1
|
Reichelt P, Bernhart S, Platzbecker U, Cross M. MicroRNA Screening Reveals Upregulation of FoxO-Signaling in Relapsed Acute Myeloid Leukemia Patients. Genes (Basel) 2024; 15:1625. [PMID: 39766892 PMCID: PMC11675194 DOI: 10.3390/genes15121625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 12/13/2024] [Accepted: 12/17/2024] [Indexed: 01/30/2025] Open
Abstract
Background/Objectives: AML is an aggressive malignant disease characterized by aberrant proliferation and accumulation of immature blast cells in the patient's bone marrow. Chemotherapeutic treatment can effectively induce remission and re-establish functional hematopoiesis. However, many patients experience chemoresistance-associated relapse and disease progression with a poor prognosis. The identification of molecular determinants of chemoresistance that could serve as potential targets for the therapeutic restoration of chemosensitivity has proven to be challenging. Methods: To address this, we have analyzed longitudinal changes in the expression of microRNAs during disease progression in a small set of four AML patients, combined with gene ontology (GO) pathway analysis and evaluation of gene expression data in patient databases. Results: MicroRNA profiling of bone marrow samples at diagnosis and after relapse revealed significant differential expression of a large number of microRNAs between the two time points. Subsequent GO pathway analysis identified 11 signal transduction pathways likely to be affected by the differential miRNA signatures. Exemplary validation of the FoxO signaling pathway by gene expression analysis confirmed significant upregulation of FOXO1 and the target genes GADD45 and SOD2. Conclusions: Here, we show how a microRNA-based pathway prediction strategy can be used to identify differentially regulated signaling pathways that represent potential targets for therapeutic intervention.
Collapse
Affiliation(s)
- Paula Reichelt
- Department of Hematology, Cell Therapy, Hemostaseology and Infectiology, University Hospital Leipzig, 04103 Leipzig, Germany; (U.P.); (M.C.)
| | - Stephan Bernhart
- Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, Germany;
| | - Uwe Platzbecker
- Department of Hematology, Cell Therapy, Hemostaseology and Infectiology, University Hospital Leipzig, 04103 Leipzig, Germany; (U.P.); (M.C.)
| | - Michael Cross
- Department of Hematology, Cell Therapy, Hemostaseology and Infectiology, University Hospital Leipzig, 04103 Leipzig, Germany; (U.P.); (M.C.)
| |
Collapse
|
2
|
Ghionescu AV, Sorop A, Linioudaki E, Coman C, Savu L, Fogarasi M, Lixandru D, Dima SO. A predicted epithelial-to-mesenchymal transition-associated mRNA/miRNA axis contributes to the progression of diabetic liver disease. Sci Rep 2024; 14:27678. [PMID: 39532948 PMCID: PMC11557572 DOI: 10.1038/s41598-024-77416-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024] Open
Abstract
Despite public health measures, type 2 diabetes (T2D) is still a significant concern worldwide, given its associated complications, including hepatic alterations. The role of epithelial-to-mesenchymal transition (EMT) in liver fibrosis is well established. However, its effects on the progression of diabetic liver diseases are not well understood. Therefore, this study aims to investigate the mRNA/miRNA axes involved in this process. Bioinformatic analysis revealed new EMT-associated genes (CDH2, ITGB1, COL4A1, COL1A1, TNC, CCN2, and JUN), which showed higher expression in obese T2D and hepatocellular carcinoma (HCC) patients. In addition, six miRNAs (miR-21-5p, miR-26a-5p, miR-34a-5p, miR-106a-5p, miR-320a-3p and miR-424-5p) have been found as potential targets. Among them, miR-26a-5p and miR-424-5p were significantly downregulated in nonalcoholic steatohepatitis (NASH) and HCC (p < 0.05), being considered potential negative regulators of the EMT process. In our hepatic mesenchymal culture model, miR-26a-5p negatively regulated cadherin 2 (also known as N-cadherin, CDH2) and promoted the cadherin 1 (also known as E-cadherin, CDH1) expression. Our results reveal potential molecules involved in liver tumor development. Moreover, we observe that miR-26a-5p impairs EMT in the initial stages of diabetic liver disease by inhibiting CDH2 and could be a valuable target in this pathology.
Collapse
Grants
- 629PED/2022 CCCDI-UEFISCDI, project number PN-III-P2-2.1-PED-2021-3180, within PNCDI III
- 629PED/2022 CCCDI-UEFISCDI, project number PN-III-P2-2.1-PED-2021-3180, within PNCDI III
- 629PED/2022 CCCDI-UEFISCDI, project number PN-III-P2-2.1-PED-2021-3180, within PNCDI III
- 629PED/2022 CCCDI-UEFISCDI, project number PN-III-P2-2.1-PED-2021-3180, within PNCDI III
- 629PED/2022 CCCDI-UEFISCDI, project number PN-III-P2-2.1-PED-2021-3180, within PNCDI III
- 629PED/2022 CCCDI-UEFISCDI, project number PN-III-P2-2.1-PED-2021-3180, within PNCDI III
- 629PED/2022 CCCDI-UEFISCDI, project number PN-III-P2-2.1-PED-2021-3180, within PNCDI III
- 28571/02.10.2023 UMFCD
Collapse
Affiliation(s)
- Alina-Veronica Ghionescu
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Ekaterini Linioudaki
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Cristin Coman
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- "Cantacuzino" National Medico-Military Institute for Research and Development, Bucharest, Romania
| | - Lorand Savu
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Marton Fogarasi
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
| | - Daniela Lixandru
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania.
