1
|
McIntyre G, Jackson Z, Colina J, Sekhar S, DiFeo A. miR-181a: regulatory roles, cancer-associated signaling pathway disruptions, and therapeutic potential. Expert Opin Ther Targets 2024; 28:1061-1091. [PMID: 39648331 PMCID: PMC12054384 DOI: 10.1080/14728222.2024.2433687] [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: 08/01/2024] [Accepted: 11/20/2024] [Indexed: 12/10/2024]
Abstract
INTRODUCTION microRNA-181a (miR-181a) is a crucial post-transcriptional regulator of many mRNA transcripts and noncoding-RNAs, influencing cell proliferation, cancer cell stemness, apoptosis, and immune responses. Its abnormal expression is well-characterized in numerous cancers, establishing it as a significant genomic vulnerability and biomarker in cancer research. AREAS COVERED Here, we summarize miR-181a's correlation with poor patient outcomes across numerous cancers and the mechanisms governing miR-181a's activity and processing. We comprehensively describe miR-181a's involvement in multiple regulatory cancer signaling pathways, cellular processes, and the tumor microenvironment. We also discuss current therapeutic approaches to targeting miR-181a, highlighting their limitations and future potential. EXPERT OPINION miR-181a is a clinically relevant pan-cancer biomarker with potential as a therapeutic target. Its regulatory control of tumorigenic signaling pathways and immune responses positions it as a promising candidate for personalized treatments. The success of miR-181a as a target relies on the development of specific therapeutics platforms. Future research on miR-181a's role in the tumor microenvironment and the RNA binding proteins that regulate its stability will help uncover new techniques to targeting miR-181a. Further research into miR-181a serum levels in patients undergoing therapy will help to better stratify patients and enhance therapeutic success.
Collapse
Affiliation(s)
- Grace McIntyre
- Department of Pathology, Rackham Graduate School, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zoe Jackson
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jose Colina
- Department of Pathology, Rackham Graduate School, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Sreeja Sekhar
- Department of Pathology, Rackham Graduate School, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Analisa DiFeo
- Department of Pathology, Rackham Graduate School, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
2
|
Cavalleri E, Cabri A, Soto-Gomez M, Bonfitto S, Perlasca P, Gliozzo J, Callahan TJ, Reese J, Robinson PN, Casiraghi E, Valentini G, Mesiti M. An ontology-based knowledge graph for representing interactions involving RNA molecules. Sci Data 2024; 11:906. [PMID: 39174566 PMCID: PMC11341713 DOI: 10.1038/s41597-024-03673-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/23/2024] [Indexed: 08/24/2024] Open
Abstract
The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.
Collapse
Affiliation(s)
- Emanuele Cavalleri
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
| | - Alberto Cabri
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
| | - Mauricio Soto-Gomez
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
| | - Sara Bonfitto
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
| | - Paolo Perlasca
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
| | - Jessica Gliozzo
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
| | - Tiffany J Callahan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Justin Reese
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter N Robinson
- Berlin Institute of Health - Charité, Universitätsmedizin, Berlin, 13353, Germany
- ELLIS, European Laboratory for Learning and Intelligent Systems, Munich, Germany
| | - Elena Casiraghi
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- ELLIS, European Laboratory for Learning and Intelligent Systems, Munich, Germany
| | - Giorgio Valentini
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy
- ELLIS, European Laboratory for Learning and Intelligent Systems, Munich, Germany
| | - Marco Mesiti
- AnacletoLab, Computer Science Department, University of Milan, Milan, 20133, Italy.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
3
|
Chatterjee B, Thakur SS. miRNA-protein-metabolite interaction network reveals the regulatory network and players of pregnancy regulation in dairy cows. Front Cell Dev Biol 2024; 12:1377172. [PMID: 39156977 PMCID: PMC11329941 DOI: 10.3389/fcell.2024.1377172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/05/2024] [Indexed: 08/20/2024] Open
Abstract
Pregnancy is a complex process involving complex molecular interaction networks, such as between miRNA-protein, protein-protein, metabolite-metabolite, and protein-metabolite interactions. Advances in technology have led to the identification of many pregnancy-associated microRNA (miRNA), protein, and metabolite fingerprints in dairy cows. An array of miRNA, protein, and metabolite fingerprints produced during the early pregnancy of dairy cows were described. We have found the in silico interaction networks between miRNA-protein, protein-protein, metabolite-metabolite, and protein-metabolite. We have manually constructed miRNA-protein-metabolite interaction networks such as bta-miR-423-3p-IGFBP2-PGF2α interactomes. This interactome is obtained by manually combining the interaction network formed between bta-miR-423-3p-IGFBP2 and the interaction network between IGFBP2-PGF2α with IGFBP2 as a common interactor with bta-miR-423-3p and PGF2α with the provided sources of evidence. The interaction between bta-miR-423-3p and IGFBP2 has many sources of evidence including a high miRanda score of 169, minimum free energy (MFE) score of -25.14, binding probability (p) of 1, and energy of -25.5. The interaction between IGFBP2 and PGF2α occurs at high confidence scores (≥0.7 or 70%). Interestingly, PGF2α is also found to interact with different metabolites, such as PGF2α-PGD2, PGF2α-thromboxane B2, PGF2α-PGE2, and PGF2α-6-keto-PGF1α at high confidence scores (≥0.7 or 70%). Furthermore, the interactions between C3-PGE2, C3-PGD2, PGE2-PGD2, PGD2-thromboxane B2, PGE2-thromboxane B2, 6-keto-PGF1α-thromboxane B2, and PGE2-6-keto-PGF1α were also obtained at high confidence scores (≥0.7 or 70%). Therefore, we propose that miRNA-protein-metabolite interactomes involving miRNA, protein, and metabolite fingerprints of early pregnancy of dairy cows such as bta-miR-423-3p, IGFBP2, PGF2α, PGD2, C3, PGE2, 6-keto-PGF1 alpha, and thromboxane B2 may form the key regulatory networks and players of pregnancy regulation in dairy cows. This is the first study involving miRNA-protein-metabolite interactomes obtained in the early pregnancy stage of dairy cows.
Collapse
|
4
|
Chen J, Liu K, Vadas MA, Gamble JR, McCaughan GW. The Role of the MiR-181 Family in Hepatocellular Carcinoma. Cells 2024; 13:1289. [PMID: 39120319 PMCID: PMC11311592 DOI: 10.3390/cells13151289] [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: 06/28/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the fourth-leading cause of cancer-related death worldwide. Due to the high mortality rate in HCC patients, discovering and developing novel systemic treatment options for HCC is a vital unmet medical need. Among the numerous molecular alterations in HCCs, microRNAs (miRNAs) have been increasingly recognised to play critical roles in hepatocarcinogenesis. We and others have recently revealed that members of the microRNA-181 (miR-181) family were up-regulated in some, though not all, human cirrhotic and HCC tissues-this up-regulation induced epithelial-mesenchymal transition (EMT) in hepatocytes and tumour cells, promoting HCC progression. MiR-181s play crucial roles in governing the fate and function of various cells, such as endothelial cells, immune cells, and tumour cells. Previous reviews have extensively covered these aspects in detail. This review aims to give some insights into miR-181s, their targets and roles in modulating signal transduction pathways, factors regulating miR-181 expression and function, and their roles in HCC.
Collapse
Affiliation(s)
- Jinbiao Chen
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
| | - Ken Liu
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
| | - Mathew A. Vadas
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Jennifer R. Gamble
- Vascular Biology Program, Healthy Ageing Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; (M.A.V.); (J.R.G.)
| | - Geoffrey W. McCaughan
- Liver Injury and Cancer Program, Cancer Innovations Centre, Centenary Institute, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia;
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW 2050, Australia
| |
Collapse
|
5
|
Khan A, Khan A, Khan MA, Malik Z, Massey S, Parveen R, Mustafa S, Shamsi A, Husain SA. Phytocompounds targeting epigenetic modulations: an assessment in cancer. Front Pharmacol 2024; 14:1273993. [PMID: 38596245 PMCID: PMC11002180 DOI: 10.3389/fphar.2023.1273993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/09/2023] [Indexed: 04/11/2024] Open
Abstract
For centuries, plants have been serving as sources of potential therapeutic agents. In recent years, there has been a growing interest in investigating the effects of plant-derived compounds on epigenetic processes, a novel and captivating Frontier in the field of epigenetics research. Epigenetic changes encompass modifications to DNA, histones, and microRNAs that can influence gene expression. Aberrant epigenetic changes can perturb key cellular processes, including cell cycle control, intercellular communication, DNA repair, inflammation, stress response, and apoptosis. Such disruptions can contribute to cancer development by altering the expression of genes involved in tumorigenesis. However, these modifications are reversible, offering a unique avenue for therapeutic intervention. Plant secondary compounds, including terpenes, phenolics, terpenoids, and sulfur-containing compounds are widely found in grains, vegetables, spices, fruits, and medicinal plants. Numerous plant-derived compounds have demonstrated the potential to target these abnormal epigenetic modifications, including apigenin (histone acetylation), berberine (DNA methylation), curcumin (histone acetylation and epi-miRs), genistein (histone acetylation and DNA methylation), lycopene (epi-miRs), quercetin (DNA methylation and epi-miRs), etc. This comprehensive review highlights these abnormal epigenetic alterations and discusses the promising efficacy of plant-derived compounds in mitigating these deleterious epigenetic signatures in human cancer. Furthermore, it addresses ongoing clinical investigations to evaluate the therapeutic potential of these phytocompounds in cancer treatment, along with their limitations and challenges.
