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Liao L, Tang Y, Zhou Y, Meng X, Li B, Zhang X. MicroRNA-126 (MiR-126): key roles in related diseases. J Physiol Biochem 2024; 80:277-286. [PMID: 38517589 DOI: 10.1007/s13105-024-01017-y] [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: 12/02/2023] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
In eukaryotes such as humans, some non-coding single-stranded RNAs (ncRNAs) help to regulate the pre- and post-transcriptional expression of certain genes, which in turn control many important physiological processes, such as cell proliferation, distinctions, invasion, angiogenesis, and embryonic development. microRNA-126 is an important member of these miRNAs that can be directly or indirectly involved in the control of angiogenesis. Recently, numerous studies have expounded that microRNA-126 can inhibit or promote angiogenesis as well as attenuate inflammatory responses through complex molecular mechanisms. As such, it serves as a biomarker or potential therapeutic target for the prediction, diagnosis, and treatment of relevant diseases. In this review, we present the advancements in research regarding microRNA-126's role in the diagnosis and treatment of related diseases, aiming to provide innovative therapeutic options for the diagnosis and treatment of clinically relevant diseases.
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Affiliation(s)
- Li Liao
- The Second People's Hospital of Yibin-Yibin Hospital of West China Hospital of Sichuan University, Yibin, 644000, China.
| | - Yan Tang
- The Second People's Hospital of Yibin-Yibin Hospital of West China Hospital of Sichuan University, Yibin, 644000, China
| | - Yanping Zhou
- The Second People's Hospital of Yibin-Yibin Hospital of West China Hospital of Sichuan University, Yibin, 644000, China
| | - Xianglin Meng
- The Second People's Hospital of Yibin-Yibin Hospital of West China Hospital of Sichuan University, Yibin, 644000, China
| | - Bo Li
- Third Affiliated Hospital of Chengdu Medical College-Chengdu Pidu District People's Hospital, Chengdu, 611700, China
| | - Xiaochun Zhang
- The Second People's Hospital of Yibin-Yibin Hospital of West China Hospital of Sichuan University, Yibin, 644000, China.
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Shaikh FS, Siegel RJ, Srivastava A, Fox DA, Ahmed S. Challenges and promise of targeting miRNA in rheumatic diseases: a computational approach to identify miRNA association with cell types, cytokines, and disease mechanisms. Front Immunol 2024; 14:1322806. [PMID: 38264662 PMCID: PMC10803576 DOI: 10.3389/fimmu.2023.1322806] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that alter the expression of target genes at the post-transcriptional level, influencing diverse outcomes in metabolism, cell differentiation, proliferation, cell survival, and cell death. Dysregulated miRNA expression is implicated in various rheumatic conditions, including ankylosing spondylitis (AS), gout, juvenile idiopathic arthritis (JIA), osteoarthritis (OA), psoriatic arthritis, rheumatoid arthritis (RA), Sjogren's syndrome, systemic lupus erythematosus (SLE) and systemic sclerosis. For this review, we used an open-source programming language- PowerShell, to scan the massive number of existing primary research publications on PubMed on miRNAs in these nine diseases to identify and count unique co-occurrences of individual miRNAs and the disease name. These counts were used to rank the top seven most relevant immuno-miRs based on their research volume in each rheumatic disease. Individual miRNAs were also screened for publication with the names of immune cells, cytokines, and pathological processes involved in rheumatic diseases. These occurrences were tabulated into matrices to identify hotspots for research relevance. Based on this information, we summarize the basic and clinical findings for the top three miRNAs - miR-146, miR-155, and miR-21 - whose relevance spans across multiple rheumatic diseases. Furthermore, we highlight some unique miRNAs for each disease and why some rheumatic conditions lack research in this emerging epigenetics field. With the overwhelming number of publications on miRNAs in rheumatic diseases, this review serves as a 'relevance finder' to guide researchers in selecting miRNAs based on the compiled existing knowledge of their involvement in disease pathogenesis. This approach applies to other disease contexts with the end goal of developing miRNA-based therapeutics.
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Affiliation(s)
- Farheen S. Shaikh
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
| | - Ruby J. Siegel
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
| | - Aayush Srivastava
- Department of Computer and Information Science and Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, United States
| | - David A. Fox
- Department of Medicine, Division of Rheumatology and Clinical Autoimmunity Center of Excellence, University of Michigan Medical System, Ann Arbor, MI, United States
| | - Salahuddin Ahmed
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
- Division of Rheumatology, University of Washington School of Medicine, Seattle, WA, United States
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3
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Solorzano J, Carrillo-de Santa Pau E, Laguna T, Busturia A. A genome-wide computational approach to define microRNA-Polycomb/trithorax gene regulatory circuits in Drosophila. Dev Biol 2023; 495:63-75. [PMID: 36596335 DOI: 10.1016/j.ydbio.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 01/02/2023]
Abstract
Characterization of gene regulatory networks is fundamental to understanding homeostatic development. This process can be simplified by analyzing relatively simple genomes such as the genome of Drosophila melanogaster. In this work we have developed a computational framework in Drosophila to explore for the presence of gene regulatory circuits between two large groups of transcriptional regulators: the epigenetic group of the Polycomb/trithorax (PcG/trxG) proteins and the microRNAs (miRNAs). We have searched genome-wide for miRNA targets in PcG/trxG transcripts as well as for Polycomb Response Elements (PREs) in miRNA genes. Our results show that 10% of the analyzed miRNAs could be controlling PcG/trxG gene expression, while 40% of those miRNAs are putatively controlled by the selected set of PcG/trxG proteins. The integration of these analyses has resulted in the predicted existence of 3 classes of miRNA-PcG/trxG crosstalk interactions that define potential regulatory circuits. In the first class, miRNA-PcG circuits are defined by miRNAs that reciprocally crosstalk with PcG. In the second, miRNA-trxG circuits are defined by miRNAs that reciprocally crosstalk with trxG. In the third class, miRNA-PcG/trxG shared circuits are defined by miRNAs that crosstalk with both PcG and trxG regulators. These putative regulatory circuits may uncover a novel mechanism in Drosophila for the control of PcG/trxG and miRNAs levels of expression. The computational framework developed here for Drosophila melanogaster can serve as a model case for similar analyses in other species. Moreover, our work provides, for the first time, a new and useful resource for the Drosophila community to consult prior to experimental studies investigating the epigenetic regulatory networks of miRNA-PcG/trxG mediated gene expression.
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Affiliation(s)
- Jacobo Solorzano
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, 28049, Madrid, Spain; Centre de Recherches en Cancerologie de Toulouse, 2 Av. Hubert Curien, 31100, Toulouse, France
| | - Enrique Carrillo-de Santa Pau
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, CEI UAM+CSIC, 28049, Madrid, Spain
| | - Teresa Laguna
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, CEI UAM+CSIC, 28049, Madrid, Spain.
| | - Ana Busturia
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, 28049, Madrid, Spain.
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Singh NP, Yang X, Bam M, Nagarkatti M, Nagarkatti P. 2,3,7,8-Tetrachlorodibenzo-p-dioxin induces multigenerational alterations in the expression of microRNA in the thymus through epigenetic modifications. PNAS NEXUS 2023; 2:pgac290. [PMID: 36712935 PMCID: PMC9833045 DOI: 10.1093/pnasnexus/pgac290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/07/2022] [Indexed: 05/11/2023]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a potent AhR ligand, is an environmental contaminant that is known for mediating toxicity across generations. However, whether TCDD can induce multigenerational changes in the expression of microRNAs (miRs) has not been previously studied. In the current study, we investigated the effect of administration of TCDD in pregnant mice (F0) on gestational day 14, on the expression of miRs in the thymus of F0 and subsequent generations (F1 and F2). Of the 3200 miRs screened, 160 miRs were dysregulated similarly in F0, F1, and F2 generations, while 46 miRs were differentially altered in F0 to F2 generations. Pathway analysis revealed that the changes in miR signature profile mediated by TCDD affected the genes that regulate cell signaling, apoptosis, thymic atrophy, cancer, immunosuppression, and other physiological pathways. A significant number of miRs that showed altered expression exhibited dioxin response elements (DRE) on their promoters. Focusing on one such miR, namely miR-203 that expressed DREs and was induced across F0 to F2 by TCDD, promoter analysis showed that one of the DREs expressed by miR-203 was functional to TCDD-mediated upregulation. Also, the histone methylation status of H3K4me3 in the miR-203 promoter was significantly increased near the transcriptional start site in TCDD-treated thymocytes across F0 to F2 generations. Genome-wide chromatin immunoprecipitation sequencing study suggested that TCDD may cause alterations in histone methylation in certain genes across the three generations. Together, the current study demonstrates that gestational exposure to TCDD can alter the expression of miRs in F0 through direct activation of DREs as well as across F0, F1, and F2 generations through epigenetic pathways.