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania.
| | - Simona Olimpia Dima
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest, Romania
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest, Romania
| |
Collapse
|
3
|
Pernar Kovač M, Tadić V, Kralj J, Milković Periša M, Orešković S, Babić I, Banović V, Zhang W, Culig Z, Brozovic A. MiRNA-mRNA integrative analysis reveals epigenetically regulated and prognostic miR-103a with a role in migration and invasion of carboplatin-resistant ovarian cancer cells that acquired mesenchymal-like phenotype. Biomed Pharmacother 2023; 166:115349. [PMID: 37634476 DOI: 10.1016/j.biopha.2023.115349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/07/2023] [Accepted: 08/19/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND DNA methylation, histone modifications, and miRNAs affect ovarian cancer (OC) progression and therapy response. PURPOSE Identification of epigenetically downregulated miRNAs in drug-resistant OC cell lines with a possible role in drug resistance and/or drug-induced mesenchymal-like phenotype. METHODS MiRNA profiling was performed on parental and carboplatin-resistant OC cells, MES-OV and MES-OV CBP. RT-qPCR validation, epigenetic modulation and other CBP-resistant OC cell lines were used to select miRNAs of interest. The integration of miRNA-predicted target genes and differentially expressed genes (DEGs), pathway and functional analysis were used for forecasting their biological role. Data mining was performed to determine their possible prognostic and predictive values. RESULTS MiRNA profiling revealed 48 downregulated miRNAs in OC cells whose drug sensitivity and metastatic potential were impacted by epigenetic modulators. Of the fourteen selected, nine were validated as changed, and seven of these restored their expression upon treatment with epigenetic inhibitors. Only three had similar expression patterns in other OC cell lines. MiRNA-mRNA integrative analysis resulted in 56 target DEGs. Pathway analysis revealed that these genes are involved in cell adhesion, migration, and invasion. The functional analysis confirmed the role of miR-103a-3p, miR-17-5p and miR-107 in cell invasion, while data mining showed their prognostic and predictive values. Only miR-103a-3p was epigenetically regulated at the constitutive level. CONCLUSION High throughput miRNA and cDNA profiling coupled with pathway analysis and data mining delivered evidence for miRNAs which can be epigenetically regulated in drug-resistant, mesenchymal-like OC cells as possible markers to combat therapy-induced short overall survival and tumor metastatic potential.
Collapse
Affiliation(s)
- Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Vanja Tadić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Juran Kralj
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marija Milković Periša
- University Hospital Centre Zagreb, Department of Pathology and Cytology, Petrova ulica 13, HR-10000 Zagreb, Croatia; University of Zagreb, School of Medicine, Institute of Pathology, Šalata 10, HR-10000 Zagreb, Croatia
| | - Slavko Orešković
- Department of Obstetrics and Gynecology, University Hospital Center Zagreb, Petrova 13, HR-10000 Zagreb, Croatia
| | - Ivan Babić
- Department of Obstetrics and Gynecology, University Hospital Center Zagreb, Petrova 13, HR-10000 Zagreb, Croatia
| | - Vladimir Banović
- Department of Obstetrics and Gynecology, University Hospital Center Zagreb, Petrova 13, HR-10000 Zagreb, Croatia
| | - Wei Zhang
- Department of Engineering Mechanics, Dalian University of Technology, Linggong Road 2, 116024 Dalian, China
| | - Zoran Culig
- Department of Urology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| |
Collapse
|
4
|
Evidence that Transcriptional Alterations in Sarcoptes scabiei Are under Tight Post-Transcriptional (microRNA) Control. Int J Mol Sci 2022; 23:ijms23179719. [PMID: 36077116 PMCID: PMC9456212 DOI: 10.3390/ijms23179719] [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: 06/21/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Here, we explored transcriptomic differences among early egg (Ee), late egg (Le) and adult female (Af) stages of the scabies mite, Sarcoptes scabiei, using an integrative bioinformatic approach. We recorded a high, negative correlation between miRNAs and genes with decreased mRNA transcription between the developmental stages, indicating substantial post-transcriptional repression; we also showed a positive correlation between miRNAs and genes with increased mRNA transcription, suggesting indirect post-transcriptional regulation. The alterations in mRNA transcription between the egg and adult female stages of S. scabiei were inferred to be linked to metabolism (including carbohydrate and lipid degradation, amino acid and energy metabolism), environmental information processing (e.g., signal transduction and signalling molecules), genetic information processing (e.g., transcription and translation) and/or organismal systems. Taken together, these results provide insight into the transcription of this socioeconomically important parasitic mite, with a particular focus on the egg stage. This work encourages further, detailed laboratory studies of miRNA regulation across all developmental stages of S. scabiei and might assist in discovering new intervention targets in the egg stage of S. scabiei.