Collapse
Affiliation(s)
- Aqsa Khan
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Asifa Khan
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Mohammad Aasif Khan
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
- Department of Radiation Oncology, The University of Texas Health Science Centre at San Antonio, San Antonio, TX, United States
| | - Zoya Malik
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Sheersh Massey
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Rabea Parveen
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Saad Mustafa
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Syed A. Husain
- Department of Bioscience, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| |
Collapse
|
6
|
Jin Z, Sheng J, Hu Y, Zhang Y, Wang X, Huang Y. Shining a spotlight on m6A and the vital role of RNA modification in endometrial cancer: a review. Front Genet 2023; 14:1247309. [PMID: 37886684 PMCID: PMC10598767 DOI: 10.3389/fgene.2023.1247309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023] Open
Abstract
RNA modifications are mostly dynamically reversible post-transcriptional modifications, of which m6A is the most prevalent in eukaryotic mRNAs. A growing number of studies indicate that RNA modification can finely tune gene expression and modulate RNA metabolic homeostasis, which in turn affects the self-renewal, proliferation, apoptosis, migration, and invasion of tumor cells. Endometrial carcinoma (EC) is the most common gynecologic tumor in developed countries. Although it can be diagnosed early in the onset and have a preferable prognosis, some cases might develop and become metastatic or recurrent, with a worse prognosis. Fortunately, immunotherapy and targeted therapy are promising methods of treating endometrial cancer patients. Gene modifications may also contribute to these treatments, as is especially the case with recent developments of new targeted therapeutic genes and diagnostic biomarkers for EC, even though current findings on the relationship between RNA modification and EC are still very limited, especially m6A. For example, what is the elaborate mechanism by which RNA modification affects EC progression? Taking m6A modification as an example, what is the conversion mode of methylation and demethylation for RNAs, and how to achieve selective recognition of specific RNA? Understanding how they cope with various stimuli as part of in vivo and in vitro biological development, disease or tumor occurrence and development, and other processes is valuable and RNA modifications provide a distinctive insight into genetic information. The roles of these processes in coping with various stimuli, biological development, disease, or tumor development in vivo and in vitro are self-evident and may become a new direction for cancer in the future. In this review, we summarize the category, characteristics, and therapeutic precis of RNA modification, m6A in particular, with the purpose of seeking the systematic regulation axis related to RNA modification to provide a better solution for the treatment of EC.
Collapse
Affiliation(s)
- Zujian Jin
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Jingjing Sheng
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yingying Hu
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Zhang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Xiaoxia Wang
- Reproductive Medicine Center, School of Medicine, The Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China
| | - Yiping Huang
- Department of Gynecology and Obstetrics, The Fourth Affiliated Hospital, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| |
Collapse
|
7
|
Mani I, Singh V. Applications of bioinformatics in epigenetics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:1-13. [PMID: 37225316 DOI: 10.1016/bs.pmbts.2023.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Epigenetic modifications such as DNA methylation, post-translational chromatin modifications and non-coding RNA-mediated mechanisms are responsible for epigenetic inheritance. Change in gene expression due to these epigenetic modifications are responsible for new traits in different organisms leading to various diseases including cancer, diabetic kidney disease (DKD), diabetic nephropathy (DN) and renal fibrosis. Bioinformatics is an effective approach for epigenomic profiling. These epigenomic data can be analyzed by a large number of bioinformatics tools and software. Many databases are available online, which comprises huge amount of information regarding these modifications. Recent methodologies include many sequencing and analytical techniques to extrapolate different types of epigenetic data. This data can be used to design drugs against diseases linked to epigenetic modifications. This chapter briefly highlights different epigenetics databases (MethDB, REBASE, Pubmeth, MethPrimerDB, Histone Database, ChromDB, MeInfoText database, EpimiR, Methylome DB, and dbHiMo), and tools (compEpiTools, CpGProD, MethBlAST, EpiExplorer, and BiQ analyzer), which are being utilized to retrieve the data and mechanistically analysis of epigenetics modifications.
Collapse
Affiliation(s)
- Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| |
Collapse
|
8
|
Aldous N, Elsayed AK, Alajez NM, Abdelalim EM. iPSC-Derived Pancreatic Progenitors Lacking FOXA2 Reveal Alterations in miRNA Expression Targeting Key Pancreatic Genes. Stem Cell Rev Rep 2023; 19:1082-1097. [PMID: 36749553 DOI: 10.1007/s12015-023-10515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2023] [Indexed: 02/08/2023]
Abstract
Recently, we reported that forkhead box A2 (FOXA2) is required for the development of human pancreatic α- and β-cells. However, whether miRNAs play a role in regulating pancreatic genes during pancreatic development in the absence of FOXA2 expression is largely unknown. Here, we aimed to capture the dysregulated miRNAs and to identify their pancreatic-specific gene targets in pancreatic progenitors (PPs) derived from wild-type induced pluripotent stem cells (WT-iPSCs) and from iPSCs lacking FOXA2 (FOXA2-/-iPSCs). To identify differentially expressed miRNAs (DEmiRs), and genes (DEGs), two different FOXA2-/-iPSC lines were differentiated into PPs. FOXA2-/- PPs showed a significant reduction in the expression of the main PP transcription factors (TFs) in comparison to WT-PPs. RNA sequencing analysis demonstrated significant reduction in the mRNA expression of genes involved in the development and function of exocrine and endocrine pancreas. Furthermore, miRNA profiling identified 107 downregulated and 111 upregulated DEmiRs in FOXA2-/- PPs compared to WT-PPs. Target prediction analysis between DEmiRs and DEGs identified 92 upregulated miRNAs, predicted to target 1498 downregulated genes in FOXA2-/- PPs. Several important pancreatic TFs essential for pancreatic development were targeted by multiple DEmiRs. Selected DEmiRs and DEGs were further validated using RT-qPCR. Our findings revealed that FOXA2 expression is crucial for pancreatic development through regulating the expression of pancreatic endocrine and exocrine genes targeted by a set of miRNAs at the pancreatic progenitor stage. These data provide novel insights of the effect of FOXA2 deficiency on miRNA-mRNA regulatory networks controlling pancreatic development and differentiation.
Collapse
Affiliation(s)
- Noura Aldous
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ahmed K Elsayed
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Essam M Abdelalim
- College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar. .,Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.
| |
Collapse
|
9
|
Alamro H, Bajic V, Macvanin MT, Isenovic ER, Gojobori T, Essack M, Gao X. Type 2 Diabetes Mellitus and its comorbidity, Alzheimer's disease: Identifying critical microRNA using machine learning. Front Endocrinol (Lausanne) 2023; 13:1084656. [PMID: 36743910 PMCID: PMC9893111 DOI: 10.3389/fendo.2022.1084656] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/23/2022] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression in healthy and diseased states, and numerous studies have established their tremendous potential as a tool for improving the diagnosis of Type 2 Diabetes Mellitus (T2D) and its comorbidities. In this regard, we computationally identify novel top-ranked hub miRNAs that might be involved in T2D. We accomplish this via two strategies: 1) by ranking miRNAs based on the number of T2D differentially expressed genes (DEGs) they target, and 2) using only the common DEGs between T2D and its comorbidity, Alzheimer's disease (AD) to predict and rank miRNA. Then classifier models are built using the DEGs targeted by each miRNA as features. Here, we show the T2D DEGs targeted by hsa-mir-1-3p, hsa-mir-16-5p, hsa-mir-124-3p, hsa-mir-34a-5p, hsa-let-7b-5p, hsa-mir-155-5p, hsa-mir-107, hsa-mir-27a-3p, hsa-mir-129-2-3p, and hsa-mir-146a-5p are capable of distinguishing T2D samples from the controls, which serves as a measure of confidence in the miRNAs' potential role in T2D progression. Moreover, for the second strategy, we show other critical miRNAs can be made apparent through the disease's comorbidities, and in this case, overall, the hsa-mir-103a-3p models work well for all the datasets, especially in T2D, while the hsa-mir-124-3p models achieved the best scores for the AD datasets. To the best of our knowledge, this is the first study that used predicted miRNAs to determine the features that can separate the diseased samples (T2D or AD) from the normal ones, instead of using conventional non-biology-based feature selection methods.