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Affiliation(s)
- Narendra P Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Marpe Bam
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA
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Vadevoo SMP, Gunassekaran GR, Yoo JD, Kwon TH, Hur K, Chae S, Lee B. Epigenetic therapy reprograms M2-type tumor-associated macrophages into an M1-like phenotype by upregulating miR-7083-5p. Front Immunol 2022; 13:976196. [PMID: 36483544 PMCID: PMC9724234 DOI: 10.3389/fimmu.2022.976196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
Abstract
Reprogramming M2-type, pro-tumoral tumor-associated macrophages (TAMs) into M1-type, anti-tumoral macrophages is a key strategy in cancer therapy. In this study, we exploited epigenetic therapy using the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) and the histone deacetylation inhibitor trichostatin A (TSA), to reprogram M2-type macrophages into an M1-like phenotype. Treatment of M2-type macrophages with the combination of 5-aza-dC and TSA decreased the levels of M2 macrophage cytokines while increasing those of M1 macrophage cytokines, as compared to the use of either therapy alone. Conditioned medium of M2 macrophages treated with the combination of 5-aza-dC and TSA sensitized the tumor cells to paclitaxel. Moreover, treatment with the combination inhibited tumor growth and improved anti-tumor immunity in the tumor microenvironment. Depletion of macrophages reduced the anti-tumor growth activity of the combination therapy. Profiling of miRNAs revealed that the expression of miR-7083-5p was remarkably upregulated in M2 macrophages, following treatment with 5-aza-dC and TSA. Transfection of miR-7083-5p reprogrammed the M2-type macrophages towards an M1-like phenotype, and adoptive transfer of M2 macrophages pre-treated with miR-7083-5p into mice inhibited tumor growth. miR-7083-5p inhibited the expression of colony-stimulating factor 2 receptor alpha and CD43 as candidate targets. These results show that epigenetic therapy upon treatment with the combination of 5-aza-dC and TSA skews M2-type TAMs towards the M1-like phenotype by upregulating miR-7083-5p, which contributes to the inhibition of tumor growth.
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Affiliation(s)
- Sri Murugan Poongkavithai Vadevoo
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea,Cell & Matrix Research Institute (CMRI), Kyungpook National University, Daegu, South Korea
| | - Gowri Rangaswamy Gunassekaran
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea,Cell & Matrix Research Institute (CMRI), Kyungpook National University, Daegu, South Korea
| | - Jae Do Yoo
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea,Cell & Matrix Research Institute (CMRI), Kyungpook National University, Daegu, South Korea
| | - Tae-Hwan Kwon
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea,Cell & Matrix Research Institute (CMRI), Kyungpook National University, Daegu, South Korea,Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu, South Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea,Cell & Matrix Research Institute (CMRI), Kyungpook National University, Daegu, South Korea,Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu, South Korea
| | - Sehyun Chae
- Korea Brain Research Institute (KBRI), Daegu, South Korea
| | - Byungheon Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea,Cell & Matrix Research Institute (CMRI), Kyungpook National University, Daegu, South Korea,Department of Biomedical Science, Graduate School, Kyungpook National University, Daegu, South Korea,*Correspondence: Byungheon Lee,
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Xu N, Liu J, Li X. Lupus nephritis: The regulatory interplay between epigenetic and MicroRNAs. Front Physiol 2022; 13:925416. [PMID: 36187762 PMCID: PMC9523357 DOI: 10.3389/fphys.2022.925416] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous, small, non-coding RNA molecules that act as epigenetic modifiers to regulate the protein levels of target messenger RNAs without altering their genetic sequences. The highly complex role of miRNAs in the epigenetics of lupus nephritis (LN) is increasingly being recognized. DNA methylation and histone modifications are focal points of epigenetic research. miRNAs play a critical role in renal development and physiology, and dysregulation may result in abnormal renal cell proliferation, inflammation, and fibrosis of the kidneys in LN. However, epigenetic and miRNA-mediated regulation are not mutually exclusive. Further research has established a link between miRNA expression and epigenetic regulation in various disorders, including LN. This review summarizes the most recent evidence regarding the interaction between miRNAs and epigenetics in LN and highlights potential therapeutic and diagnostic targets.
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Affiliation(s)
- Ning Xu
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jie Liu
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xiangling Li
- Department of Nephrology, Affiliated Hospital of Weifang Medical University, Weifang, China
- *Correspondence: Xiangling Li,
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7
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Valle F, Osella M, Caselle M. Multiomics Topic Modeling for Breast Cancer Classification. Cancers (Basel) 2022; 14:1150. [PMID: 35267458 PMCID: PMC8909787 DOI: 10.3390/cancers14051150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
The integration of transcriptional data with other layers of information, such as the post-transcriptional regulation mediated by microRNAs, can be crucial to identify the driver genes and the subtypes of complex and heterogeneous diseases such as cancer. This paper presents an approach based on topic modeling to accomplish this integration task. More specifically, we show how an algorithm based on a hierarchical version of stochastic block modeling can be naturally extended to integrate any combination of 'omics data. We test this approach on breast cancer samples from the TCGA database, integrating data on messenger RNA, microRNAs, and copy number variations. We show that the inclusion of the microRNA layer significantly improves the accuracy of subtype classification. Moreover, some of the hidden structures or "topics" that the algorithm extracts actually correspond to genes and microRNAs involved in breast cancer development and are associated to the survival probability.
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Affiliation(s)
- Filippo Valle
- Physics Department, University of Turin and INFN, via P. Giuria 1, 10125 Turin, Italy; (M.O.); (M.C.)
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microRNA-Mediated Encoding and Decoding of Time-Dependent Signals in Tumorigenesis. Biomolecules 2022; 12:biom12020213. [PMID: 35204714 PMCID: PMC8961662 DOI: 10.3390/biom12020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
microRNAs, pivotal post-transcriptional regulators of gene expression, in the past decades have caught the attention of researchers for their involvement in different biological processes, ranging from cell development to cancer. Although lots of effort has been devoted to elucidate the topological features and the equilibrium properties of microRNA-mediated motifs, little is known about how the information encoded in frequency, amplitude, duration, and other features of their regulatory signals can affect the resulting gene expression patterns. Here, we review the current knowledge about microRNA-mediated gene regulatory networks characterized by time-dependent input signals, such as pulses, transient inputs, and oscillations. First, we identify the general characteristic of the main motifs underlying temporal patterns. Then, we analyze their impact on two commonly studied oncogenic networks, showing how their dysfunction can lead to tumorigenesis.
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Ahmad Z, Somanath PR. AKT Isoforms in the Immune Response in Cancer. Curr Top Microbiol Immunol 2022; 436:349-366. [PMID: 36243852 DOI: 10.1007/978-3-031-06566-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
AKT is a protein kinase that exists in three isoforms: AKT1, AKT2, and AKT3. Though similar in structure, these isoforms display different effects. AKT is activated downstream of PI3K, and together, this signaling pathway helps regulate cellular processes including cell growth, proliferation, metabolism, survival, and apoptosis. Disruption in these pathways has been associated with disorders including cardiovascular diseases, developmental disorders, inflammatory responses, autoimmune diseases, neurologic disorders, type 2 diabetes, and several cancers. In cancer, deregulation in the PI3K/AKT pathway can be manifested as tumorigenesis, pathological angiogenesis, and metastasis. Increased activity has been correlated with tumor progression and resistance to cancer treatments. Recent studies have suggested that inhibition of the PI3K/AKT pathway plays a significant role in the development, expansion, and proliferation of cells of the immune system. Additionally, AKT has been found to play an important role in differentiating regulatory T cells, activating B cells, and augmenting tumor immunosurveillance. This emphasizes AKT as a potential target for inhibition in cancer therapy. This chapter reviews AKT structure and regulation, its different isoforms, its role in immune cells, and its modulation in oncotherapy.
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Affiliation(s)
- Zayd Ahmad
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, 30912, USA
| | - Payaningal R Somanath
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, 30912, USA.
- Georgia Cancer Center, Vascular Biology Center and Department of Medicine, Augusta University, Augusta, GA, 30912, USA.
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Gurbuz V, Sozen S, Bilen CY, Konac E. miR-148a, miR-152 and miR-200b promote prostate cancer metastasis by targeting DNMT1 and PTEN expression. Oncol Lett 2021; 22:805. [PMID: 34630712 PMCID: PMC8488332 DOI: 10.3892/ol.2021.13066] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRs) modulate the expression of target genes in the signal pathway on transcriptome level. The present study investigated the ‘epigenetic-based miRNA (epi-miRNA)-mRNA’ regulatory network of miR-34b, miR-34c, miR-148a, miR-152, miR-200a and miR-200b epi-miRNAs and their target genes, DNA methyltransferase (DNMT1, 3a and 3b), phosphate and tensin homolog (PTEN) and NK3 Homeobox 1 (NKX3.1), in prostate cancer (PCa) using reverse transcription-quantitative PCR. The expression level of NKX3.1 were not significantly different between the PCa, Met-PCa and control groups. However, in the PCa and Met-PCa groups, the expression level of DNMT1 was upregulated, while DNMT3a, DNMT3b and PTEN were downregulated. Overexpression of DNMT1 (~5 and ~6-fold increase in the PCa and Met-PCa groups respectively) was accompanied by a decreased expression in PTEN, indicating a potential negative association. Both groups indicated that a high level of DNMT1 is associated with the aggressiveness of cancer, and there is a a directly proportional relationship between this gene and PSA, GS and TNM staging. A significant ~2 to ~5-fold decrease in the expression levels of DNMT3a and DNMT3b was found in both groups. In the PCa group, significant associations were identified between miR-34b and DNMT1/DNMT3b; between miR-34c/miR-148a and all target genes; between miR-152 and DNMT1/DNMT3b and PTEN; and between miR-200a/b and DNMT1. In the Met-PCa group, miR-148a, miR-152 and miR-200b exhibited a significant association with all target genes. A significant negative association was identified between PTEN and DNMT1 in the Met-PCa group. It was also revealed that that miR-148a, miR-152 and miR-200b increased the expression of DNMT1 and suppressed PTEN. Furthermore, the ‘epi-miRNA-mRNA’ bidirectional feedback loop was emphasised and the methylation pattern in PCa anti-cancer therapeutics was highlighted.