Collapse
|
5
|
Li Y, Yang M, Lou A, Yun J, Ren C, Li X, Xia G, Nam K, Yoon D, Jin H, Seo K, Jin X. Integrated analysis of expression profiles with meat quality traits in cattle. Sci Rep 2022; 12:5926. [PMID: 35396568 PMCID: PMC8993808 DOI: 10.1038/s41598-022-09998-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.
Collapse
Affiliation(s)
- Yunxiao Li
- College of Life Science, Shandong University, Qingdao, China
| | - Miaosen Yang
- Department of Chemistry, Northeast Electric Power University, Jilin, China
| | - Angang Lou
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Jinyan Yun
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Chunyu Ren
- Animal Husbandry Bureau of Yanbian Autonomous Prefecture, Yanji, China
| | - Xiangchun Li
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Guangjun Xia
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Kichang Nam
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University, Sunchon, South Korea
| | - Duhak Yoon
- Department of Animal Science, Kyungpook National University, Taegu, South Korea
| | - Haiguo Jin
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Kangseok Seo
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University, Sunchon, South Korea.
| | - Xin Jin
- Engineering Research Center of North-East Cold Region Beef Cattle Science and Technology Innovation, Ministry of Education, Yanbian University, Yanji, China.
| |
Collapse
|
6
|
Afshari A, Yaghobi R, Rezaei G. Inter-regulatory role of microRNAs in interaction between viruses and stem cells. World J Stem Cells 2021; 13:985-1004. [PMID: 34567421 PMCID: PMC8422934 DOI: 10.4252/wjsc.v13.i8.985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/11/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are well known for post-transcriptional regulatory ability over specific mRNA targets. miRNAs exhibit temporal or tissue-specific expression patterns and regulate the cell and tissue developmental pathways. They also have determinative roles in production and differentiation of multiple lineages of stem cells and might have therapeutic advantages. miRNAs are a part of some viruses' regulatory machinery, not a byproduct. The trace of miRNAs was detected in the genomes of viruses and regulation of cell reprograming and viral pathogenesis. Combination of inter-regulatory systems has been detected for miRNAs during viral infections in stem cells. Contraction between viruses and stem cells may be helpful in therapeutic tactics, pathogenesis, controlling viral infections and defining stem cell developmental strategies that is programmed by miRNAs as a tool. Therefore, in this review we intended to study the inter-regulatory role of miRNAs in the interaction between viruses and stem cells and tried to explain the advantages of miRNA regulatory potentials, which make a new landscape for future studies.
Collapse
Affiliation(s)
- Afsoon Afshari
- Shiraz Nephro-Urology Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran.
| | - Ghazal Rezaei
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz 7193711351, Iran
| |
Collapse
|
7
|
Mohammadi A, Mansoori B, Duijf PHG, Safarzadeh E, Tebbi L, Najafi S, Shokouhi B, Sorensen GL, Holmskov U, Baradaran B. Restoration of miR-330 expression suppresses lung cancer cell viability, proliferation, and migration. J Cell Physiol 2020; 236:273-283. [PMID: 32583462 DOI: 10.1002/jcp.29840] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/29/2020] [Accepted: 05/21/2020] [Indexed: 12/15/2022]
Abstract
Lung cancer is one of the most common cancers and its incidence is rising around the world. Various studies suggest that miR-330 acts as a tumor-suppressor microRNA (miRNA) in different types of cancers, but precisely how has remained unclear. In this study, we investigate miR-330 expression in lung cancer patient samples, as well as in vitro, by studying how normalization of miR-330 expression affects lung cancer cellular phenotypes such as viability, apoptosis, proliferation, and migration. We establish that low miR-330 expression predicts poor lung cancer prognosis. Stable restoration of reduced miR-330 expression in lung cancer cells reduces cell viability, increases the fraction of apoptotic cells, causes G2/M cell cycle arrest, and inhibits cell migration. These findings are substantiated by increased mRNA and protein expression of markers for apoptosis via the intrinsic pathway, such as caspase 9, and decreased mRNA and protein expression of markers for cell migration, such as vimentin, C-X-C chemokine receptor type 4, and matrix metalloproteinase 9. We showed that reduced miR-330 expression predicts poor lung cancer survival and that stable restoration of miR-330 expression in lung cancer cells has a broad range of tumor-suppressive effects. This indicates that miR-330 is a promising candidate for miRNA replacement therapy for lung cancer patients.