Collapse
Affiliation(s)
- Hind Alamro
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- College of Computer and Information Systems, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Vladan Bajic
- Department of Radiology and Molecular Genetics, VINCA Institute of Nuclear Science - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Mirjana T. Macvanin
- Department of Radiology and Molecular Genetics, VINCA Institute of Nuclear Science - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Esma R. Isenovic
- Department of Radiology and Molecular Genetics, VINCA Institute of Nuclear Science - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Takashi Gojobori
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| |
Collapse
|
10
|
Abstract
MicroRNAs exert their effects in the context of gene regulatory networks. The recent development of high-throughput experimental approaches and the growing availability of gene expression data have permitted comprehensive functional studies of miRNAs. However, the data interpretation is often challenging due to the fact that miRNAs not only act cooperatively with other miRNAs but also participate in complex networks by interacting with other functional elements, including non-coding RNAs or transcription factors that often have extensive effects on cell biology. This chapter provides detailed practical procedures on how to use miRNet 2.0 ( https://www.mirnet.ca ) to perform miRNA regulatory network analytics to gain functional insights.
Collapse
Affiliation(s)
- Le Chang
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jianguo Xia
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Institute of Parasitology, McGill University, Montreal, QC, Canada.
- Department of Animal Science, McGill University, Montreal, QC, Canada.
| |
Collapse
|
11
|
Bhatia G, Prall W, Sharma B, Gregory BD. Covalent RNA modifications and their budding crosstalk with plant epigenetic processes. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102287. [PMID: 35988352 DOI: 10.1016/j.pbi.2022.102287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/29/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Our recent cognizance of diverse RNA classes undergoing dynamic covalent chemical modifications (or epitranscriptomic marks) in plants has provided fresh insight into the underlying molecular mechanisms of gene expression regulation. Comparatively, epigenetic marks comprising heritable modifications of DNA and histones have been extensively studied in plants and their impact on plant gene expression is quite established. Based on our growing knowledge of the plant epitranscriptome and epigenome, it is logical to explore how the two regulatory layers intermingle to intricately determine gene expression levels underlying key biological processes such as development and response to stress. Herein, we focus on the emerging evidence of crosstalk between the plant epitranscriptome with epigenetic regulation involving DNA modification, histone modification, and non-coding RNAs.
Collapse
Affiliation(s)
- Garima Bhatia
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Bishwas Sharma
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA.
| |
Collapse
|
12
|
Tumor-Suppressive and Oncogenic Roles of microRNA-149-5p in Human Cancers. Int J Mol Sci 2022; 23:ijms231810823. [PMID: 36142734 PMCID: PMC9501226 DOI: 10.3390/ijms231810823] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Malignant tumors are always a critical threat to human health, with complex pathogenesis, numerous causative factors, and poor prognosis. The features of cancers, such as gene mutations, epigenetic alterations, and the activation and inhibition of signaling pathways in the organism, play important roles in tumorigenesis and prognosis. MicroRNA (miRNA) enables the control of various molecular mechanisms and plays a variety of roles in human cancers, such as radiation sensitivity and tumor immunity, through the regulation of target genes. MiR-149-5p participates in the process and is closely related to lipogenesis, the migration of vascular endothelial cells, and the expression of stem-cell-related proteins. In recent years, its role in cancer has dramatically increased. In this review, we summarize the regular physiological roles of miRNAs, specifically miR-149-5p, in the organism and discuss the tumor-suppressive or oncogenic roles of miR-149-5p in different human cancers with respect to signaling pathways involved in regulation. Possible clinical applications of miR-149-5p in future targeted therapies and prognosis improvement in oncology are suggested.
Collapse
|
13
|
Liu B, Tian Y, He J, Gu Q, Jin B, Shen H, Li W, Shi L, Yu H, Shan G, Cai X. The potential of mecciRNA in hepatic stellate cell to regulate progression of nonalcoholic hepatitis. J Transl Med 2022; 20:393. [PMID: 36058953 PMCID: PMC9441041 DOI: 10.1186/s12967-022-03595-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nonalcoholic steatohepatitis (NASH) occupies a substantial proportion of chronic liver disease worldwide, of which pathogenesis needs further research. Recent studies have demonstrated the significant roles of circular RNAs (circRNAs) in NASH, while the function of a novel type of circRNAs, namely mitochondria-encoded circRNAs (mecciRNAs), remains elusive. Therefore, we aimed to investigate their potential to regulate the progression of NASH in this study. METHODS GSE134146 was used to screen for differentially expressed mecciRNAs in NASH, while GSE46300 was used to identify NASH-related genes. To establish the mecciRNA-miRNA-mRNA networks, circMINE and miRNet databases were used for predicting downstream targets. Then, consensus clustering analysis was used to determine immune subtypes of NASH. Finally, we successfully validated our findings in vitro (LPS-treated hepatic stellate cells [HSCs]) and in vivo (MCD-diet mice) NASH models. RESULTS We confirmed that circRNomics balance is disrupted in HSCs of NASH, while two mecciRNAs (hsa_circ_0089761 and hsa_circ_0089763) could function as competing for endogenous RNAs (ceRNAs) to regulate fibrosis-related signals. Furthermore, we constructed two ceRNA networks based on mecciRNAs for the first time. Cell and animal NASH models validated our findings that c-MYC and SMAD2/3 were upregulated in HSCs, while THBS1 and p-STAT3 were upregulated in hepatocytes. Moreover, we identified 21 core genes by overlapping the differentially expressed genes (NASH vs. Normal) with mecciRNA-targeted genes. According to their expression profiles, NASH patients could be divided in 2 different clusters, in which proinflammatory signals (TNF and IL-17 pathways) are significantly activated in Cluster 1. CONCLUSION We successfully established two novel mecciRNA-miRNA-mRNA networks in HSCs and hepatocytes, which were further confirmed by in vitro and in vivo models. Meanwhile, the novel immunotyping model revealed the heterogeneity of NASH, thereby might guiding treatment options. Altogether, our study brought a distinct perspective on the relationship between mecciRNAs and NASH.
Collapse
Affiliation(s)
- Boqiang Liu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China.,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China.,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China
| | - Yuanshi Tian
- Department of Diagnostic Ultrasound & Echocardiography, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Jing He
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China.,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China.,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China
| | - Qiuxia Gu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China.,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China.,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China
| | - Binghan Jin
- Department of Endocrinology, The Children's Hospital, School of Medicine, National Clinical Research Center for Child Health, Zhejiang University, Hangzhou, 310053, China
| | - Hao Shen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China.,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China.,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China
| | - Weiqi Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China.,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China.,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China
| | - Liang Shi
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China.,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China.,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China
| | - Hong Yu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China.,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China.,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China.,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China
| | - Ge Shan
- Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China. .,Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China. .,Department of Clinical Laboratory, First Affiliated Hospital of the USTC, Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, China.
| | - Xiujun Cai
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China. .,Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou, 310016, China. .,Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou, 310016, China. .,Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou, 310016, China. .,Zhejiang University Cancer Center, Zhejiang University, Hangzhou, 310030, China.
| |
Collapse
|
14
|
Jain CK, Srivastava P, Pandey AK, Singh N, Kumar RS. miRNA therapeutics in precision oncology: a natural premium to nurture. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:511-532. [PMID: 36071981 PMCID: PMC9446160 DOI: 10.37349/etat.2022.00098] [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: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The dynamic spectrum of microRNA (miRNA) has grown significantly over the years with its identification and exploration in cancer therapeutics and is currently identified as an important resource for innovative strategies due to its functional behavior for gene regulation and modulation of complex biological networks. The progression of cancer is the consequence of uncontrolled, nonsynchronous procedural faults in the biological system. Diversified and variable cellular response of cancerous cells has always raised challenges in effective cancer therapy. miRNAs, a class of non-coding RNAs (ncRNAs), are the natural genetic gift, responsible to preserve the homeostasis of cell to nurture. The unprecedented significance of endogenous miRNAs has exhibited promising therapeutic potential in cancer therapeutics. Currently, miRNA mimic miR-34, and an antimiR aimed against miR-122 has entered the clinical trials for cancer treatments. This review, highlights the recent breakthroughs, challenges, clinical trials, and advanced delivery vehicles in the administration of miRNA therapies for precision oncology.
