheng D, Pu J, Guo Z, Wu Z. Identification and interaction analysis of key genes and microRNAs in hepatocellular carcinoma by bioinformatics analysis. World J Surg Oncol 2017; 15:63. [PMID: 28302149 PMCID: PMC5356276 DOI: 10.1186/s12957-017-1127-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/06/2017] [Indexed: 12/20/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the most common liver malignancy worldwide. However, present studies of its multiple gene interaction and cellular pathways still could not explain the initiation and development of HCC perfectly. To find the key genes and miRNAs as well as their potential molecular mechanisms in HCC, microarray data GSE22058, GSE25097, and GSE57958 were analyzed. Methods The microarray datasets GSE22058, GSE25097, and GSE57958, including mRNA and miRNA profiles, were downloaded from the GEO database and were analyzed using GEO2R. Functional and pathway enrichment analyses were performed using the DAVID database, and the protein–protein interaction (PPI) network was constructed using the Cytoscape software. Finally, miRDB was applied to predict the targets of the differentially expressed miRNAs (DEMs). Results A total of 115 differentially expressed genes (DEGs) were found in HCC, including 52 up-regulated genes and 63 down-regulated genes. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses from DAVID showed that up-regulated genes were significantly enriched in chromosome segregation and cell division, while the down-regulated genes were mainly involved in complement activation, protein activation cascades, carboxylic acid metabolic processes, oxoacid metabolic processes, and the immune response. From the PPI network, the 18 nodes with the highest degree were screened as hub genes. Among them, ESR1 was found to have close interactions with FOXO1, CXCL12, and GNAO1. In addition, a total of 64 DEMs were identified, which included 58 up-regulated miRNAs and 6 down-regulated miRNAs. ESR1 was potentially targeted by five miRNAs, including hsa-mir-18a and hsa-mir-221. Conclusions The roles of DEMs like hsa-mir-221 in HCC through interactions with DEGs such as ESR1 and CXCL12 may provide new clues for the diagnosis and treatment of HCC patients. Electronic supplementary material The online version of this article (doi:10.1186/s12957-017-1127-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tong Mou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Di Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Xufu Wei
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Tingting Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Daofeng Zheng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Junliang Pu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Zhen Guo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Zhongjun Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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Long non-coding RNAs and genes contributing to the generation of cancer stem cells in hepatocellular carcinoma identified by RNA sequencing analysis. Oncol Rep 2016; 36:2619-2624. [DOI: 10.3892/or.2016.5120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/22/2016] [Indexed: 11/05/2022] Open
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14
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Identification of More Feasible MicroRNA-mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction. Int J Mol Sci 2016; 17:ijms17050696. [PMID: 27171078 PMCID: PMC4881522 DOI: 10.3390/ijms17050696] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 04/13/2016] [Accepted: 04/27/2016] [Indexed: 12/28/2022] Open
Abstract
MicroRNA(miRNA)–mRNA interactions are important for understanding many biological processes, including development, differentiation and disease progression, but their identification is highly context-dependent. When computationally derived from sequence information alone, the identification should be verified by integrated analyses of mRNA and miRNA expression. The drawback of this strategy is the vast number of identified interactions, which prevents an experimental or detailed investigation of each pair. In this paper, we overcome this difficulty by the recently proposed principal component analysis (PCA)-based unsupervised feature extraction (FE), which reduces the number of identified miRNA–mRNA interactions that properly discriminate between patients and healthy controls without losing biological feasibility. The approach is applied to six cancers: hepatocellular carcinoma, non-small cell lung cancer, esophageal squamous cell carcinoma, prostate cancer, colorectal/colon cancer and breast cancer. In PCA-based unsupervised FE, the significance does not depend on the number of samples (as in the standard case) but on the number of features, which approximates the number of miRNAs/mRNAs. To our knowledge, we have newly identified miRNA–mRNA interactions in multiple cancers based on a single common (universal) criterion. Moreover, the number of identified interactions was sufficiently small to be sequentially curated by literature searches.
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Lee S, Lee M, Kim JB, Jo A, Cho EJ, Yu SJ, Lee JH, Yoon JH, Kim YJ. 17β-estradiol exerts anticancer effects in anoikis-resistant hepatocellular carcinoma cell lines by targeting IL-6/STAT3 signaling. Biochem Biophys Res Commun 2016; 473:1247-1254. [PMID: 27091428 DOI: 10.1016/j.bbrc.2016.04.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 04/11/2016] [Indexed: 02/07/2023]
Abstract
17β-Estradiol (E2) has been proven to exert protective effects against HCC; however, its mechanism on HCC proliferation and suppression of invasion remains to be further explored. Because HCC up-regulates serum Interleukin-6 (IL-6) levels and Signal Transducer and Activator of Transcription 3 (STAT3), molecular agents that attenuate IL-6/STAT3 signaling can potentially suppress HCC development. In this study, we examined involvement of E2 in anoikis resistance that induces invasion capacities and chemo-resistance. Huh-BAT and HepG2 cells grown under anchorage-independent condition were selected. The anoikis-resistant (AR) cells showed stronger chemo-resistance against sorafenib, doxorubicin, 5-fluorouracil and cisplatin compared to adherent HCC cells. AR HCC cells exhibited decreased expression of E-cadherin and increased expression of the N-cadherin and vimentin compared to adherent HCC cells. We then demonstrated that E2 suppressed cell proliferation in AR HCC cells. IL-6 treatment enhanced invasive characteristics, and E2 reversed it. Regarding mechanism of E2, it decreased in the phosphorylation of STAT3 that overexpressed on AR HCC cells. The inhibitory effect of E2 on cell growth was accompanied with cell cycle arrest at G2/M phase and caspase-3/9/PARP activation through c-Jun N-terminal Kinase (JNK) phosphorylation. Taken together, these findings suggested that E2 inhibited the proliferation of AR HCC cells through down-regulation of IL-6/STAT3 signaling. Thus, E2 can be a potential therapeutic drug for treatment of metastatic or chemo-resistant HCC.
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Affiliation(s)
- Seulki Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, South Korea.
| | - Minjong Lee
- Division of Gastroenterology, Department of Internal Medicine, Kangwon National University Hospital, 156 Baengnyeong-ro, Chuncheon-si, Gangwon-do, South Korea.
| | - Jong Bin Kim
- Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA.
| | - Ara Jo
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, South Korea.
| | - Eun Ju Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, South Korea.
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, South Korea.
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, South Korea.
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, South Korea.
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 110-799, South Korea.
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