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Affiliation(s)
- Venhar Gurbuz
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Ankara 06510, Turkey
| | - Sinan Sozen
- Department of Urology, Faculty of Medicine, Gazi University, Ankara 06510, Turkey
| | - Cenk Y Bilen
- Department of Urology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Ece Konac
- Department of Medical Biology and Genetics, Faculty of Medicine, Gazi University, Ankara 06510, Turkey
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11
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Krishnan A, Chilton E, Raman J, Saxena P, McFarlane C, Trollope AF, Kinobe R, Chilton L. Are Interactions between Epicardial Adipose Tissue, Cardiac Fibroblasts and Cardiac Myocytes Instrumental in Atrial Fibrosis and Atrial Fibrillation? Cells 2021; 10:2501. [PMID: 34572150 PMCID: PMC8467050 DOI: 10.3390/cells10092501] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Atrial fibrillation is very common among the elderly and/or obese. While myocardial fibrosis is associated with atrial fibrillation, the exact mechanisms within atrial myocytes and surrounding non-myocytes are not fully understood. This review considers the potential roles of myocardial fibroblasts and myofibroblasts in fibrosis and modulating myocyte electrophysiology through electrotonic interactions. Coupling with (myo)fibroblasts in vitro and in silico prolonged myocyte action potential duration and caused resting depolarization; an optogenetic study has verified in vivo that fibroblasts depolarized when coupled myocytes produced action potentials. This review also introduces another non-myocyte which may modulate both myocardial (myo)fibroblasts and myocytes: epicardial adipose tissue. Epicardial adipocytes are in intimate contact with myocytes and (myo)fibroblasts and may infiltrate the myocardium. Adipocytes secrete numerous adipokines which modulate (myo)fibroblast and myocyte physiology. These adipokines are protective in healthy hearts, preventing inflammation and fibrosis. However, adipokines secreted from adipocytes may switch to pro-inflammatory and pro-fibrotic, associated with reactive oxygen species generation. Pro-fibrotic adipokines stimulate myofibroblast differentiation, causing pronounced fibrosis in the epicardial adipose tissue and the myocardium. Adipose tissue also influences myocyte electrophysiology, via the adipokines and/or through electrotonic interactions. Deeper understanding of the interactions between myocytes and non-myocytes is important to understand and manage atrial fibrillation.
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Affiliation(s)
- Anirudh Krishnan
- College of Medicine and Dentistry, James Cook University, Townsville, QLD 4811, Australia;
| | - Emily Chilton
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Jaishankar Raman
- Austin & St Vincent’s Hospitals, Melbourne University, Melbourne, VIC 3010, Australia;
- Applied Artificial Intelligence Institute, Deakin University, Melbourne, VIC 3217, Australia
- Department of Surgery, Oregon Health and Science University, Portland, OR 97239, USA
- School of Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
| | - Pankaj Saxena
- Department of Cardiothoracic Surgery, Townsville University Hospital, Townsville, QLD 4814, Australia;
| | - Craig McFarlane
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
| | - Alexandra F. Trollope
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, College of Medicine and Dentistry, James Cook University, Townsville, QLD 4811, Australia;
| | - Robert Kinobe
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
| | - Lisa Chilton
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia;
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12
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Hati S, Duddu AS, Jolly MK. Operating principles of circular toggle polygons. Phys Biol 2021; 18. [PMID: 33730700 DOI: 10.1088/1478-3975/abef79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/17/2021] [Indexed: 11/12/2022]
Abstract
Decoding the dynamics of cellular decision-making and cell differentiation is a central question in cell and developmental biology. A common network motif involved in many cell-fate decisions is a mutually inhibitory feedback loop between two self-activating 'master regulators' A and B, also called as toggle switch. Typically, it can allow for three stable states-(high A, low B), (low A, high B) and (medium A, medium B). A toggle triad-three mutually repressing regulators A, B and C, i.e. three toggle switches arranged circularly (between A and B, between B and C, and between A and C)-can allow for six stable states: three 'single positive' and three 'double positive' ones. However, the operating principles of larger toggle polygons, i.e. toggle switches arranged circularly to form a polygon, remain unclear. Here, we simulate using both discrete and continuous methods the dynamics of different sized toggle polygons. We observed a pattern in their steady state frequency depending on whether the polygon was an even or odd numbered one. The even-numbered toggle polygons result in two dominant states with consecutive components of the network expressing alternating high and low levels. The odd-numbered toggle polygons, on the other hand, enable more number of states, usually twice the number of components with the states that follow 'circular permutation' patterns in their composition. Incorporating self-activations preserved these trends while increasing the frequency of multistability in the corresponding network. Our results offer insights into design principles of circular arrangement of regulatory units involved in cell-fate decision making, and can offer design strategies for synthesizing genetic circuits.
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Affiliation(s)
- Souvadra Hati
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.,Undergraduate Programme, Indian Institute of Science, Bangalore, India
| | - Atchuta Srinivas Duddu
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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13
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Favier A, Rocher G, Larsen AK, Delangle R, Uzan C, Sabbah M, Castela M, Duval A, Mehats C, Canlorbe G. MicroRNA as Epigenetic Modifiers in Endometrial Cancer: A Systematic Review. Cancers (Basel) 2021; 13:cancers13051137. [PMID: 33800944 PMCID: PMC7961497 DOI: 10.3390/cancers13051137] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/02/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Endometrial cancer (EC) is the 2nd most common gynecologic cancer worldwide. MicroRNAs (miRNAs) are small noncoding RNAs that contribute to epigenetic regulation. The objective of this systematic review is to summarize our current knowledge on the role of miRNAs in the epigenetic deregulation of tumor-related genes in EC. It includes all miRNAs reported to be involved in EC including their roles in DNA methylation and RNA-associated silencing. This systematic review should be useful for development of novel strategies to improve diagnosis and risk assessment as well as for new treatments aimed at miRNAs, their target genes or DNA methylation. Abstract The objective of this systematic review is to summarize our current knowledge on the influence of miRNAs in the epigenetic deregulation of tumor-related genes in endometrial cancer (EC). We conducted a literature search on the role of miRNAs in the epigenetic regulation of EC applying the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The following terms were used: microRNA, miRNA, miR, endometrial cancer, endometrium, epigenetic, epimutation, hypermethylation, lynch, deacetylase, DICER, novel biomarker, histone, chromatin. The miRNAs were classified and are presented according to their function (tumor suppressor or onco-miRNA), their targets (when known), their expression levels in EC tissue vs the normal surrounding tissue, and the degree of DNA methylation in miRNA loci and CpG sites. Data were collected from 201 articles, including 190 original articles, published between November 1, 2008 and September 30, 2020 identifying 313 different miRNAs implicated in epigenetic regulation of EC. Overall, we identified a total of 148 miRNAs with decreased expression in EC, 140 miRNAs with increased expression in EC, and 22 miRNAs with discordant expression levels. The literature implicated different epigenetic phenomena including altered miRNA expression levels (miR-182, -230), changes in the methylation of miRNA loci (miR-34b, -129-2, -130a/b, -152, -200b, -625) and increased/decreased methylation of target genes (miR-30d,-191). This work provides an overview of all miRNAs reported to be involved in epigenetic regulation in EC including DNA methylation and RNA-associated silencing. These findings may contribute to novel strategies in diagnosis, risk assessment, and treatments aimed at miRNAs, their target genes or DNA methylation.
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Affiliation(s)
- Amélia Favier
- Centre de Recherche Saint-Antoine (CRSA), INSERM UMR_S_938, Cancer Biology and Therapeutics, Sorbonne University, 75012 Paris, France; (A.K.L.); (C.U.); (M.S.)
- Department of Gynecological and Breast Surgery and Oncology, Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris (AP-HP), University Hospital, 75013 Paris, France; (G.R.); (R.D.)
- Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, INSERM, Sorbonne Université, 75012 Paris, France;
- Correspondence: (A.F.); (G.C.)
| | - Grégoire Rocher
- Department of Gynecological and Breast Surgery and Oncology, Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris (AP-HP), University Hospital, 75013 Paris, France; (G.R.); (R.D.)
- Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, INSERM, Sorbonne Université, 75012 Paris, France;
| | - Annette K. Larsen
- Centre de Recherche Saint-Antoine (CRSA), INSERM UMR_S_938, Cancer Biology and Therapeutics, Sorbonne University, 75012 Paris, France; (A.K.L.); (C.U.); (M.S.)
| | - Romain Delangle
- Department of Gynecological and Breast Surgery and Oncology, Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris (AP-HP), University Hospital, 75013 Paris, France; (G.R.); (R.D.)
| | - Catherine Uzan
- Centre de Recherche Saint-Antoine (CRSA), INSERM UMR_S_938, Cancer Biology and Therapeutics, Sorbonne University, 75012 Paris, France; (A.K.L.); (C.U.); (M.S.)
- Department of Gynecological and Breast Surgery and Oncology, Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris (AP-HP), University Hospital, 75013 Paris, France; (G.R.); (R.D.)
| | - Michèle Sabbah
- Centre de Recherche Saint-Antoine (CRSA), INSERM UMR_S_938, Cancer Biology and Therapeutics, Sorbonne University, 75012 Paris, France; (A.K.L.); (C.U.); (M.S.)
| | - Mathieu Castela
- Scarcell Therapeutics, 101 rue de Sèvres, 75006 Paris, France;
| | - Alex Duval
- Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, INSERM, Sorbonne Université, 75012 Paris, France;
| | - Céline Mehats
- U1016, CNRS, UMR8104, Institut Cochin, INSERM, Université de Paris, 75014 Paris, France;
| | - Geoffroy Canlorbe
- Centre de Recherche Saint-Antoine (CRSA), INSERM UMR_S_938, Cancer Biology and Therapeutics, Sorbonne University, 75012 Paris, France; (A.K.L.); (C.U.); (M.S.)