Collapse
Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Poornima Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, GIFT city 382355, India
| | - R Suresh Kumar
- Molecular Genetics Lab, Molecular Biology Group, National Institute of Cancer Prevention and Research (ICMR), Noida 201307, India
| |
Collapse
|
15
|
Chao HM, Wang TW, Chern E, Hsu SH. Regulatory RNAs, microRNA, long-non coding RNA and circular RNA roles in colorectal cancer stem cells. World J Gastrointest Oncol 2022; 14:748-764. [PMID: 35582099 PMCID: PMC9048531 DOI: 10.4251/wjgo.v14.i4.748] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 08/18/2021] [Accepted: 03/27/2022] [Indexed: 02/06/2023] Open
Abstract
The properties of cancer stem cells (CSCs), such as self-renewal, drug resistance, and metastasis, have been indicated to be responsible for the poor prognosis of patients with colon cancers. The epigenetic regulatory network plays a crucial role in CSC properties. Regulatory non-coding RNA (ncRNA), including microRNAs, long noncoding RNAs, and circular RNAs, have an important influence on cell physiopathology. They modulate cells by regulating gene expression in different ways. This review discusses the basic characteristics and the physiological functions of colorectal cancer (CRC) stem cells. Elucidation of these ncRNAs will help us understand the pathological mechanism of CRC progression, and they could become a new target for cancer treatment.
Collapse
Affiliation(s)
- Hsiao-Mei Chao
- Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Teh-Wei Wang
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Edward Chern
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Shan-hui Hsu
- Institute of Polymer Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
16
|
Prashanth G, Vastrad B, Vastrad C, Kotrashetti S. Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. Bioinform Biol Insights 2022; 15:11779322211067365. [PMID: 34992355 PMCID: PMC8725226 DOI: 10.1177/11779322211067365] [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: 09/16/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022] Open
Abstract
Introduction: Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infections
(COVID 19) is a progressive viral infection that has been investigated
extensively. However, genetic features and molecular pathogenesis underlying
remdesivir treatment for SARS-CoV-2 infection remain unclear. Here, we used
bioinformatics to investigate the candidate genes associated in the
molecular pathogenesis of remdesivir-treated SARS-CoV-2-infected
patients. Methods: Expression profiling by high-throughput sequencing dataset (GSE149273) was
downloaded from the Gene Expression Omnibus, and the differentially
expressed genes (DEGs) in remdesivir-treated SARS-CoV-2 infection samples
and nontreated SARS-CoV-2 infection samples with an adjusted
P value of <.05 and a |log fold change| > 1.3
were first identified by limma in R software package. Next, pathway and gene
ontology (GO) enrichment analysis of these DEGs was performed. Then, the hub
genes were identified by the NetworkAnalyzer plugin and the other
bioinformatics approaches including protein-protein interaction network
analysis, module analysis, target gene—miRNA regulatory network, and target
gene—TF regulatory network. Finally, a receiver-operating characteristic
analysis was performed for diagnostic values associated with hub genes. Results: A total of 909 DEGs were identified, including 453 upregulated genes and 457
downregulated genes. As for the pathway and GO enrichment analysis, the
upregulated genes were mainly linked with influenza A and defense response,
whereas downregulated genes were mainly linked with drug
metabolism—cytochrome P450 and reproductive process. In addition, 10 hub
genes (VCAM1, IKBKE, STAT1, IL7R, ISG15, E2F1, ZBTB16, TFAP4, ATP6V1B1, and
APBB1) were identified. Receiver-operating characteristic analysis showed
that hub genes (CIITA, HSPA6, MYD88, SOCS3, TNFRSF10A, ADH1A, CACNA2D2,
DUSP9, FMO5, and PDE1A) had good diagnostic values. Conclusion: This study provided insights into the molecular mechanism of
remdesivir-treated SARS-CoV-2 infection that might be useful in further
investigations.
Collapse
Affiliation(s)
- G Prashanth
- Department of General Medicine, Basaveshwara Medical College, Chitradurga, India
| | - Basavaraj Vastrad
- Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, India
| | | | | |
Collapse
|
17
|
Abstract
MicroRNAs (miRNAs) are small noncoding elements that play essential roles in the posttranscriptional regulation of biochemical processes. miRNAs recognize and target multiple mRNAs; therefore, investigating miRNA dysregulation is an indispensable strategy to understand pathological conditions and to design innovative drugs. Targeting miRNAs in diseases improve outcomes of several therapeutic strategies thus, this present study highlights miRNA targeting methods through experimental assays and bioinformatics tools. The first part of this review focuses on experimental miRNA targeting approaches for elucidating key biochemical pathways. A growing body of evidence about the miRNA world reveals the fact that it is not possible to uncover these molecules' structural and functional characteristics related to the biological processes with a deterministic approach. Instead, a systemic point of view is needed to truly understand the facts behind the natural complexity of interactions and regulations that miRNA regulations present. This task heavily depends both on computational and experimental capabilities. Fortunately, several miRNA bioinformatics tools catering to nonexperts are available as complementary wet-lab approaches. For this purpose, this work provides recent research and information about computational tools for miRNA targeting research.
Collapse
Affiliation(s)
- Hossein Ghanbarian
- Biotechnology Department & Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehmet Taha Yıldız
- Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey
| | - Yusuf Tutar
- Division of Biochemistry, Department of Basic Pharmaceutical Sciences, Hamidiye Faculty of Pharmacy & Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey.
| |
Collapse
|
18
|
Abstract
In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.
Collapse
Affiliation(s)
- Tharcísio Soares de Amorim
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Daniel Longhi Fernandes Pedro
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil.
| |
Collapse
|
19
|
Aslani M, Mortazavi-Jahromi SS, Mirshafiey A. Cytokine storm in the pathophysiology of COVID-19: Possible functional disturbances of miRNAs. Int Immunopharmacol 2021; 101:108172. [PMID: 34601331 PMCID: PMC8452524 DOI: 10.1016/j.intimp.2021.108172] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2, as the causative agent of COVID-19, is an enveloped positives-sense single-stranded RNA virus that belongs to the Beta-CoVs sub-family. A sophisticated hyper-inflammatory reaction named cytokine storm is occurred in patients with severe/critical COVID-19, following an imbalance in immune-inflammatory processes and inhibition of antiviral responses by SARS-CoV-2, which leads to pulmonary failure, ARDS, and death. The miRNAs are small non-coding RNAs with an average length of 22 nucleotides which play various roles as one of the main modulators of genes expression and maintenance of immune system homeostasis. Recent evidence has shown that Homo sapiens (hsa)-miRNAs have the potential to work in three pivotal areas including targeting the virus genome, regulating the inflammatory signaling pathways, and reinforcing the production/signaling of IFNs-I. However, it seems that several SARS-CoV-2-induced interfering agents such as viral (v)-miRNAs, cytokine content, competing endogenous RNAs (ceRNAs), etc. preclude efficient function of hsa-miRNAs in severe/critical COVID-19. This subsequently leads to increased virus replication, intense inflammatory processes, and secondary complications development. In this review article, we provide an overview of hsa-miRNAs roles in viral genome targeting, inflammatory pathways modulation, and IFNs responses amplification in severe/critical COVID-19 accompanied by probable interventional factors and their function. Identification and monitoring of these interventional elements can help us in designing the miRNAs-based therapy for the reduction of complications/mortality rate in patients with severe/critical forms of the disease.
Collapse
Affiliation(s)
- Mona Aslani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Abbas Mirshafiey
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
20
|
Dragomir MP, Knutsen E, Calin GA. Classical and noncanonical functions of miRNAs in cancers. Trends Genet 2021; 38:379-394. [PMID: 34728089 DOI: 10.1016/j.tig.2021.10.002] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Alterations in microRNAs (miRNAs) expression are causative in the initiation and progression of human cancers. The molecular events responsible for the widespread differential expression of miRNAs in malignancy are exemplified by their location in cancer-associated genomic regions, epigenetic mechanisms, transcriptional dysregulation, chemical modifications and editing, and alterations in miRNA biogenesis proteins. The classical miRNA function is synonymous with post-transcriptional repression of target protein genes. However, several studies have reported miRNAs functioning outside this paradigm and some of these novel modes of regulation of gene expression have been implicated in cancers. Here, we summarize key aspects of miRNA involvement in cancer, with a special focus on these lesser-studied mechanisms of action.