Collapse
Affiliation(s)
- Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pascal H G Duijf
- University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
| | - Elham Safarzadeh
- Department of Microbiology & Immunology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Leila Tebbi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Souzan Najafi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behrooz Shokouhi
- Departmentof Infectious Diseases, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Grith L Sorensen
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Uffe Holmskov
- Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
8
|
Shirjang S, Mansoori B, Mohammadi A, Shajari N, H G Duijf P, Najafi S, Abedi Gaballu F, Nofouzi K, Baradaran B. miR-330 Regulates Colorectal Cancer Oncogenesis by Targeting BACH1. Adv Pharm Bull 2020; 10:444-451. [PMID: 32665904 PMCID: PMC7335988 DOI: 10.34172/apb.2020.054] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/28/2019] [Accepted: 12/08/2019] [Indexed: 12/24/2022] Open
Abstract
Purpose: Based on WHO report, colorectal cancer (CRC) is the second cause of death among patients with cancer worldwide. Dysregulation of miRNAs expressions has been demonstrated in different human cancers, especially CRC. Studies have shown that miR-330 could act as both TS-miR and/or oncomiR in different types of cancers. BACH1 is also identified as a transcription factor, which is involved in ontogenesis. In this study, we evaluated the CRC suppression via silencing of BACH1 by small silencer molecule called miR-330. Methods: Firstly, we analyzed the BACH1, miR-330-3p and miR-330-5p expressions according to the colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) project established from a patient of the colon and rectal cancer patients in The Cancer Genome Atlas (TCGA) database. The targeting of BACH1 via miR-330 in human CRC cells was evaluated by Vejnar bioinformatics methods, and confirmed by qRT-PCR and western blot analysis. Proliferation was performed by MTT assay. The MMP9, CXCR4, and VEGFR proteins were measured by western blotting. Results: The analysis of BACH1, miR-330-3p, and miR-330-5p expressions according to the COAD and READ projects showed that BACH1 was overexpressed, but miR-330-3p and miR330-5p were reduced in CRC tumors compared to normal controls. The miR-330 induction prevented proliferation of CRC cell by targeting BACH1 mRNA, which represses MMP9, C-X-C chemokine receptor type 4 (CXCR4), and vascular endothelial growth factor receptor (VEGFR) proteins expressions. Conclusion: Our results suggested that BACH1 is a potential target for miR-330 in CRC cells. The miR-330 induction inhibits CRC cells proliferation by suppressing BACH1 expression in posttranscriptional level. It was suggested that targeting of BACH1 via miRNA such as miR-330 could be a valid strategy in the field of CRC targeted therapy via modulating the oncogenic signaling pathway.
Collapse
Affiliation(s)
- Solmaz Shirjang
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Neda Shajari
- Department of Immunology, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
| | - Pascal H G Duijf
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Souzan Najafi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Katayoon Nofouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
9
|
Panagaki T, Randi EB, Szabo C. Role of 3-Mercaptopyruvate Sulfurtransferase in the Regulation of Proliferation and Cellular Bioenergetics in Human Down Syndrome Fibroblasts. Biomolecules 2020; 10:biom10040653. [PMID: 32340322 PMCID: PMC7226246 DOI: 10.3390/biom10040653] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Down syndrome (trisomy of human chromosome 21) is a common genetic disorder. Overproduction of the gaseous mediator hydrogen sulfide (H2S) has been implicated in the pathogenesis of neurological and metabolic deficits associated with Down syndrome. Several lines of data indicate that an important enzyme responsible for H2S overproduction in Down syndrome is cystathionine-β-synthase (CBS), an enzyme localized on chromosome 21. The current study explored the possibility that a second H2S-producing enzyme, 3-mercaptopyruvate sulfurtransferase (3-MST), may also contribute to the development of functional deficits of Down syndrome cells. Western blotting analysis demonstrated a significantly higher level of 3-MST protein expression in human Down syndrome fibroblasts compared to cells from healthy control individuals; the excess 3-MST was mainly localized to the mitochondrial compartment. Pharmacological inhibition of 3-MST activity improved mitochondrial electron transport and oxidative phosphorylation parameters (but did not affect the suppressed glycolytic parameters) and enhanced cell proliferation in Down syndrome cells (but not in healthy control cells). The findings presented in the current report suggest that in addition to the indisputable role of CBS, H2S produced from 3-MST may also contribute to the development of mitochondrial metabolic and functional impairments in Down syndrome cells.
Collapse
|
10
|
Jeffery N, Harries LW. miRNAs responsive to the diabetic microenvironment in the human beta cell line EndoC-βH1 may target genes in the FOXO, HIPPO and Lysine degradation pathways. Exp Cell Res 2019; 384:111559. [PMID: 31425691 DOI: 10.1016/j.yexcr.2019.111559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/13/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022]
Abstract
Altered expression of miRNAs is evident in the islets of diabetic human donors, but the effects of specific aspects of the diabetic microenvironment and identity of gene ontology pathways demonstrating target gene enrichment in response to each is understudied. We assessed changes in the miRNA milieu in response to high/low glucose, hypoxia, dyslipidaemia and inflammatory factors in a humanised EndoC-βH1 beta cell culture system and performed miRPath analysis for each treatment individually. The 10 miRNAs demonstrating the greatest dysregulation across treatments were then independently validated and Gene Set Enrichment Analysis to confirm targeted pathways undertaken. 171 of 392 miRNAs displayed altered expression in response to one or more cellular stressors. miRNA changes were treatment specific, but their target genes were enriched in conserved pathways. 5 miRNAs (miR-136-5p, miR299-5p, miR-454-5p, miR-152 and miR-185) were dysregulated in response to multiple stressors and survived validation in independent samples (p = 0.008, 0.002, 0.012, 0.005 and 0.024 respectively). Target genes of dysregulated miRNAs were clustered into FOXO1, HIPPO and Lysine degradation pathways (p = 0.02, p = 5.84 × 10-5 and p = 3.00 × 10-3 respectively). We provide evidence that the diabetic microenvironment may induce changes to the expression of miRNAs targeting genes enriched in pathways involved in cell stress response and cell survival.