- Department of Gynecological and Breast Surgery and Oncology, Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris (AP-HP), University Hospital, 75013 Paris, France; (G.R.); (R.D.)
- Correspondence: (A.F.); (G.C.)
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14
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Fernández-Ponce C, Navarro Quiroz R, Díaz Perez A, Aroca Martinez G, Cadena Bonfanti A, Acosta Hoyos A, Gómez Escorcia L, Hernández Agudelo S, Orozco Sánchez C, Villarreal Camacho J, Atencio Ibarra L, Consuegra Machado J, Espinoza Garavito A, García-Cózar F, Navarro Quiroz E. MicroRNAs overexpressed in Crohn's disease and their interactions with mechanisms of epigenetic regulation explain novel aspects of Crohn's disease pathogenesis. Clin Epigenetics 2021; 13:39. [PMID: 33602320 PMCID: PMC7890887 DOI: 10.1186/s13148-021-01022-8] [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: 11/05/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Background In this review, we were interested to identify the wide universe of enzymes associated with epigenetic modifications, whose gene expression is regulated by miRNAs with a high relative abundance in Crohn's disease (CD) affected tissues, with the aim to determine their impact in the pathogenesis and evolution of the disease. Methods We used HMDD and Bibliometrix R-package in order to identify the miRNAs overexpressed in CD. The identified enzymes associated with epigenetic mechanisms and post-translational modifications, regulated by miRNAs upregulated in CD, were analyzed using String v11 database. Results We found 190 miRNAs with great abundance in patients with CD, of which 26 miRNAs regulate the gene expression of enzymes known to catalyze epigenetic modifications involved in essentials pathophysiological processes, such as chromatin architecture reorganization, immune response regulation including CD4+ T cells polarization, integrity of gut mucosa, gut microbiota composition and tumorigenesis. Conclusion The integrated analysis of miRNAs with a high relative abundance in patients with CD showed a combined and superimposed gene expression regulation of enzymes associated with relevant epigenetic mechanisms and that could explain, in part, the pathogenesis of CD. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01022-8.
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Affiliation(s)
- Cecilia Fernández-Ponce
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz, Cadiz, Spain
| | - Roberto Navarro Quiroz
- CMCC-Centro de Matemática, Computação E Cognição, Laboratório do Biología Computacional e Bioinformática-LBCB, Universidade Federal Do ABC, Sao Paulo, 01023, Brazil
| | - Anderson Díaz Perez
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia.,Universidad Rafael Nuñez, 130001, Cartagena, Colombia
| | - Gustavo Aroca Martinez
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia.,Department of Nephrology, Clinica de La Costa, 080001, Barranquilla, Colombia
| | - Andrés Cadena Bonfanti
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia.,Department of Nephrology, Clinica de La Costa, 080001, Barranquilla, Colombia
| | - Antonio Acosta Hoyos
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia
| | - Lorena Gómez Escorcia
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia.,Universidad Rafael Nuñez, 130001, Cartagena, Colombia
| | - Sandra Hernández Agudelo
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia.,Department of Nephrology, Clinica de La Costa, 080001, Barranquilla, Colombia
| | - Christian Orozco Sánchez
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia
| | | | | | | | - Alberto Espinoza Garavito
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia
| | - Francisco García-Cózar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz, Cadiz, Spain
| | - Elkin Navarro Quiroz
- Facultad de Ciencias Básicas y Biomédicas, Universidad Simon Bolivar, 080001, Barranquilla, Colombia. .,Centro de Investigación E Innovación en Biomoléculas, C4U S.A.S, 080001, Barranquilla, Colombia.
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15
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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: 72] [Impact Index Per Article: 18.0] [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.
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16
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Aljaibeji H, Elemam NM, Mohammed AK, Hasswan H, Thahyabat MA, Alkhayyal N, Sulaiman N, Taneera J. Let7b-5p is Upregulated in the Serum of Emirati Patients with Type 2 Diabetes and Regulates Insulin Secretion in INS-1 Cells. Exp Clin Endocrinol Diabetes 2020; 130:22-29. [PMID: 33036033 DOI: 10.1055/a-1261-5282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Let7b-5p is a member of the Let-7 miRNA family and one of the top expressed miRNAs in human islets that implicated in glucose homeostasis. The levels of Let7b-5p in type 2 diabetes (T2DM) patients or its role in β-cell function is still unclear. In the current study, we measured the serum levels of let7b-5p in Emirati patients with T2DM (with/without complications) and control subjects. Overexpression or silencing of let7b-5p in INS-1 (832/13) cells was performed to investigate the impact on insulin secretion, content, cell viability, apoptosis, and key functional genes. We found that serum levels of let7b-5p are significantly (p<0.05) higher in T2DM-patients or T2DM with complications compared to control subjects. Overexpression of let7b-5p increased insulin content and decreased glucose-stimulated insulin secretion, whereas silencing of let7b-5p reduced insulin content and secretion. Modulation of the expression levels of let7b-5p did not influence cell viability nor apoptosis. Analysis of mRNA and protein expression of hallmark genes in let7b-5p transfected cells revealed a marked dysregulation of Insulin, Pancreatic And Duodenal Homeobox 1 (PDX1), glucokinase (GCK), glucose transporter 2 (GLUT2), and INSR. In conclusion, an appropriate level of let7b-5p is essential to maintain β-cell function and may be regarded as a biomarker for T2DM.
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Affiliation(s)
- Hayat Aljaibeji
- Sharjah Institute for Medical Research, University of Sharjah
| | | | | | - Hind Hasswan
- Sharjah Institute for Medical Research, University of Sharjah
| | | | - Noura Alkhayyal
- Sharjah Institute for Medical Research, University of Sharjah
| | - Nabil Sulaiman
- Department of Family Medicine, College of Medicine, University of Sharjah.,Baker/IDI Heart and Diabetes Institute, Melbourne, Victoria
| | - Jalal Taneera
- Sharjah Institute for Medical Research, University of Sharjah.,Department of Basic Medical Sciences, College of Medicine, University of Sharjah
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17
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Kandettu A, Radhakrishnan R, Chakrabarty S, Sriharikrishnaa S, Kabekkodu SP. The emerging role of miRNA clusters in breast cancer progression. Biochim Biophys Acta Rev Cancer 2020; 1874:188413. [PMID: 32827583 DOI: 10.1016/j.bbcan.2020.188413] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/01/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
Micro RNAs (miRNAs) are small non-coding RNAs that are essential for regulation of gene expression of the target genes. Large number of miRNAs are organized into defined units known as miRNA clusters (MCs). The MCs consist of two or more than two miRNA encoding genes driven by a single promoter, transcribed together in the same orientation, that are not separated from each other by a transcription unit. Aberrant miRNA clusters expression is reported in breast cancer (BC), exhibiting both pro-tumorogenic and anti-tumorigenic role. Altered MCs expression facilitates to breast carcinogenesis by promoting the breast cells to acquire the various hallmarks of the cancer. Since miRNA clusters contain multiple miRNA encoding genes, targeting cluster may be more attractive than targeting individual miRNAs. Besides targeting dysregulated miRNA clusters in BC, studies have focused on the mechanism of action, and its contribution to the progression of the BC. The present review provides a comprehensive overview of dysregulated miRNA clusters and its role in the acquisition of cancer hallmarks in BC. More specifically, we have presented the regulation, differential expression, classification, targets, mechanism of action, and signaling pathways of miRNA clusters in BC. Additionally, we have also discussed the potential utility of the miRNA cluster as a diagnostic and prognostic indicator in BC.
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Affiliation(s)
- Amoolya Kandettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India; Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - S Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576106, India; Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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18
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. microRNA-mediated noise processing in cells: A fight or a game? Comput Struct Biotechnol J 2020; 18:642-649. [PMID: 32257047 PMCID: PMC7103774 DOI: 10.1016/j.csbj.2020.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/17/2022] Open
Abstract
In the past decades, microRNAs (miRNA) have much attracted the attention of researchers at the interface between life and theoretical sciences for their involvement in post-transcriptional regulation and related diseases. Thanks to the always more sophisticated experimental techniques, the role of miRNAs as "noise processing units" has been further elucidated and two main ways of miRNA noise-control have emerged by combinations of theoretical and experimental studies. While on one side miRNAs were thought to buffer gene expression noise, it has recently been suggested that miRNAs could also increase the cell-to-cell variability of their targets. In this Mini Review, we focus on the role of miRNAs in molecular noise processing and on the advantages as well as current limitations of theoretical modelling.
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Affiliation(s)
- Elsi Ferro
- Italian Institute for Genomic Medicine, Italy
| | | | - Silvia Grigolon
- The Francis Crick Institute, 1, Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- Italian Institute for Genomic Medicine, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Italy
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19
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview. Cells 2019; 8:E1540. [PMID: 31795372 PMCID: PMC6952906 DOI: 10.3390/cells8121540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and the type of interactions amongst them. Depending on their topology, these molecular circuits may carry out specific functions that years of studies have related to the processing of gene expression noise. In this review, we first present the different over-represented network motifs involving microRNAs and their specific role in implementing relevant biological functions, reviewing both theoretical and experimental studies. We then illustrate the recent advances in synthetic biology, such as the construction of artificially synthesised circuits, which provide a controlled tool to test experimentally the possible microRNA regulatory tasks and constitute a starting point for clinical applications.