Collapse
Affiliation(s)
- Mihnea P Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
21
|
Gregorova J, Vychytilova-Faltejskova P, Sevcikova S. Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development. Cancers (Basel) 2021; 13:1333. [PMID: 33809566 PMCID: PMC8002357 DOI: 10.3390/cancers13061333] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are small non-coding single-stranded RNA molecules regulating gene expression on a post-transcriptional level based on the seed sequence similarity. They are frequently clustered; thus, they are either simultaneously transcribed into a single polycistronic transcript or they may be transcribed independently. Importantly, microRNA families that contain the same seed region and thus target related signaling proteins, may be localized in one or more clusters, which are in a close relationship. MicroRNAs are involved in basic physiological processes, and their deregulation is associated with the origin of various pathologies, including solid tumors or hematologic malignancies. Recently, the interplay between the expression of microRNA clusters and families and epigenetic machinery was described, indicating aberrant DNA methylation or histone modifications as major mechanisms responsible for microRNA deregulation during cancerogenesis. In this review, the most studied microRNA clusters and families affected by hyper- or hypomethylation as well as by histone modifications are presented with the focus on particular mechanisms. Finally, the diagnostic and prognostic potential of microRNA clusters and families is discussed together with technologies currently used for epigenetic-based cancer therapies.
Collapse
Affiliation(s)
- Jana Gregorova
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
| | - Petra Vychytilova-Faltejskova
- Department of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic;
| | - Sabina Sevcikova
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
- Department of Clinical Hematology, University Hospital Brno, 625 00 Brno, Czech Republic
| |
Collapse
|
22
|
Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. GENE REPORTS 2020; 21:100956. [PMID: 33553808 PMCID: PMC7854084 DOI: 10.1016/j.genrep.2020.100956] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection is a leading cause of pneumonia and death. The aim of this investigation is to identify the key genes in SARS-CoV-2 infection and uncover their potential functions. We downloaded the expression profiling by high throughput sequencing of GSE152075 from the Gene Expression Omnibus database. Normalization of the data from primary SARS-CoV-2 infected samples and negative control samples in the database was conducted using R software. Then, joint analysis of the data was performed. Pathway and Gene ontology (GO) enrichment analyses were performed, and the protein-protein interaction (PPI) network, target gene - miRNA regulatory network, target gene - TF regulatory network of the differentially expressed genes (DEGs) were constructed using Cytoscape software. Identification of diagnostic biomarkers was conducted using receiver operating characteristic (ROC) curve analysis. 994 DEGs (496 up regulated and 498 down regulated genes) were identified. Pathway and GO enrichment analysis showed up and down regulated genes mainly enriched in the NOD-like receptor signaling pathway, Ribosome, response to external biotic stimulus and viral transcription in SARS-CoV-2 infection. Down and up regulated genes were selected to establish the PPI network, modules, target gene - miRNA regulatory network, target gene - TF regulatory network revealed that these genes were involved in adaptive immune system, fluid shear stress and atherosclerosis, influenza A and protein processing in endoplasmic reticulum. In total, ten genes (CBL, ISG15, NEDD4, PML, REL, CTNNB1, ERBB2, JUN, RPS8 and STUB1) were identified as good diagnostic biomarkers. In conclusion, the identified DEGs, hub genes and target genes contribute to the understanding of the molecular mechanisms underlying the advancement of SARS-CoV-2 infection and they may be used as diagnostic and molecular targets for the treatment of patients with SARS-CoV-2 infection in the future.
Collapse
Key Words
- Bioinformatics
- CBL, Cbl proto-oncogene
- DEGs, differentially expressed genes
- Diagnosis
- GO, Gene ontology
- ISG15, ISG15 ubiquitin like modifier
- Key genes
- NEDD4, NEDD4 E3 ubiquitin protein ligase
- PML, promyelocyticleukemia
- PPI, protein-protein interaction
- Pathways
- REL, REL proto-oncogene, NF-kB subunit
- ROC, receiver operating characteristic
- SARS-CoV-2 infection
- SARS-CoV-2, Severe acute respiratory syndrome corona virus 2
Collapse
|
23
|
Regulatory Mechanisms of Epigenetic miRNA Relationships in Human Cancer and Potential as Therapeutic Targets. Cancers (Basel) 2020; 12:cancers12102922. [PMID: 33050637 PMCID: PMC7600069 DOI: 10.3390/cancers12102922] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary By the virtue of targeting multiple genes, a microRNA (miRNA) can infer variable consequences on tumorigenesis by appearing as both a tumour suppressor and oncogene. miRNAs can regulate gene expression by modulating genome-wide epigenetic status of genes that are involved in various cancers. These miRNAs perform direct inhibition of key mediators of the epigenetic machinery, such as DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) genes. Along with miRNAs gene expression, similar to other protein-coding genes, miRNAs are also controlled by epigenetic mechanisms. Overall, this reciprocal interaction between the miRNAs and the epigenetic architecture is significantly implicated in the aberrant expression of miRNAs detected in various human cancers. Comprehensive knowledge of the miRNA-epigenetic dynamics in cancer is essential for the discovery of novel anticancer therapeutics. Abstract Initiation and progression of cancer are under both genetic and epigenetic regulation. Epigenetic modifications including alterations in DNA methylation, RNA and histone modifications can lead to microRNA (miRNA) gene dysregulation and malignant cellular transformation and are hereditary and reversible. miRNAs are small non-coding RNAs which regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. miRNAs can target epigenetic modifier enzymes involved in epigenetic modulation, establishing a trilateral regulatory “epi–miR–epi” feedback circuit. The intricate association between miRNAs and the epigenetic architecture is an important feature through which to monitor gene expression profiles in cancer. This review summarises the involvement of epigenetically regulated miRNAs and miRNA-mediated epigenetic modulations in various cancers. In addition, the application of bioinformatics tools to study these networks and the use of therapeutic miRNAs for the treatment of cancer are also reviewed. A comprehensive interpretation of these mechanisms and the interwoven bond between miRNAs and epigenetics is crucial for understanding how the human epigenome is maintained, how aberrant miRNA expression can contribute to tumorigenesis and how knowledge of these factors can be translated into diagnostic and therapeutic tool development.
Collapse
|
24
|
Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. 3 Biotech 2020; 10:422. [PMID: 33251083 PMCID: PMC7679428 DOI: 10.1007/s13205-020-02406-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
The goal of the present investigation is to identify the differentially expressed genes (DEGs) between SARS-CoV-2 infected and normal control samples to investigate the molecular mechanisms of infection with SARS-CoV-2. The microarray data of the dataset E-MTAB-8871 were retrieved from the ArrayExpress database. Pathway and Gene Ontology (GO) enrichment study, protein–protein interaction (PPI) network, modules, target gene–miRNA regulatory network, and target gene–TF regulatory network have been performed. Subsequently, the key genes were validated using an analysis of the receiver operating characteristic (ROC) curve. In SARS-CoV-2 infection, a total of 324 DEGs (76 up- and 248 down-regulated genes) were identified and enriched in a number of associated SARS-CoV-2 infection pathways and GO terms. Hub and target genes such as TP53, HRAS, MAPK11, RELA, IKZF3, IFNAR2, SKI, TNFRSF13C, JAK1, TRAF6, KLRF2, CD1A were identified from PPI network, target gene–miRNA regulatory network, and target gene–TF regulatory network. Study of the ROC showed that ten genes (CCL5, IFNAR2, JAK2, MX1, STAT1, BID, CD55, CD80, HAL-B, and HLA-DMA) were substantially involved in SARS-CoV-2 patients. The present investigation identified key genes and pathways that deepen our understanding of the molecular mechanisms of SARS-CoV-2 infection, and could be used for SARS-CoV-2 infection as diagnostic and therapeutic biomarkers.
Collapse
|
25
|
MicroRNAs: Diverse Mechanisms of Action and Their Potential Applications as Cancer Epi-Therapeutics. Biomolecules 2020; 10:biom10091285. [PMID: 32906681 PMCID: PMC7565521 DOI: 10.3390/biom10091285] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022] Open
Abstract
Usually, miRNAs function post-transcriptionally, by base-pairing with the 3′UTR of target mRNAs, repressing protein synthesis in the cytoplasm. Furthermore, other regions including gene promoters, as well as coding and 5′UTR regions of mRNAs are able to interact with miRNAs. In recent years, miRNAs have emerged as important regulators of both translational and transcriptional programs. The expression of miRNA genes, similar to protein-coding genes, can be epigenetically regulated, in turn miRNA molecules (named epi-miRs) are able to regulate epigenetic enzymatic machinery. The most recent line of evidence indicates that miRNAs can influence physiological processes, such as embryonic development, cell proliferation, differentiation, and apoptosis as well as pathological processes (e.g., tumorigenesis) through epigenetic mechanisms. Some tumor types show repression of tumor-suppressor epi-miRs resulting in cancer progression and metastasis, hence these molecules have become novel therapeutic targets in the last few years. This review provides information about miRNAs involvement in the various levels of transcription and translation regulation, as well as discusses therapeutic potential of tumor-suppressor epi-miRs used in in vitro and in vivo anti-cancer therapy.