Collapse
Affiliation(s)
- Nicola Jeffery
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
11
|
MiR-190a potentially ameliorates postoperative cognitive dysfunction by regulating Tiam1. BMC Genomics 2019; 20:670. [PMID: 31438846 PMCID: PMC6704709 DOI: 10.1186/s12864-019-6035-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/15/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Postoperative cognitive dysfunction (POCD) affects a large number of post-surgery patients, especially for the elderly. However, the etiology of this neurocognitive disorder is largely unknown. Even if several studies have reported a small number of miRNAs as the essential modulatory factors in POCD, these findings are still rather limited. The aim of current study was to screen the POCD-related miRNAs in the hippocampus tissues and investigate the target genes of differentially expressed miRNAs and their biological functions underlying POCD pathophysiology. METHODS The miRNA microarray was used to find the abnormal expression of miRNAs in the hippocampus tissues from the POCD model mice to normal mice (Discovery cohort, 3 vs 3). The nominal significant results were validated in an independent sample of hippocampus tissues of 10 mice based on same miRNA microarray (Replication cohort, 5 vs 5). Expression level of the most significantly abnormal miRNA was further validated by real-time quantitative polymerase chain reaction (PCR). To determine the expression pattern among miRNAs and genes and detect the interactions, we conducted a weighted gene co-expression network analysis (WGCNA) in the miRNAs and genes expression data from hippocampus tissue of wild type mice (n = 24). The target genes of miRNAs were predicted using the miRWalk3.0 software. Furthermore, we used the ClueGO software to decipher the pathways network and reveal the biological functions of target genes of miRNAs. RESULTS We found that nine miRNAs showed significant associations with POCD in both datasets. Among these miRNAs, mmu-miR-190a-3p was the most significant one. By performing WGCNA analysis, we found 25 co-expression modules, of which mmu-miR-190a-3p was significantly anti-correlated with red module. Moreover, in the red module, 314 genes were significantly enriched in four pathways such as axon guidance and calcium signaling pathway, which are well-documented to be associated with psychiatric disorders and brain development. Also, 169 of the 314 genes were highly correlated with mmu-miR-190a-3p, and four genes (Sphkap, Arhgef25, Tiam1, and Ntrk3) had putative binding sites at 3'-UTR of mmu-miR-190a-3p. Based on protein-protein network analysis, we detected that Tiam1 was a central gene regulated by the mmu-miR-190a-3p. CONCLUSIONS Taken together, we conclude that mmu-miR-190a-3p is involved in the etiology of POCD and may serve as a novel predictive indicator for POCD.
Collapse
|
12
|
Liang HB, He JR, Tu XQ, Ding KQ, Yang GY, Zhang Y, Zeng LL. MicroRNA-140-5p: A novel circulating biomarker for early warning of late-onset post-stroke depression. J Psychiatr Res 2019; 115:129-141. [PMID: 31129437 DOI: 10.1016/j.jpsychires.2019.05.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/12/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
We aimed to explore the circulating microRNAs biomarkers in the acute stage following cerebral ischemia to earlier warn late-onset post-stroke depression (PSD). A total of 251 consecutive patients with acute ischemic stroke were recruited. They were divided into three groups depending on whether PSD had occurred at 2 weeks or 3 months since stroke: early-onset PSD, late-onset PSD, and non-depressed group. Microarray assay was conducted to identify the different expression profiles of plasma miRNAs. Comprehensive bioinformatics analysis for their integrating putative target genes was performed. The key miRNA was validated in a larger cohort and its function was further studied in ischemic mice brain. We screened three differentially expressed miRNAs in the late-onset PSD individuals, miR-140-5p and miR-221-3p were significantly upregulated while miR-1246 was downregulated. The bioinformatics analysis demonstrated that their predicted target genes were mainly enriched in axon development and Ras signaling pathway. Logistic regression analysis revealed that miR-140-5p was an independent risk factor for late-onset PSD (P = 0.017, OR = 2.313, 95%CI 1.158 to 4.617). The miR-140-5p expression on admission was significantly positively correlated with HDRS scores assessed at 3 months after stroke (P = 0.0007). The predictive value of miR-140-5p for late-onset PSD is 83.3% sensitivity and 72.6% specificity (AUC = 0.8127, P < 0.0001). AAV-mediated overexpression of miR-140-5p decreased the protein level of IL1rap, IL1rapl1, VEGF, and MEGF10 in the ischemic mouse hippocampus and inhibited neurogenesis and capillary density. MiR-140-5p might be involved in the pathogenesis of late-onset PSD and used as a novel early warning biomarker.