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Affiliation(s)
- Elsi Ferro
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Chiara Enrico Bena
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Silvia Grigolon
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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20
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Reale E, Taverna D, Cantini L, Martignetti L, Osella M, De Pittà C, Virga F, Orso F, Caselle M. Investigating the epi-miRNome: identification of epi-miRNAs using transfection experiments. Epigenomics 2019; 11:1581-1599. [PMID: 31693439 DOI: 10.2217/epi-2019-0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Growing evidence shows a strong interplay between post-transcriptional regulation, mediated by miRNAs (miRs) and epigenetic regulation. Nevertheless, the number of experimentally validated miRs (called epi-miRs) involved in these regulatory circuitries is still very small. Material & methods: We propose a pipeline to prioritize candidate epi-miRs and to identify potential epigenetic interactors of any given miR starting from miR transfection experiment datasets. Results & conclusion: We identified 34 candidate epi-miRs: 19 of them are known epi-miRs, while 15 are new. Moreover, using an in-house generated gene expression dataset, we experimentally proved that a component of the polycomb-repressive complex 2, the histone methyltransferase enhancer of zeste homolog 2 (EZH2), interacts with miR-214, a well-known prometastatic miR in melanoma and breast cancer, highlighting a miR-214-EZH2 regulatory axis potentially relevant in tumor progression.
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Affiliation(s)
- Elisa Reale
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
| | - Daniela Taverna
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy.,Center for Complex Systems in Molecular Biology & Medicine, University of Torino, 10123, Torino, Italy
| | - Laura Cantini
- Institut Curie, PSL Research University, INSERM U900, Paris, France.,Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, 75005 Paris, France
| | | | - Matteo Osella
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
| | | | - Federico Virga
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy
| | - Francesca Orso
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy.,Center for Complex Systems in Molecular Biology & Medicine, University of Torino, 10123, Torino, Italy
| | - Michele Caselle
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
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21
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Bertucci A, Pierron F, Ye T, Gonzalez P, Couture P, Baudrimont M. Identification and expression of microRNAs in european eels Anguilla anguilla from two natural sites with different pollution levels. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:274-283. [PMID: 30999204 DOI: 10.1016/j.envpol.2019.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/25/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNA that control multiple biological processes through negative post-transcriptional regulation of gene expression. Recently a role of miRNAs in the response of aquatic organisms to environmental toxicants emerged. Toxicant-induced changes in miRNA expression might then represent novel biomarkers to evaluate the health status of these organisms. In this study, we aimed to identify the miRNA repertoire in the liver of the European eel Anguilla anguilla and to compare their differential expression between a polluted site located in the Gironde Estuary and a pristine site in Arcachon Bay (France). A total of 299 mature miRNAs were identified. In polluted water, 19 miRNAs were up-regulated and 22 were down-regulated. We predicted that these differentially expressed miRNAs could target 490 genes that were involved in ribosome biogenesis, response to hormones, response to chemical and chromatin modification. Moreover, we observed only few examples (29) of negative correlation between the expression levels of miRNAs and their targets suggesting that, in the system studied, miRNAs might not only regulate gene expression directly by degrading mRNA but also by inhibiting protein translation or by regulating other epigenetic processes. This study is the first example of in situ investigation of the role of miRNAs in the response of a fish species to water quality. Our findings provide new insights into the involvement of epigenetic mechanisms in the response of animals chronically exposed to pollution and pave the way for the utilization of miRNAs in aquatic ecotoxicology.
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Affiliation(s)
| | - Fabien Pierron
- Univ. Bordeaux, UMR EPOC CNRS 5805, 33615, Pessac, France
| | - Tao Ye
- IGBMC - CNRS UMR 7104 - Inserm U 964, 1 BP 10142, 67404, Illkirch Cedex, France
| | | | - Patrice Couture
- Institut National de La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 rue De La Couronne, Québec, QC, G1K 9A9, Canada
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22
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Sankrityayan H, Kulkarni YA, Gaikwad AB. Diabetic nephropathy: The regulatory interplay between epigenetics and microRNAs. Pharmacol Res 2019; 141:574-585. [PMID: 30695734 DOI: 10.1016/j.phrs.2019.01.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/20/2022]
Abstract
Diabetic nephropathy (DN) is still one of the leading causes of end-stage renal disease despite the emergence of different therapies to counter the metabolic, hemodynamic and fibrotic pathways, implicating a prominent role of genetic and epigenetic factors in its progression. Epigenetics is the study of changes in the expression of genes which may be inheritable and does not involve a change in the genome sequence. Thrust areas of epigenetic research are DNA methylation and histone modifications. Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) control the expression of genes via post-transcriptional mechanisms. However, the regulation by epigenetic mechanisms and miRNAs are not completely distinct. A number of emerging reports have revealed the interplay between epigenetic machinery and miRNA expression, particularly in cancer. Further research has proved that a feedback loop exists between miRNA expression and epigenetic regulation in disorders including DN. Studies showed that different miRNAs (miR-200, miR-29 etc.) were found to be regulated by epigenetic mechanisms viz. DNA methylation and histone modifications. Conversely, miRNAs (miR-301, miR-449 etc.) themselves modulated levels of DNA methyltranferases (DNMTs) and Histone deacetylases (HDACs), enzymes vital to epigenetic modifications. With already few FDA approved epigenetic -modulating drugs (Vorinostat, Decitabine) in the market and miRNA therapeutic drugs under clinical trial it becomes imperative to analyze the possible interaction between the two classes of drugs in the modulation of a disease process. The purpose of this review is to articulate the interplay between miRNA expression and epigenetic modifications with a particular focus on its impact on the development and progression of DN.
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Affiliation(s)
- Himanshu Sankrityayan
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Yogesh A Kulkarni
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai 400056, India
| | - Anil Bhanudas Gaikwad
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India.
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23
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Akemann C, Meyer DN, Gurdziel K, Baker TR. Developmental Dioxin Exposure Alters the Methylome of Adult Male Zebrafish Gonads. Front Genet 2019; 9:719. [PMID: 30687390 PMCID: PMC6336703 DOI: 10.3389/fgene.2018.00719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 12/21/2018] [Indexed: 01/20/2023] Open
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental toxicant and endocrine disrupting compound with reproductive and developmental effects in humans and model organisms, including zebrafish. Our previous microarray and histological studies found defects in spermatogenesis and fertility of zebrafish in response to acute developmental TCDD exposure. These effects are apparent following exposure during reproductive development, modeling fetal basis of adult-onset disease. Some outcomes of these previous studies (reduced fertility, changes in sex ratio, transcriptomic alterations) are also transgenerational – persisting to unexposed generations – through the male germline. We hypothesized that DNA methylation could be a possible mechanism for these reproductive effects and performed whole genome bisulfite sequencing (WGBS), which identifies whole genome DNA methylation status at the base pair level, on testes of adult zebrafish exposed to TCDD (two separate hour-long exposures to 50 pg/mL TCDD at 3 and 7 weeks post fertilization). In response to TCDD exposure, multiple genes were differentially methylated; many of which are involved in reproductive processes or epigenetic modifications, suggesting a role of DNA methylation in later-life health outcomes. Additionally, several differentially methylated genes corresponded with gene expression changes identified in TCDD-exposed zebrafish testes, indicating a potential link between DNA methylation and gene expression. Ingenuity pathway analysis of WGBS and microarray data revealed genes involved in reproductive processes and development, RNA regulation, the cell cycle, and cellular morphology and development. We conclude that site-specific changes in DNA methylation of adult zebrafish testes occur in response to acute developmental TCDD exposure.
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Affiliation(s)
- Camille Akemann
- Department of Pharmacology, Wayne State University, Detroit, MI, United States
| | - Danielle N Meyer
- Department of Pharmacology, Wayne State University, Detroit, MI, United States.,Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States
| | - Katherine Gurdziel
- Applied Genome Technology Center, School of Medicine, Wayne State University, Detroit, MI, United States
| | - Tracie R Baker
- Department of Pharmacology, Wayne State University, Detroit, MI, United States.,Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States
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24
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Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs. Methods Mol Biol 2019; 1912:367-409. [PMID: 30635902 DOI: 10.1007/978-1-4939-8982-9_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Non-coding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA-RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting, e.g., the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell's proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.
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25
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Stappert L, Klaus F, Brüstle O. MicroRNAs Engage in Complex Circuits Regulating Adult Neurogenesis. Front Neurosci 2018; 12:707. [PMID: 30455620 PMCID: PMC6230569 DOI: 10.3389/fnins.2018.00707] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/18/2018] [Indexed: 12/27/2022] Open
Abstract
The finding that the adult mammalian brain is still capable of producing neurons has ignited a new field of research aiming to identify the molecular mechanisms regulating adult neurogenesis. An improved understanding of these mechanisms could lead to the development of novel approaches to delay cognitive decline and facilitate neuroregeneration in the adult human brain. Accumulating evidence suggest microRNAs (miRNAs), which represent a class of post-transcriptional gene expression regulators, as crucial part of the gene regulatory networks governing adult neurogenesis. This review attempts to illustrate how miRNAs modulate key processes in the adult neurogenic niche by interacting with each other and with transcriptional regulators. We discuss the function of miRNAs in adult neurogenesis following the life-journey of an adult-born neuron from the adult neural stem cell (NSCs) compartment to its final target site. We first survey how miRNAs control the initial step of adult neurogenesis, that is the transition of quiescent to activated proliferative adult NSCs, and then go on to discuss the role of miRNAs to regulate neuronal differentiation, survival, and functional integration of the newborn neurons. In this context, we highlight miRNAs that converge on functionally related targets or act within cross talking gene regulatory networks. The cooperative manner of miRNA action and the broad target repertoire of each individual miRNA could make the miRNA system a promising tool to gain control on adult NSCs in the context of therapeutic approaches.