Collapse
|
26
|
Screening and identification of potential prognostic biomarkers in bladder urothelial carcinoma: Evidence from bioinformatics analysis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
27
|
Karakaidos P, Karagiannis D, Rampias T. Resolving DNA Damage: Epigenetic Regulation of DNA Repair. Molecules 2020; 25:molecules25112496. [PMID: 32471288 PMCID: PMC7321228 DOI: 10.3390/molecules25112496] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
Epigenetic research has rapidly evolved into a dynamic field of genome biology. Chromatin regulation has been proved to be an essential aspect for all genomic processes, including DNA repair. Chromatin structure is modified by enzymes and factors that deposit, erase, and interact with epigenetic marks such as DNA and histone modifications, as well as by complexes that remodel nucleosomes. In this review we discuss recent advances on how the chromatin state is modulated during this multi-step process of damage recognition, signaling, and repair. Moreover, we examine how chromatin is regulated when different pathways of DNA repair are utilized. Furthermore, we review additional modes of regulation of DNA repair, such as through the role of global and localized chromatin states in maintaining expression of DNA repair genes, as well as through the activity of epigenetic enzymes on non-nucleosome substrates. Finally, we discuss current and future applications of the mechanistic interplays between chromatin regulation and DNA repair in the context cancer treatment.
Collapse
Affiliation(s)
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA;
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
- Correspondence: ; Tel.: +30-210-659-7469
| |
Collapse
|
28
|
Hernández-Romero IA, Guerra-Calderas L, Salgado-Albarrán M, Maldonado-Huerta T, Soto-Reyes E. The Regulatory Roles of Non-coding RNAs in Angiogenesis and Neovascularization From an Epigenetic Perspective. Front Oncol 2019; 9:1091. [PMID: 31709179 PMCID: PMC6821677 DOI: 10.3389/fonc.2019.01091] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
Angiogenesis is a crucial process for organ morphogenesis and growth during development, and it is especially relevant during the repair of wounded tissue in adults. It is coordinated by an equilibrium of pro- and anti-angiogenic factors; nevertheless, when affected, it promotes several diseases. Lately, a growing body of evidence is indicating that non-coding RNAs (ncRNAs), such as miRNAs, circRNAs, and lncRNAs, play critical roles in angiogenesis. These ncRNAs can act in cis or trans and alter gene transcription by several mechanisms including epigenetic processes. In the following pages, we will discuss the functions of ncRNAs in the regulation of angiogenesis and neovascularization, both in normal and disease contexts, from an epigenetic perspective. Additionally, we will describe the contribution of Next-Generation Sequencing (NGS) techniques to the discovery and understanding of the role of ncRNAs in angiogenesis.
Collapse
Affiliation(s)
| | | | | | | | - Ernesto Soto-Reyes
- Natural Sciences Department, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| |
Collapse
|
29
|
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. Med Oncol 2019; 36:73. [PMID: 31321566 DOI: 10.1007/s12032-019-1296-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022]
|
30
|
Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
Collapse
|
31
|
Alshabi AM, Vastrad B, Shaikh IA, Vastrad C. Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. Biomolecules 2019; 9:biom9050201. [PMID: 31137733 PMCID: PMC6571969 DOI: 10.3390/biom9050201] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 02/07/2023] Open
Abstract
The present study aimed to investigate the molecular mechanisms underlying glioblastoma multiform (GBM) and its biomarkers. The differentially expressed genes (DEGs) were diagnosed using the limma software package. The ToppGene (ToppFun) was used to perform pathway and Gene Ontology (GO) enrichment analysis of the DEGs. Protein-protein interaction (PPI) networks, extracted modules, miRNA-target genes regulatory network and TF-target genes regulatory network were used to obtain insight into the actions of DEGs. Survival analysis for DEGs was carried out. A total of 590 DEGs, including 243 up regulated and 347 down regulated genes, were diagnosed between scrambled shRNA expression and Lin7A knock down. The up-regulated genes were enriched in ribosome, mitochondrial translation termination, translation, and peptide biosynthetic process. The down-regulated genes were enriched in focal adhesion, VEGFR3 signaling in lymphatic endothelium, extracellular matrix organization, and extracellular matrix. The current study screened the genes in the PPI network, extracted modules, miRNA-target genes regulatory network, and TF-target genes regulatory network with higher degrees as hub genes, which included NPM1, CUL4A, YIPF1, SHC1, AKT1, VLDLR, RPL14, P3H2, DTNA, FAM126B, RPL34, and MYL5. Survival analysis indicated that the high expression of RPL36A and MRPL35 were predicting longer survival of GBM, while high expression of AP1S1 and AKAP12 were predicting shorter survival of GBM. High expression of RPL36A and AP1S1 were associated with pathogenesis of GBM, while low expression of ALPL was associated with pathogenesis of GBM. In conclusion, the current study diagnosed DEGs between scrambled shRNA expression and Lin7A knock down samples, which could improve our understanding of the molecular mechanisms in the progression of GBM, and these crucial as well as new diagnostic markers might be used as therapeutic targets for GBM.
Collapse
Affiliation(s)
- Ali Mohamed Alshabi
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran 61441, Saudi Arabia.
| | - Basavaraj Vastrad
- Department of Pharmaceutics, SET`S College of Pharmacy, Dharwad, Karnataka 580002, India.
| | - Ibrahim Ahmed Shaikh
- Department of Pharmacology, College of Pharmacy, Najran University, Najran 61441, Saudi Arabia.
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India.
| |
Collapse
|
32
|
Fan Y, Xia J. miRNet-Functional Analysis and Visual Exploration of miRNA-Target Interactions in a Network Context. Methods Mol Biol 2019; 1819:215-233. [PMID: 30421406 DOI: 10.1007/978-1-4939-8618-7_10] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To gain functional insights into microRNAs (miRNAs), researchers usually look for pathways or biological processes that are overrepresented in their target genes. The interpretation is often complicated by the fact that a single miRNA can target many genes and multiple miRNAs can regulate a single gene. Here we introduce miRNet ( www.mirnet.ca ), an easy-to-use web-based tool designed for creation, customization, visual exploration and functional interpretation of miRNA-target interaction networks. By integrating multiple high-quality miRNA-target data sources and advanced statistical methods into a powerful network visualization system, miRNet allows researchers to easily navigate the complex landscape of miRNA-target interactions to obtain deep biological insights. This tutorial provides a step-by-step protocol on how to use miRNet to create miRNA-target networks for visual exploration and functional analysis from different types of data inputs.
Collapse
Affiliation(s)
- Yannan Fan
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada. .,Department of Animal Science, McGill University, Montreal, Quebec, Canada.
| |
Collapse
|
33
|
Macharia LW, Wanjiru CM, Mureithi MW, Pereira CM, Ferrer VP, Moura-Neto V. MicroRNAs, Hypoxia and the Stem-Like State as Contributors to Cancer Aggressiveness. Front Genet 2019; 10:125. [PMID: 30842790 PMCID: PMC6391339 DOI: 10.3389/fgene.2019.00125] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/04/2019] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that play key regulatory roles in cancer acting as both oncogenes and tumor suppressors. Due to their potential roles in improving cancer prognostic, predictive, diagnostic and therapeutic approaches, they have become an area of intense research focus in recent years. Several studies have demonstrated an altered expression of several miRNAs under hypoxic condition and even shown that the hypoxic microenvironment drives the selection of a more aggressive cancer cell population through cellular adaptations referred as the cancer stem-like cell. These minor fractions of cells are characterized by their self-renewal abilities and their ability to maintain the tumor mass, suggesting their crucial roles in cancer development. This review aims to highlight the interconnected role between miRNAs, hypoxia and the stem-like state in contributing to the cancer aggressiveness as opposed to their independent contributions, and it is based in four aggressive tumors, namely glioblastoma, cervical, prostate, and breast cancers.