Collapse
Affiliation(s)
- Huai-Bin Liang
- Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Ji-Rong He
- Department of Neurology, Ruijin Hospital Luwan Branch, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200020, China
| | - Xuan-Qiang Tu
- Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Kai-Qi Ding
- Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Guo-Yuan Yang
- Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yu Zhang
- Department of Neurology, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201801, China.
| | - Li-Li Zeng
- Department of Neurology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| |
Collapse
|
13
|
Circulating microRNAs as potential diagnostic biomarkers and therapeutic targets in prostate cancer: Current status and future perspectives. J Cell Biochem 2019; 120:16316-16329. [DOI: 10.1002/jcb.29053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/04/2019] [Indexed: 12/19/2022]
|
14
|
Mura M, Jaksik R, Lalik A, Biernacki K, Kimmel M, Rzeszowska-Wolny J, Fujarewicz K. A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes. BMC Genomics 2019; 20:114. [PMID: 30727966 PMCID: PMC6366035 DOI: 10.1186/s12864-019-5464-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023] Open
Abstract
Background Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation, since the amounts of miRNAs in cells also vary upon irradiation. To address this possibility, we designed experiments using cancer-derived cell lines transfected with luciferase reporter gene containing sequences targeted by different miRNA species in its 3′- untranslated region. We focus on the early time-course response (1 h past irradiation) to eliminate secondary mRNA expression waves. Results Experiments revealed that the irradiation-induced changes in the mRNA expression depend on the miRNAs which interact with mRNA. To identify the strongest interactions, we propose a mathematical model which predicts the mRNA fold expression changes, caused by perturbation of microRNA-mRNA interactions. Model was applied to experimental data including various cell lines, irradiation doses and observation times, both ours and literature-based. Comparison of modelled and experimental mRNA expression levels given miRNA level changes allows estimating how many and which miRNAs play a significant role in transcriptome response to stress conditions in different cell types. As an example, in the human melanoma cell line the comparison suggests that, globally, a major part of the irradiation-induced changes of mRNA expression can be explained by perturbed miRNA-mRNA interactions. A subset of about 30 out of a few hundred miRNAs expressed in these cells appears to account for the changes. These miRNAs play crucial roles in regulatory mechanisms observed after irradiation. In addition, these miRNAs have a higher average content of GC and a higher number of targeted transcripts, and many have been reported to play a role in the development of cancer. Conclusions Our proposed mathematical modeling approach may be used to identify miRNAs which participate in responses of cells to ionizing radiation, and other stress factors such as extremes of temperature, exposure to toxins, and drugs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5464-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marzena Mura
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland. .,, Ardigen S.A., ul. Bobrzyńskiego 14, 30-348, Cracow, Poland.
| | - Roman Jaksik
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland
| | - Anna Lalik
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland
| | - Krzysztof Biernacki
- Department of Medical and Molecular Biology, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, USA
| | - Marek Kimmel
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Departments of Statistics and Bioengineering, Rice University, MS 138, 6100 Main, Houston, TX, 77005, USA
| | - Joanna Rzeszowska-Wolny
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland. .,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland.
| | - Krzysztof Fujarewicz
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland
| |
Collapse
|
15
|
MiR-34b Protects Against Focal Cerebral Ischemia-Reperfusion (I/R) Injury in Rat by Targeting Keap1. J Stroke Cerebrovasc Dis 2019; 28:1-9. [DOI: 10.1016/j.jstrokecerebrovasdis.2018.08.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/01/2018] [Accepted: 08/08/2018] [Indexed: 02/07/2023] Open
|
16
|
Lnc-ISG20 Inhibits Influenza A Virus Replication by Enhancing ISG20 Expression. J Virol 2018; 92:JVI.00539-18. [PMID: 29899085 DOI: 10.1128/jvi.00539-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in many aspects of cellular processes, including the antiviral immune response. To identify influenza A virus (IAV)-related lncRNAs, we performed RNA deep sequencing to compare the profiles of lncRNAs in A549 and HEK293T cells with or without IAV infection. We identified an IAV-upregulated lncRNA named lnc-ISG20 because it shares most of its sequence with ISG20. We found that lnc-ISG20 is an interferon-stimulated gene similar to ISG20. Overexpression of lnc-ISG20 inhibited IAV replication, while lnc-ISG20 knockdown favored viral replication, suggesting that lnc-ISG20 is inhibitory to IAV replication. Further study indicated that overexpression of lnc-ISG20 enhances ISG20 protein levels, while knockdown of lnc-ISG20 reduces ISG20 protein levels in A549 cells induced with poly(I·C) and Sendai virus. We demonstrated that lnc-ISG20 inhibits IAV replication in an ISG20-dependent manner. As lnc-ISG20 did not affect the mRNA level of ISG20, we postulated that lnc-ISG20 may function as endogenous RNA competing with ISG20 to enhance its translation. Indeed, we identified that microRNA 326 (miR-326) is a mutual microRNA for both ISG20 and lnc-ISG20 that targets the 3' untranslated region of ISG20 mRNA to inhibit its translation. We confirmed that lnc-ISG20 can bind miR-326, which in turn decreased the amount of miR-326 bound to ISG20 mRNA. In conclusion, we identified that the IAV-upregulated lnc-ISG20 is a novel interferon-stimulated gene that elicits its inhibitory effect on IAV replication by enhancing ISG20 expression. We demonstrated that lnc-ISG20 functions as a competitive endogenous RNA to bind miR-326 to reduce its inhibition of ISG20 translation. Our results revealed the mechanism by which lnc-ISG20 inhibits IAV replication.IMPORTANCE The replication of influenza A virus is regulated by host factors. However, the mechanisms by which lncRNAs regulate IAV infection are not well understood. We identified that lnc-ISG20 is upregulated during IAV infection and is also an interferon-stimulated gene. We demonstrated that lnc-ISG20 can enhance ISG20 expression, which in turn inhibits IAV replication. Our studies indicate that lnc-ISG20 functions as a competing endogenous RNA that binds miR-326 and reduces its inhibitory effect on ISG20. Taken together, our findings reveal the mechanistic details of lnc-ISG20 negatively regulating IAV replication. These findings indicate that lnc-ISG20 plays an important role during the host antiviral immune response.