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Affiliation(s)
- Laura Stappert
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Center, Bonn, Germany
| | - Frederike Klaus
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Center, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn Medical Center, Bonn, Germany
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26
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Paul ABM, Sadek ST, Mahesan AM. The role of microRNAs in human embryo implantation: a review. J Assist Reprod Genet 2018; 36:179-187. [PMID: 30315515 DOI: 10.1007/s10815-018-1326-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as important in human embryo implantation, and we present here a review of the literature from a clinical perspective. Implantation involves complex interactions between the blastocyst and endometrium. miRNAs have been shown to be differentially expressed in implanted compared with non-implanted blastocysts and euploid compared with aneuploid blastocysts. Further, miRNAs are differentially expressed in proliferative compared with decidualized endometrium, and in receptive compared with pre-receptive endometrium. miRNAs are also differentially expressed in endometrium of women who failed implantation, and in endometrium of women with recurrent implantation failure. Due to the complexity of miRNA signaling, studies have suffered from inconsistency in reproducibility of results. However, miRNAs show potential as biomarkers in the pursuit of more reliable prediction of embryo implantation.
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Affiliation(s)
- Anthea B M Paul
- Department of Pathology and Laboratory Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Seifeldin T Sadek
- The Jones Institute for Reproductive Medicine, Eastern Virginia Medical School, 601 Colley Ave., Norfolk, VA, 23507, USA
| | - Arnold M Mahesan
- The Jones Institute for Reproductive Medicine, Eastern Virginia Medical School, 601 Colley Ave., Norfolk, VA, 23507, USA.
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27
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Casciaro M, Di Salvo E, Brizzi T, Rodolico C, Gangemi S. Involvement of miR-126 in autoimmune disorders. Clin Mol Allergy 2018; 16:11. [PMID: 29743819 PMCID: PMC5930861 DOI: 10.1186/s12948-018-0089-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Micro-RNA represent a great family of small non-condign ribonucleic acid molecules; in particular microRNA-126 is an important member of this family and is expressed in many human cells such as cardiomyocytes, endothelial and lung cells. Some studies have shown the implication of miR-126 in cancer, but recently significant progresses have also been made in determining the role of miR-126 regulating immune-related diseases; probably, in a near future, they could potentially serve as diagnostic biomarkers or therapeutic targets. OBJECTIVE The purpose of this review is to investigate the role of miR-126 in autoimmune diseases, so as to offer innovative therapies. RESULTS According literature, it was concluded that miRNAs, especially miR-126, are involved in many pathologies and that their expression levels increase in autoimmune diseases because they interfere with the transcription of the proteins involved. Since microRNAs can be detected from several biological sources, they may be attractive as potential biomarkers for the diagnosis, prognosis, disease activity and severity of various diseases. In fact, once confirmed the involvement of miR-126 in autoimmune diseases, it was speculated that it could be used as a promising biomarker. These discovers implicate that miR-126 have a central role in many pathways leading to the development and sustain of autoimmune diseases. Its key role make this microRNA a potential therapeutic target in autoimmunity. CONCLUSION Although miR-126 relevant role in several immune-related diseases, further studies are needed to clear its molecular mechanisms; the final step of these novel researches could be the blockage or the prevention of the diseases onset by creating of new targeted therapy.
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Affiliation(s)
- Marco Casciaro
- School and Division of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, Messina University Hospital, 98125 Messina, Italy
| | - Eleonora Di Salvo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Teresa Brizzi
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Carmelo Rodolico
- Department of Clinical and Experimental Medicine, University of Messina, 98125 Messina, Italy
| | - Sebastiano Gangemi
- School and Division of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, Messina University Hospital, 98125 Messina, Italy
- Operative Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
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28
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Galatenko VV, Galatenko AV, Samatov TR, Turchinovich AA, Shkurnikov MY, Makarova JA, Tonevitsky AG. Comprehensive network of miRNA-induced intergenic interactions and a biological role of its core in cancer. Sci Rep 2018; 8:2418. [PMID: 29402894 PMCID: PMC5799291 DOI: 10.1038/s41598-018-20215-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of short noncoding RNAs that posttranscriptionally regulate gene expression and play an important role in multiple cellular processes. A significant percentage of miRNAs are intragenic, which is often functionally related to their host genes playing either antagonistic or synergistic roles. In this study, we constructed and analyzed the entire network of intergenic interactions induced by intragenic miRNAs. We further focused on the core of this network, which was defined as a union of nontrivial strongly connected components, i.e., sets of nodes (genes) mutually connected via directed paths. Both the entire network and its core possessed statistically significant non-random properties. Specifically, genes forming the core had high expression levels and low expression variance. Furthermore, the network core did not split into separate components corresponding to individual signalling or metabolic pathways, but integrated genes involved in key cellular processes, including DNA replication, transcription, protein homeostasis and cell metabolism. We suggest that the network core, consisting of genes mutually regulated by their intragenic miRNAs, could coordinate adjacent pathways or homeostatic control circuits, serving as a horizontal inter-circuit link. Notably, expression patterns of these genes had an efficient prognostic potential for breast and colorectal cancer patients.
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Affiliation(s)
- Vladimir V Galatenko
- Lomonosov Moscow State University, Leninskie Gory 1, 119991, Moscow, Russia. .,SRC Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia. .,Tauber Bioinformatics Research Center, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, 3498838, Haifa, Israel.
| | - Alexey V Galatenko
- Lomonosov Moscow State University, Leninskie Gory 1, 119991, Moscow, Russia
| | - Timur R Samatov
- SRC Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia.,Evotec International GmbH, Marie-Curie Str. 7, 37079, Göttingen, Germany
| | | | - Maxim Yu Shkurnikov
- P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, Second Botkinsky lane 3, 125284, Moscow, Russia
| | - Julia A Makarova
- P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, Second Botkinsky lane 3, 125284, Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, 119991, Moscow, Russia
| | - Alexander G Tonevitsky
- SRC Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia. .,P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, Second Botkinsky lane 3, 125284, Moscow, Russia.
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29
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Tang Y, Zhang L, Tu T, Li Y, Murray D, Tu Q, Chen JJ. MicroRNA-99a is a novel regulator of KDM6B-mediated osteogenic differentiation of BMSCs. J Cell Mol Med 2018; 22:2162-2176. [PMID: 29377540 PMCID: PMC5867145 DOI: 10.1111/jcmm.13490] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/12/2017] [Indexed: 12/19/2022] Open
Abstract
Skeletal tissue originates from mesenchymal stem cells (MSCs) with differentiation potential into the osteoblast lineage regulated by essential transcriptional and post‐transcriptional mechanisms. Recently, miRNAs and histone modifications have been identified as novel key regulators of osteogenic differentiation of MSCs. Here, we identified miR‐99a and its target lysine (K)‐specific demethylase 6B (KDM6B) gene as novel modulators of osteogenic differentiation of bone mesenchymal stem cells (BMSCs). Microarray profiling and further validation by quantitative real‐time RT‐PCR revealed that miR‐99a was up‐regulated during osteoblastic differentiation of BMSCs, and decreased in differentiated osteoblasts. Transfection of miR‐99a mimics inhibited osteoblastic commitment and differentiation of BMSCs, whereas inhibition of miR‐99a by inhibitors enhances these processes. KDM6B was determined as one of important targets of miR‐99a, which was further confirmed by luciferase assay of 3′‐UTR of KDM6B. Moreover, HOX gene level decreased after transfection of miR‐99a mimics in BMSCs, which indicated that KDM6B is a bona fide target of miR‐99a. Furthermore, in a model of in vivo bone regeneration, osteoblast‐specific gain‐ and loss‐of‐function experiments performed using cranial bone defects revealed that miR‐99a mimics‐transfected BMSCs reduced bone formation, and conversely, miR‐99a inhibitors‐transfected BMSCs increased in vivo bone formation. Tissue‐specific inhibition of miR‐99a may be a potential novel therapeutic approach for enhancing BMSCs‐based bone formation and regeneration.
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Affiliation(s)
- Yin Tang
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA.,State Key Laboratory of Oral Disease, West China School & Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Lan Zhang
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA.,State Key Laboratory of Oral Disease, West China School & Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Tianchi Tu
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Yijia Li
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Dana Murray
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Qisheng Tu
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA
| | - Jake Jinkun Chen
- Division of Oral Biology, Tufts University School of Dental Medicine, Boston, MA, USA.,Department of Anatomy and Cell Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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30
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Quintanilha BJ, Reis BZ, Duarte GBS, Cozzolino SMF, Rogero MM. Nutrimiromics: Role of microRNAs and Nutrition in Modulating Inflammation and Chronic Diseases. Nutrients 2017; 9:nu9111168. [PMID: 29077020 PMCID: PMC5707640 DOI: 10.3390/nu9111168] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 12/12/2022] Open
Abstract
Nutrimiromics studies the influence of the diet on the modification of gene expression due to epigenetic processes related to microRNAs (miRNAs), which may affect the risk for the development of chronic diseases. miRNAs are a class of non-coding endogenous RNA molecules that are usually involved in post-transcriptional gene silencing by inducing mRNA degradation or translational repression by binding to a target messenger RNA. They can be controlled by environmental and dietary factors, particularly by isolated nutrients or bioactive compounds, indicating that diet manipulation may hold promise as a therapeutic approach in modulating the risk of chronic diseases. This review summarizes the evidence regarding the influence of nutrients and bioactive compounds on the expression of miRNAs related to inflammation and chronic disease in several models (cell culture, animal models, and human trials).