Collapse
Affiliation(s)
- Lucy Wanjiku Macharia
- Instituto Estadual do Cérebro Paulo Niemeyer - Secretaria de Estado de Saúde, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Anatomia Patológica, Faculdade de Medicina da Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Caroline Muriithi Wanjiru
- Instituto Estadual do Cérebro Paulo Niemeyer - Secretaria de Estado de Saúde, Rio de Janeiro, Brazil.,Instituto de Ciências Biomédicas da Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Valéria Pereira Ferrer
- Instituto Estadual do Cérebro Paulo Niemeyer - Secretaria de Estado de Saúde, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Anatomia Patológica, Faculdade de Medicina da Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vivaldo Moura-Neto
- Instituto Estadual do Cérebro Paulo Niemeyer - Secretaria de Estado de Saúde, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Anatomia Patológica, Faculdade de Medicina da Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
34
|
Understanding the molecular mechanisms underlying mood stabilizer treatments in bipolar disorder: Potential involvement of epigenetics. Neurosci Lett 2018; 669:24-31. [DOI: 10.1016/j.neulet.2016.06.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 11/23/2022]
|
35
|
Bansal A, Singh TR, Chauhan RS. A novel miRNA analysis framework to analyze differential biological networks. Sci Rep 2017; 7:14604. [PMID: 29097749 PMCID: PMC5668248 DOI: 10.1038/s41598-017-14973-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/19/2017] [Indexed: 01/30/2023] Open
Abstract
For understanding complex biological systems, a systems biology approach, involving both the top-down and bottom-up analyses, is often required. Numerous system components and their connections are best characterised as networks, which are primarily represented as graphs, with several nodes connected at multiple edges. Inefficient network visualisation is a common problem related to transcriptomic and genomic datasets. In this article, we demonstrate an miRNA analysis framework with the help of Jatropha curcas healthy and disease transcriptome datasets, functioning as a pipeline derived from the graph theory universe, and discuss how the network theory, along with gene ontology (GO) analysis, can be used to infer biological properties and other important features of a network. Network profiling, combined with GO, correlation, and co-expression analyses, can aid in efficiently understanding the biological significance of pathways, networks, as well as a studied system. The proposed framework may help experimental and computational biologists to analyse their own data and infer meaningful biological information.
Collapse
Affiliation(s)
- Ankush Bansal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat-, 173234, Solan, H.P., India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat-, 173234, Solan, H.P., India
| | - Rajinder Singh Chauhan
- Department of Biotechnology, Bennett University- A Times Group Initiative, TechZone II, Greater Noida, 201310, Uttar Pradesh, India.
| |
Collapse
|
36
|
Shukla V, Varghese VK, Kabekkodu SP, Mallya S, Satyamoorthy K. A compilation of Web-based research tools for miRNA analysis. Brief Funct Genomics 2017; 16:249-273. [PMID: 28334134 DOI: 10.1093/bfgp/elw042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features. This review provides a comprehensive assessment of web-based tools for the miRNA analysis that does not require prior knowledge of any computing languages.
Collapse
|
37
|
Russo F, Belling K, Jensen AB, Scoyni F, Brunak S, Pellegrini M. MicroRNAs, Regulatory Networks, and Comorbidities: Decoding Complex Systems. Methods Mol Biol 2017; 1580:281-295. [PMID: 28439840 DOI: 10.1007/978-1-4939-6866-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of messenger RNAs (mRNAs). Each miRNA targets a specific set of mRNAs. Upon binding the miRNA inhibits mRNA translation or facilitate mRNA degradation. miRNAs are frequently deregulated in several pathologies including cancer and cardiovascular diseases. Since miRNAs have a crucial role in fine-tuning the expression of their targets, they have been proposed as biomarkers of disease progression and prognostication.In this chapter we discuss different approaches for computational predictions of miRNA targets based on sequence complementarity and integration of expression data. In the last section of the chapter we discuss new opportunities in the study of miRNA regulatory networks in the context of temporal disease progression and comorbidities.
Collapse
Affiliation(s)
- Francesco Russo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, København N, Bygning 6, Denmark.
| | - Kirstine Belling
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, København N, Bygning 6, Denmark
| | - Anders Boeck Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, København N, Bygning 6, Denmark
| | - Flavia Scoyni
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, København N, Bygning 6, Denmark
| | - Marco Pellegrini
- Institute of Informatics and Telematics, National Research Council (CNR), Pisa, Italy
| |
Collapse
|
38
|
miR-194-5p/BCLAF1 deregulation in AML tumorigenesis. Leukemia 2017; 31:2315-2325. [PMID: 28216661 PMCID: PMC5668498 DOI: 10.1038/leu.2017.64] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/28/2016] [Accepted: 02/14/2017] [Indexed: 02/07/2023]
Abstract
Deregulation of epigenetic mechanisms, including microRNA, contributes to leukemogenesis and drug resistance by interfering with cancer-specific molecular pathways. Here, we show that the balance between miR-194-5p and its newly discovered target BCL2-associated transcription factor 1 (BCLAF1) regulates differentiation and survival of normal hematopoietic progenitors. In acute myeloid leukemias this balance is perturbed, locking cells into an immature, potentially ‘immortal’ state. Enhanced expression of miR-194-5p by treatment with the histone deacetylase inhibitor SAHA or by exogenous miR-194-5p expression re-sensitizes cells to differentiation and apoptosis by inducing BCLAF1 to shuttle between nucleus and cytosol. miR-194-5p/BCLAF1 balance was found commonly deregulated in 60 primary acute myeloid leukemia patients and was largely restored by ex vivo SAHA treatment. Our findings link treatment responsiveness to re-instatement of miR-194-5p/BCLAF1 balance.
Collapse
|
39
|
Lin Y, Chen J, Shen B. Interactions Between Genetics, Lifestyle, and Environmental Factors for Healthcare. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1005:167-191. [PMID: 28916933 DOI: 10.1007/978-981-10-5717-5_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The occurrence and progression of diseases are strongly associated with a combination of genetic, lifestyle, and environmental factors. Understanding the interplay between genetic and nongenetic components provides deep insights into disease pathogenesis and promotes personalized strategies for people healthcare. Recently, the paradigm of systems medicine, which integrates biomedical data and knowledge at multidimensional levels, is considered to be an optimal way for disease management and clinical decision-making in the era of precision medicine. In this chapter, epigenetic-mediated genetics-lifestyle-environment interactions within specific diseases and different ethnic groups are systematically discussed, and data sources, computational models, and translational platforms for systems medicine research are sequentially presented. Moreover, feasible suggestions on precision healthcare and healthy longevity are kindly proposed based on the comprehensive review of current studies.
Collapse
Affiliation(s)
- Yuxin Lin
- Center for Systems Biology, Soochow University, No.1 Shizi Street, Suzhou, Jiangsu, 215006, China
| | - Jiajia Chen
- School of Chemistry, Biology and Materials Engineering, Suzhou University of Science and Technology, No.1 Kerui road, Suzhou, Jiangsu, 215011, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, No.1 Shizi Street, Suzhou, Jiangsu, 215006, China. .,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China. .,Medical College of Guizhou University, Guiyang, 550025, China.
| |
Collapse
|
40
|
de Araújo MA, Marques TEBS, Octacílio-Silva S, de Arroxelas-Silva CL, Pereira MGAG, Peixoto-Santos JE, Kandratavicius L, Leite JP, Garcia-Cairasco N, Castro OW, Duzzioni M, Passos GA, Paçó-Larson ML, Góes Gitaí DL. Identification of microRNAs with Dysregulated Expression in Status Epilepticus Induced Epileptogenesis. PLoS One 2016; 11:e0163855. [PMID: 27695061 PMCID: PMC5047645 DOI: 10.1371/journal.pone.0163855] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/15/2016] [Indexed: 11/18/2022] Open
Abstract
The involvement of miRNA in mesial temporal lobe epilepsy (MTLE) pathogenesis has increasingly become a focus of epigenetic studies. Despite advances, the number of known miRNAs with a consistent expression response during epileptogenesis is still small. Addressing this situation requires additional miRNA profiling studies coupled to detailed individual expression analyses. Here, we perform a miRNA microarray analysis of the hippocampus of Wistar rats 24 hours after intra-hippocampal pilocarpine-induced Status Epilepticus (H-PILO SE). We identified 73 miRNAs that undergo significant changes, of which 36 were up-regulated and 37 were down-regulated. To validate, we selected 5 of these (10a-5p, 128a-3p, 196b-5p, 352 and 324-3p) for RT-qPCR analysis. Our results confirmed that miR-352 and 196b-5p levels were significantly higher and miR-128a-3p levels were significantly lower in the hippocampus of H-PILO SE rats. We also evaluated whether the 3 miRNAs show a dysregulated hippocampal expression at three time periods (0h, 24h and chronic phase) after systemic pilocarpine-induced status epilepticus (S-PILO SE). We demonstrate that miR-128a-3p transcripts are significantly reduced at all time points compared to the naïve group. Moreover, miR-196b-5p was significantly higher only at 24h post-SE, while miR-352 transcripts were significantly up-regulated after 24h and in chronic phase (epileptic) rats. Finally, when we compared hippocampi of epileptic and non-epileptic humans, we observed that transcript levels of miRNAs show similar trends to the animal models. In summary, we successfully identified two novel dysregulated miRNAs (196b-5p and 352) and confirmed miR-128a-3p downregulation in SE-induced epileptogenesis. Further functional assays are required to understand the role of these miRNAs in MTLE pathogenesis.