Collapse
|
17
|
Hou L, Luo P, Ma Y, Jia C, Yu F, Lv Z, Wu C, Fu D. MicroRNA-125a-3p downregulation correlates with tumorigenesis and poor prognosis in patients with non-small cell lung cancer. Oncol Lett 2017; 14:4441-4448. [PMID: 29085440 PMCID: PMC5649526 DOI: 10.3892/ol.2017.6809] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 12/20/2016] [Indexed: 11/05/2022] Open
Abstract
MicroRNA (miR)-125a-3p is derived from the 3'-end of pre-miR-125a, which is associated with several types of cancer, such as gastric and prostate cancer, and glioma. The aim of the present study was to identify the prognostic significance of miR-125a-3p expression levels in patients with NSCLC. The gene expression omnibus database was used to analyze miR-125a-3p expression in NSCLC in silico, and 148 NSCLC samples and 30 adjacent normal lung tissue specimens were analyzed for the expression of miR-125a-3p by qPCR. The results showed that the expression levels of miR-125a-3p in the adjacent normal tissues was higher than the expression level in the NSCLC tissues. There were several clinical parameters demonstrated to be associated with miR-125a-3p expression, such as lymph node metastasis, tumor node metastasis classification of malignant tumor stage and tumor diameter. Furthermore, high expression levels of miR-125a-3p with chemotherapy prolonged the overall survival rate and disease free survival rate compared with untreated patients with low expression of miR-125a-3p. Thus, miR-125a-3p is a significant prognostic biomarker for patients with NSCLC, from which a novel therapeutic strategy to combat NSCLC may be derived.
Collapse
Affiliation(s)
- Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Pei Luo
- Veterinary Faculty, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Yushui Ma
- Department of Nuclear Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Chengyou Jia
- Department of Nuclear Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Fei Yu
- Department of Nuclear Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, P.R. China
| | - Da Fu
- Department of Nuclear Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China.,Central Laboratory for Medical Research, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| |
Collapse
|
18
|
Lee I, Baxter D, Lee MY, Scherler K, Wang K. The Importance of Standardization on Analyzing Circulating RNA. Mol Diagn Ther 2017; 21:259-268. [PMID: 28039578 PMCID: PMC5426982 DOI: 10.1007/s40291-016-0251-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Circulating RNAs, especially microRNAs (miRNAs), have recently emerged as non-invasive disease biomarkers. Despite enthusiasm and numerous reports on disease-associated circulating miRNAs, currently there is no circulating miRNA-based diagnostic in use. In addition, there are many contradictory reports on the concentration changes of specific miRNA in circulation. Here we review the impact of various technical and non-technical factors related to circulating miRNA measurement and elucidate the importance of having a general guideline for sample preparation and concentration measurement in studying circulating RNA.
Collapse
Affiliation(s)
- Inyoul Lee
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - David Baxter
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - Min Young Lee
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - Kelsey Scherler
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA
| | - Kai Wang
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98019, USA.
| |
Collapse
|
19
|
Luo P, Yang Q, Cong LL, Wang XF, Li YS, Zhong XM, Xie RT, Jia CY, Yang HQ, Li WP, Cong XL, Xia Q, Fu D, Zeng QH, Ma YS. Identification of miR‑124a as a novel diagnostic and prognostic biomarker in non‑small cell lung cancer for chemotherapy. Mol Med Rep 2017; 16:238-246. [PMID: 28534972 PMCID: PMC5482144 DOI: 10.3892/mmr.2017.6595] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/20/2017] [Indexed: 01/18/2023] Open
Abstract
Previous studies have suggested that dysregulation of microRNA (miR) −124a is associated with various types of human cancer. However, there are few studies reporting the level of miR-124a expression in non-small cell lung cancer (NSCLC). The present study investigated the association between miR-124a and NSCLC by analyzing the differential expression of miR-124a in NSCLC using the GEO database, as well as subsequently performing reverse transcription-quantitative polymerase chain reaction analysis on 160 NSCLC biopsies, 32 of which were paired with adjacent normal tissues. The results indicated that mir-124a expression levels were decreased in NSCLC tumor biopsies compared with adjacent normal tissues. The overall survival (OS) in patients with a high expression of miR-124a was prolonged relative to patients with low expression of miR-124a. The expression levels of miR-124a were associated with clinical characteristics, including lymph-node metastasis, tumor differentiation, tumor node metastasis (TNM) stage and diameter. Frequently, lymph-node metastasis, TNM stage, diameter and lack of chemotherapy have been associated with a worse prognosis in patients. In addition, the present study identified that high expression of miR-124awith chemotherapy may increase OS. In conclusion, the current study demonstrated that miR-124a was downregulated in NSCLC, and miR-124a was a potential prognostic tumor biomarker response to chemotherapy.