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Affiliation(s)
- Bruna J Quintanilha
- Nutritional Genomics and Inflammation Laboratory, Department of Nutrition, School of Public Health, University of São Paulo, 01246-904 São Paulo, Brazil.
- Food Research Center (FoRC), 05508-000 São Paulo, Brazil.
| | - Bruna Z Reis
- Nutrition and Minerals Laboratory, Department of Food and Experimental Nutrition, University of São Paulo, 05508-000 São Paulo, Brazil.
| | - Graziela B Silva Duarte
- Nutrition and Minerals Laboratory, Department of Food and Experimental Nutrition, University of São Paulo, 05508-000 São Paulo, Brazil.
| | - Silvia M F Cozzolino
- Nutrition and Minerals Laboratory, Department of Food and Experimental Nutrition, University of São Paulo, 05508-000 São Paulo, Brazil.
| | - Marcelo M Rogero
- Nutritional Genomics and Inflammation Laboratory, Department of Nutrition, School of Public Health, University of São Paulo, 01246-904 São Paulo, Brazil.
- Food Research Center (FoRC), 05508-000 São Paulo, Brazil.
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31
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Yakovlev IA, Fossdal CG. In Silico Analysis of Small RNAs Suggest Roles for Novel and Conserved miRNAs in the Formation of Epigenetic Memory in Somatic Embryos of Norway Spruce. Front Physiol 2017; 8:674. [PMID: 28943851 PMCID: PMC5596105 DOI: 10.3389/fphys.2017.00674] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022] Open
Abstract
Epigenetic memory in Norway spruce affects the timing of bud burst and bud set, vitally important adaptive traits for this long-lived forest species. Epigenetic memory is established in response to the temperature conditions during embryogenesis. Somatic embryogenesis at different epitype inducing (EpI) temperatures closely mimics the natural processes of epigenetic memory formation in seeds, giving rise to epigenetically different clonal plants in a reproducible and predictable manner, with respect to altered bud phenology. MicroRNAs (miRNAs) and other small non-coding RNAs (sRNAs) play an essential role in the regulation of plant gene expression and may affect this epigenetic mechanism. We used NGS sequencing and computational in silico methods to identify and profile conserved and novel miRNAs among small RNAs in embryogenic tissues of Norway spruce at three EpI temperatures (18, 23 and 28°C). We detected three predominant classes of sRNAs related to a length of 24 nt, followed by a 21–22 nt class and a third 31 nt class of sRNAs. More than 2100 different miRNAs within the prevailing length 21–22 nt were identified. Profiling these putative miRNAs allowed identification of 1053 highly expressed miRNAs, including 523 conserved and 530 novels. 654 of these miRNAs were found to be differentially expressed (DEM) depending on EpI temperature. For most DEMs, we defined their putative mRNA targets. The targets represented mostly by transcripts of multiple-repeats proteins, like TIR, NBS-LRR, PPR and TPR repeat, Clathrin/VPS proteins, Myb-like, AP2, etc. Notably, 124 DE miRNAs targeted 203 differentially expressed epigenetic regulators. Developing Norway spruce embryos possess a more complex sRNA structure than that reported for somatic tissues. A variety of the predicted miRNAs showed distinct EpI temperature dependent expression patterns. These putative EpI miRNAs target spruce genes with a wide range of functions, including genes known to be involved in epigenetic regulation, which in turn could provide a feedback process leading to the formation of epigenetic marks. We suggest that TIR, NBS and LRR domain containing proteins could fulfill more general functions for signal transduction from external environmental stimuli and conversion them into molecular response. Fine-tuning of the miRNA production likely participates in both developmental regulation and epigenetic memory formation in Norway spruce.
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32
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Cora' D, Re A, Caselle M, Bussolino F. MicroRNA-mediated regulatory circuits: outlook and perspectives. Phys Biol 2017; 14:045001. [PMID: 28586314 DOI: 10.1088/1478-3975/aa6f21] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs have been found to be necessary for regulating genes implicated in almost all signaling pathways, and consequently their dysfunction influences many diseases, including cancer. Understanding of the complexity of the microRNA-mediated regulatory network has grown in terms of size, connectivity and dynamics with the development of computational and, more recently, experimental high-throughput approaches for microRNA target identification. Newly developed studies on recurrent microRNA-mediated circuits in regulatory networks, also known as network motifs, have substantially contributed to addressing this complexity, and therefore to helping understand the ways by which microRNAs achieve their regulatory role. This review provides a summarizing view of the state-of-the-art, and perspectives of research efforts on microRNA-mediated regulatory motifs. In this review, we discuss the topological properties characterizing different types of circuits, and the regulatory features theoretically enabled by such properties, with a special emphasis on examples of circuits typifying their biological significance in experimentally validated contexts. Finally, we will consider possible future developments, in particular regarding microRNA-mediated circuits involving long non-coding RNAs and epigenetic regulators.
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Affiliation(s)
- Davide Cora'
- Department of Oncology, University of Torino, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Candiolo Cancer Institute-FPO, IRCCS, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Center for Molecular Systems Biology, University of Torino, Regione Gonzole 10, I-10043 Orbassano, Italy. Current address: Department of Translational Medicine, Piemonte Orientale University 'Amedeo Avogadro', Via Solaroli 17, I-28100 Novara, Italy
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33
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Tian XJ, Zhang H, Zhang J, Xing J. Reciprocal regulation between mRNA and microRNA enables a bistable switch that directs cell fate decisions. FEBS Lett 2016; 590:3443-3455. [PMID: 27578189 DOI: 10.1002/1873-3468.12379] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022]
Abstract
Micro RNAs (miRNAs) serve as crucial post-transcriptional regulators in a variety of essential cell fate decisions. However, the contribution of mRNA-miRNA mutual regulation to bistability is not fully understood. In the present study, we built a set of mathematical models of mRNA-miRNA interactions and systematically analyzed the sensitivity of the response curves under various conditions. Our findings indicate that mRNA-miRNA reciprocal regulation could manifest ultrasensitivity to subserve the generation of bistability when equipped with a positive feedback loop. We also find that the region of bistability is expanded by a stronger competing endogenous mRNA. Interestingly, bistability can be generated without a feedback loop if multiple miRNA binding sites exist on a target mRNA. Thus, we demonstrate the importance of simple mRNA-miRNA reciprocal regulation in cell fate decisions.
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Affiliation(s)
- Xiao-Jun Tian
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA.
| | - Hang Zhang
- Genetics, Bioinformatics and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jingyu Zhang
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA. .,Computational Science Research Center, Beijing, China.
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34
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Sang W, Sun C, Zhang C, Zhang D, Wang Y, Xu L, Zhang Z, Wei X, Pan B, Yan D, Zhu F, Yan Z, Cao J, Loughran TP, Xu K. MicroRNA-150 negatively regulates the function of CD4(+) T cells through AKT3/Bim signaling pathway. Cell Immunol 2016; 306-307:35-40. [PMID: 27329362 DOI: 10.1016/j.cellimm.2016.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/28/2016] [Accepted: 05/29/2016] [Indexed: 12/21/2022]
Abstract
Donor-derived CD4(+) T lymphocytes are the major effector cells directly involved in the development of graft-versus-host disease (GVHD). As a negative regulator of immune cell differentiation and development, microRNA-150 (miR-150) induces immunological tolerance in CD4(+) T cells after transplantation. However, the specific mechanisms have not been fully elucidated. In this study, we demonstrated that miR-150 is capable of not only inhibiting proliferation and activation of CD4(+) T cells but also promoting apoptosis. Mechanistically, miR-150 targets v-akt murine thymoma viral oncogene homolog 3 (AKT3), and subsequently downregulates B-cell lymphoma 2 (Bcl-2) interacting mediator of cell death (BIM). We have also demonstrated that re-expression of AKT3 reversed miR-150-mediated inhibition of CD4(+) T lymphocyte development. Therefore, we conclude that miR-150 negatively regulates CD4(+) T cell function by inhibiting the AKT3/BIM signaling pathway. These findings also suggest that manipulating the levels of miRNA-150 could be a valuable strategy in prevention and/or treatment of acute graft-versus-host disease.
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Affiliation(s)
- Wei Sang
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Cai Sun
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Cong Zhang
- Department of hematology, Huaibei Miners General Hospital, Anhui Province, China
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, USA
| | - Ying Wang
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Linyan Xu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Zhe Zhang
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Xiangyu Wei
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Bin Pan
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Dongmei Yan
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Feng Zhu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Zhiling Yan
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Jiang Cao
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China
| | - Thomas P Loughran
- Department of Medicine, University of Virginia Cancer Center, VA, USA.
| | - Kailin Xu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, China; The Key Laboratory of Transplantation Immunity, Affiliated Hospital of Xuzhou Medical University, Jiangsu Province, China.