Collapse
Affiliation(s)
- Mykaella Andrade de Araújo
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | | | - Shirley Octacílio-Silva
- Department of Morphology, Health and Biological Sciences Center, Federal University of Sergipe, Aracajú, Sergipe, Brazil
| | - Carmem Lúcia de Arroxelas-Silva
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | | | - José Eduardo Peixoto-Santos
- Division of Neurology, Department of Neurosciences and Behavioral Sciences, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ludmyla Kandratavicius
- Division of Neurology, Department of Neurosciences and Behavioral Sciences, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João Pereira Leite
- Division of Neurology, Department of Neurosciences and Behavioral Sciences, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Norberto Garcia-Cairasco
- Department of Physiology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Olagide Wagner Castro
- Department of Physiology and Pharmacology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - Marcelo Duzzioni
- Department of Physiology and Pharmacology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
| | - Geraldo Aleixo Passos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Maria Luisa Paçó-Larson
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Leite Góes Gitaí
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceio, Alagoas, Brazil
- * E-mail:
| |
Collapse
|
41
|
Fan Y, Siklenka K, Arora SK, Ribeiro P, Kimmins S, Xia J. miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis. Nucleic Acids Res 2016; 44:W135-41. [PMID: 27105848 PMCID: PMC4987881 DOI: 10.1093/nar/gkw288] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/01/2016] [Accepted: 04/08/2016] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs) can regulate nearly all biological processes and their dysregulation is implicated in various complex diseases and pathological conditions. Recent years have seen a growing number of functional studies of miRNAs using high-throughput experimental technologies, which have produced a large amount of high-quality data regarding miRNA target genes and their interactions with small molecules, long non-coding RNAs, epigenetic modifiers, disease associations, etc These rich sets of information have enabled the creation of comprehensive networks linking miRNAs with various biologically important entities to shed light on their collective functions and regulatory mechanisms. Here, we introduce miRNet, an easy-to-use web-based tool that offers statistical, visual and network-based approaches to help researchers understand miRNAs functions and regulatory mechanisms. The key features of miRNet include: (i) a comprehensive knowledge base integrating high-quality miRNA-target interaction data from 11 databases; (ii) support for differential expression analysis of data from microarray, RNA-seq and quantitative PCR; (iii) implementation of a flexible interface for data filtering, refinement and customization during network creation; (iv) a powerful fully featured network visualization system coupled with enrichment analysis. miRNet offers a comprehensive tool suite to enable statistical analysis and functional interpretation of various data generated from current miRNA studies. miRNet is freely available at http://www.mirnet.ca.
Collapse
Affiliation(s)
- Yannan Fan
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada
| | - Keith Siklenka
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec H3G 1Y6, Canada
| | - Simran K Arora
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada
| | - Paula Ribeiro
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Québec H3G 1Y6, Canada Department of Animal Science, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Centre for Host-Parasite Interactions, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada Department of Animal Science, McGill University, Sainte Anne de Bellevue, Québec H9X 3V9, Canada
| |
Collapse
|
42
|
Bai W, Yang W, Wang W, Wang Y, Liu C, Jiang Q, Hua J, Liao M. GED: a manually curated comprehensive resource for epigenetic modification of gametogenesis. Brief Bioinform 2016; 18:98-104. [DOI: 10.1093/bib/bbw007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/29/2015] [Indexed: 12/13/2022] Open
|
43
|
Wang J, Meng X, Yuan C, Harrison AP, Chen M. The roles of cross-talk epigenetic patterns in Arabidopsis thaliana. Brief Funct Genomics 2015; 15:278-87. [PMID: 26141715 DOI: 10.1093/bfgp/elv025] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The epigenetic mechanisms, including histone modifications, DNA cytosine methylation, histone variants and noncoding RNAs (ncRNAs), play a key role in determining transcriptional outcomes. Recently, many studies have demonstrated that the different epigenetic mechanisms interplay with each other rather than work independently. In this article, we outline a framework for how different epigenetic mechanisms work with each other in Arabidopsis thalianaWe build a network of cross-talk between chromatin marks based on six classes of cross-talk interactions. The first pattern details coordinated modifications that act together to enhance or repress gene expression. The second pattern details bivalent modifications that act antagonistically toward gene expression. The third pattern is for unilateral promotion of one modification by the existence of another modification. The fourth pattern is for unilateral inhibition of one modification by another modification. The fifth pattern is for mutual inhibitory patterns. The sixth pattern is for epigenetic modifications that appear independent.We also explore the mutual regulation between chromatin marks and ncRNAs in various ways. These regulations can be divided into six parts: how ncRNA affects the binding of chromatin mark, such as miR2Epi, siR2Epi and lncR2Epi; how chromatin mark regulates ncRNA, such as Epi2miR, Epi2siR and Epi2lncR.A comprehensive network of cross-talk between different epigenetic mechanisms will help in fully understanding the functional roles and biological impacts of epigenetic regulation.
Collapse
|
44
|
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs, 18-23 nucleotides long, which act as post-transcriptional regulators of gene expression. miRNAs are strongly implicated in the pathogenesis of many common diseases, including IBDs. This review aims to outline the history, biogenesis and regulation of miRNAs. The role of miRNAs in the development and regulation of the innate and adaptive immune system is discussed, with a particular focus on mechanisms pertinent to IBD and the potential translational applications.
Collapse
Affiliation(s)
- R Kalla
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - N T Ventham
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - N A Kennedy
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - J F Quintana
- Centre for Immunity, Infection and Evolution, Ashworth laboratories, University of Edinburgh, Edinburgh, UK
| | - E R Nimmo
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - A H Buck
- Centre for Immunity, Infection and Evolution, Ashworth laboratories, University of Edinburgh, Edinburgh, UK
| | - J Satsangi
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| |
Collapse
|
45
|
Tye CE, Gordon JAR, Martin-Buley LA, Stein JL, Lian JB, Stein GS. Could lncRNAs be the missing links in control of mesenchymal stem cell differentiation? J Cell Physiol 2015; 230:526-34. [PMID: 25258250 DOI: 10.1002/jcp.24834] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/31/2022]
Abstract
Long suspected, recently recognized, and increasingly studied, non protein-coding RNAs (ncRNAs) are emerging as key drivers of biological control and pathology. Since their discovery in 1993, microRNAs (miRNAs) have been the subject of intense research focus and investigations have revealed striking findings, establishing that these molecules can exert a substantial level of biological control in numerous tissues. More recently, long ncRNAs (lncRNAs), the lesser-studied siblings of miRNA, have been suggested to have a similar robust role in developmental and adult tissue regulation. Mesenchymal stem cells (MSCs) are an important source of multipotent cells for normal and therapeutic tissue repair. Much is known about the critical role of miRNAs in biogenesis and differentiation of MSCs however; recent studies have suggested lncRNAs may play an equally important role in the regulation of these cells. Here we highlight the role of lncRNAs in the regulation of mesenchymal stem cell lineages including adipocytes, chondrocytes, myoblasts, and osteoblasts. In addition, the potential for these noncoding RNAs to be used as biomarkers for disease or therapeutic targets is also discussed.
Collapse
Affiliation(s)
- Coralee E Tye
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont
| | | | | | | | | | | |
Collapse
|
46
|
Santulli G. A Fleeting Glimpse Inside microRNA, Epigenetics, and Micropeptidomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 887:1-14. [PMID: 26662983 PMCID: PMC4871246 DOI: 10.1007/978-3-319-22380-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRs) are important regulators of gene expression in numerous biological processes. Their maturation process is herein described, including the most updated insights from the current literature. Circa 2000 miR sequences have been identified in the human genome, with over 50,000 miR-target interactions, including enzymes involved in epigenetic modulation of gene expression. Moreover, some "pieces of RNA" previously annotated as noncoding have been recently found to encode micropeptides that carry out critical mechanistic functions in the cell. Advanced techniques now available will certainly allow a precise scanning of the genome looking for micropeptides hidden within the "noncoding" RNA.
Collapse
|