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Seidl CI, Martinez-Sanchez A, Murphy CL. Derepression of MicroRNA-138 Contributes to Loss of the Human Articular Chondrocyte Phenotype. Arthritis Rheumatol 2016; 68:398-409. [PMID: 26359943 DOI: 10.1002/art.39428] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 09/03/2015] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To investigate the function of microRNA-138 (miR-138) in human articular chondrocytes (HACs). METHODS The expression of miR-138 in intact cartilage and cultured chondrocytes and the effects of miR-138 overexpression on chondrocyte marker genes were investigated. Targets of miR-138 relevant to chondrocytes were identified and verified by overexpression of synthetic miRNA mimics and inhibitors, luciferase assays, chromatin immunoprecipitation, and RNA immunoprecipitation of native argonaute 2, using quantitative polymerase chain reaction, Western blotting, and luciferase assays. RESULTS Expression levels of miR-138 were maintained at relatively low levels in intact human cartilage but were greatly increased upon loss of the differentiated phenotype in culture, with a concomitant decrease in the major cartilage extracellular matrix component COL2A1. We showed that miR-138 is able to repress the expression of COL2A1 by directly targeting Sp-1 and hypoxia-inducible factor 2α (HIF-2α), 2 transcription factors that are essential for COL2A1 transcription. We further demonstrated a direct association of these targets with miR-138 in the RNA-induced silencing complex and confirmed binding of Sp-1 to the COL2A1 promoter region in HACs. CONCLUSION We propose that an evolutionary pressure helps to suppress expression levels of miR-138 in human cartilage, thus enabling expression of appropriate tissue-specific matrix genes. Inhibition of miR-138 may serve as a potential therapeutic strategy to maintain the chondrocyte phenotype or reduce the progression of dedifferentiation in cultured HACs.
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Affiliation(s)
- Christine I Seidl
- Kennedy Institute of Rheumatology and University of Oxford, Oxford, UK
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Singh B, Owens KM, Bajpai P, Desouki MM, Srinivasasainagendra V, Tiwari HK, Singh KK. Mitochondrial DNA Polymerase POLG1 Disease Mutations and Germline Variants Promote Tumorigenic Properties. PLoS One 2015; 10:e0139846. [PMID: 26468652 PMCID: PMC4607296 DOI: 10.1371/journal.pone.0139846] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/17/2015] [Indexed: 02/04/2023] Open
Abstract
Germline mutations in mitochondrial DNA polymerase gamma (POLG1) induce mitochondrial DNA (mtDNA) mutations, depletion, and decrease oxidative phosphorylation. Earlier, we identified somatic mutations in POLG1 and the contribution of these mutations in human cancer. However, a role for germline variations in POLG1 in human cancers is unknown. In this study, we examined a role for disease associated germline variants of POLG1, POLG1 gene expression, copy number variation and regulation in human cancers. We analyzed the mutations, expression and copy number variation in POLG1 in several cancer databases and validated the analyses in primary breast tumors and breast cancer cell lines. We discovered 5-aza-2'-deoxycytidine led epigenetic regulation of POLG1, mtDNA-encoded genes and increased mitochondrial respiration. We conducted comprehensive race based bioinformatics analyses of POLG1 gene in more than 33,000 European-Americans and 5,000 African-Americans. We identified a mitochondrial disease causing missense variation in polymerase domain of POLG1 protein at amino acid 1143 (E1143G) to be 25 times more prevalent in European-Americans (allele frequency 0.03777) when compared to African-American (allele frequency 0.00151) population. We identified T251I and P587L missense variations in exonuclease and linker region of POLG1 also to be more prevalent in European-Americans. Expression of these variants increased glucose consumption, decreased ATP production and increased matrigel invasion. Interestingly, conditional expression of these variants revealed that matrigel invasion properties conferred by these germline variants were reversible suggesting a role of epigenetic regulators. Indeed, we identified a set of miRNA whose expression was reversible after variant expression was turned off. Together, our studies demonstrate altered genetic and epigenetic regulation of POLG1 in human cancers and suggest a role for POLG1 germline variants in promoting tumorigenic properties.
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Affiliation(s)
- Bhupendra Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Kjerstin M. Owens
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, United States of America
| | - Prachi Bajpai
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Mohamed Mokhtar Desouki
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, United States of America
| | - Vinodh Srinivasasainagendra
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Hemant K. Tiwari
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Keshav K. Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States of America
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Environmental Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Center for Aging, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Birmingham Veterans Affairs Medical Center, Birmingham, AL, 35294, United States of America
- * E-mail:
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Wang X, Zheng G, Dong D. Coordinated action of histone modification and microRNA regulations in human genome. Gene 2015; 570:277-81. [PMID: 26095801 DOI: 10.1016/j.gene.2015.06.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/24/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
Abstract
Both histone modifications and microRNAs (miRNAs) play pivotal role in gene expression regulation. Although numerous studies have been devoted to explore the gene regulation by miRNA and epigenetic regulations, their coordinated actions have not been comprehensively examined. In this work, we systematically investigated the combinatorial relationship between miRNA and epigenetic regulation by taking advantage of recently published whole genome-wide histone modification data and high quality miRNA targeting data. The results showed that miRNA targets have distinct histone modification patterns compared with non-targets in their promoter regions. Based on this finding, we proposed a machine learning approach to fit predictive models on the task to discern whether a gene is targeted by a specific miRNA. We found a considerable advantage in both sensitivity and specificity in diverse human cell lines. Finally, we found that our predicted miRNA targets are consistently annotated with Gene Ontology terms. Our work is the first genome-wide investigation of the coordinated action of miRNA and histone modification regulations, which provide a guide to deeply understand the complexity of transcriptional regulation.
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Affiliation(s)
- Xuan Wang
- Institute of Molecular Ecology and Evolution, SKLEC & IECR, East China Normal University, Shanghai, China
| | - Guantao Zheng
- Institute of Molecular Ecology and Evolution, SKLEC & IECR, East China Normal University, Shanghai, China
| | - Dong Dong
- Institute of Molecular Ecology and Evolution, SKLEC & IECR, East China Normal University, Shanghai, China.
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38
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Zhang G, Estève PO, Chin HG, Terragni J, Dai N, Corrêa IR, Pradhan S. Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation. Nucleic Acids Res 2015; 43:6112-24. [PMID: 25990724 PMCID: PMC4499142 DOI: 10.1093/nar/gkv518] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/06/2015] [Indexed: 01/04/2023] Open
Abstract
Mammalian cells contain copious amounts of RNA including both coding and noncoding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylation targeting and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1) co-purifies with inhibitory ncRNAs. MicroRNAs (miRNAs) bind directly to DNMT1 with high affinity. The binding of miRNAs, such as miR-155-5p, leads to inhibition of DNMT1 enzyme activity. Exogenous miR-155-5p in cells induces aberrant DNA methylation of the genome, resulting in hypomethylation of low to moderately methylated regions. And small shift of hypermethylation of previously hypomethylated region was also observed. Furthermore, hypomethylation led to activation of genes. Based on these observations, overexpression of miR-155-5p resulted in aberrant DNA methylation by inhibiting DNMT1 activity, resulting in altered gene expression.
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Affiliation(s)
- Guoqiang Zhang
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Hang Gyeong Chin
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Jolyon Terragni
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Sriharsa Pradhan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
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Zhang P, Kofron CM, Mende U. Heterotrimeric G protein-mediated signaling and its non-canonical regulation in the heart. Life Sci 2015; 129:35-41. [PMID: 25818188 PMCID: PMC4415990 DOI: 10.1016/j.lfs.2015.02.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/31/2015] [Accepted: 02/11/2015] [Indexed: 11/20/2022]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) regulate a multitude of signaling pathways in mammalian cells by transducing signals from G protein-coupled receptors (GPCRs) to effectors, which in turn regulate cellular function. In the myocardium, G protein signaling occurs in all cardiac cell types and is centrally involved in the regulation of heart rate, pump function, and vascular tone and in the response to hemodynamic stress and injury. Perturbations in G protein-mediated signaling are well known to contribute to cardiac hypertrophy, failure, and arrhythmias. Most of the currently used drugs for cardiac and other diseases target GPCR signaling. In the canonical G protein signaling paradigm, G proteins that are located at the cytoplasmic surface of the plasma membrane become activated after an agonist-induced conformational change of GPCRs, which then allows GTP-bound Gα and free Gβγ subunits to activate or inhibit effector proteins. Research over the past two decades has markedly broadened the original paradigm with a GPCR-G protein-effector at the cell surface at its core by revealing novel binding partners and additional subcellular localizations for heterotrimeric G proteins that facilitate many previously unrecognized functional effects. In this review, we focus on non-canonical and epigenetic-related mechanisms that regulate heterotrimeric G protein expression, activation, and localization and discuss functional consequences using cardiac examples where possible. Mechanisms reviewed involve microRNAs, histone deacetylases, chaperones, alternative modes of G protein activation, and posttranslational modifications. Some of these newly characterized mechanisms may be further developed into novel strategies for the treatment of cardiac disease and beyond.
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Affiliation(s)
- Peng Zhang
- Cardiovascular Research Center, Cardiology Division, Rhode Island Hospital, Providence, RI, USA; Alpert Medical School of Brown University, Providence, RI, USA
| | - Celinda M Kofron
- Cardiovascular Research Center, Cardiology Division, Rhode Island Hospital, Providence, RI, USA; Alpert Medical School of Brown University, Providence, RI, USA
| | - Ulrike Mende
- Cardiovascular Research Center, Cardiology Division, Rhode Island Hospital, Providence, RI, USA; Alpert Medical School of Brown University, Providence, RI, USA.
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Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T. The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells. J Biotechnol 2015; 199:38-46. [DOI: 10.1016/j.jbiotec.2015.02.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/09/2015] [Accepted: 02/11/2015] [Indexed: 12/14/2022]
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Robinson MD, Pelizzola M. Computational epigenomics: challenges and opportunities. Front Genet 2015; 6:88. [PMID: 25798147 PMCID: PMC4350413 DOI: 10.3389/fgene.2015.00088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 12/31/2022] Open
Affiliation(s)
- Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich Zurich, Switzerland ; SIB Swiss Institute of Bioinformatics, University of Zurich Zurich, Switzerland
| | - Mattia Pelizzola
- Computational Epigenomics, Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia Milano, Italy
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