Collapse
Affiliation(s)
- Pei Luo
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Qing Yang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Le-Le Cong
- Department of Neurology, China Japan Union Hospital, Jilin University, Changchun, Jilin 130031, P.R. China
| | - Xiao-Feng Wang
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Sheng Li
- Department of Orthopedics, Xiangya Hospital, Central‑South University, Changsha, Hunan 410008, P.R. China
| | - Xiao-Ming Zhong
- Department of Radiology, Jiangxi Provincial Tumor Hospital, Nanchang, Jiangxi 330029, P.R. China
| | - Ru-Ting Xie
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Hui-Qiong Yang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Wen-Ping Li
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, P.R. China
| | - Xian-Ling Cong
- Tissue Bank, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Qing Xia
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Da Fu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| | - Qing-Hua Zeng
- Department of Respiratory, The First Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, P.R. China
| |
Collapse
|
20
|
Gim JA, Kim HS. Identification and Expression of Equine MER-Derived miRNAs. Mol Cells 2017; 40:262-270. [PMID: 28320202 PMCID: PMC5424272 DOI: 10.14348/molcells.2017.2295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 11/27/2022] Open
Abstract
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns. The MER5A1, MER53, and MER91C sequences obtained from RepeatMasker were matched with the eca-miR-544b, eca-miR-1302, and eca-miR-652 precursor sequences derived from Ensembl transcript database, respectively. Each precursor form was anticipated to yield two mature forms, and we confirmed miRNA expression in six different tissues (cerebrum, cerebellum, lung, spleen, adrenal gland, and duodenum) of one thorough-bred horse. MER5A1-derived miRNAs generally showed significantly higher expression in the lung than in other tissues. MER91C-derived miRNA-5p also showed significantly higher expression in the duodenum than in other tissues (cerebellum, lung, spleen, and adrenal gland). The MER117-overlapped expressed sequence tag generated polycistronic miRNAs, which showed higher expression in the duodenum than other tissues. These data indicate that horse MER transposons encode miR-NAs that are expressed in several tissues and are thought to have biological functions.
Collapse
Affiliation(s)
- Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
- Genetic Engineering Institute, Pusan National University, Busan 46241,
Korea
- The Genomics Institute, Life Sciences Department, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
- Genetic Engineering Institute, Pusan National University, Busan 46241,
Korea
| |
Collapse
|
21
|
Yi H, Huang Y, Yang F, Liu W, He S, Hu X. MicroRNA-182 aggravates cerebral ischemia injury by targeting inhibitory member of the ASPP family (iASPP). Arch Biochem Biophys 2017; 620:52-58. [DOI: 10.1016/j.abb.2016.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/04/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
|
22
|
Oduor CI, Movassagh M, Kaymaz Y, Chelimo K, Otieno J, Ong'echa JM, Moormann AM, Bailey JA. Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma. Front Microbiol 2017; 8:501. [PMID: 28400759 PMCID: PMC5368269 DOI: 10.3389/fmicb.2017.00501] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 03/10/2017] [Indexed: 11/17/2022] Open
Abstract
Endemic Burkitt lymphoma (eBL) is an aggressive B cell lymphoma and is associated with Epstein-Barr virus (EBV) and Plasmodium falciparum malaria co-infections. Central to BL oncogenesis is the over-expression of the MYC proto-oncogene which is caused by a translocation of an Ig enhancer in approximation to the myc gene. While whole genome/transcriptome sequencing methods have been used to define driver mutations and transcriptional dysregulation, microRNA (miRNA) dysregulation and differential expression has yet to be fully characterized. We hypothesized that both human and EBV miRNAs contribute to eBL clinical presentation, disease progression, and poor outcomes. Using sensitive and precise deep sequencing, we identified miRNAs from 17 Kenyan eBL patient tumor samples and delineated the complement of both host and EBV miRNAs. One human miRNA, hsa-miR-10a-5p was found to be differentially expressed (DE), being down-regulated in jaw tumors relative to abdominal and in non-survivors compared to survivors. We also examined EBV miRNAs, which made up 2.7% of the miRNA composition in the eBL samples. However, we did not find any significant associations regarding initial patient outcome or anatomical presentation. Gene ontology analysis and pathway enrichment of previously validated targets of miR-10a-5p suggest that it can promote tumor cell survival as well as aid in evasion of apoptosis. To examine miR-10a-5p regulatory effect on gene expression in eBL, we performed a pairwise correlation coefficient analysis on the expression levels of all its validated targets. We found a significant enrichment of correlated target genes consistent with miR-10a-5p impacting expression. The functions of genes and their correlation fit with multiple target genes impacting tumor resilience. The observed downregulation of miR-10a and associated genes suggests a role for miRNA in eBL patient outcomes and has potential as a predictive biomarker that warrants further investigation.
Collapse
Affiliation(s)
- Cliff I Oduor
- Center for Global Health Research, Kenya Medical Research InstituteKisumu, Kenya; Department of Biomedical Sciences and Technology, Maseno UniversityMaseno, Kenya
| | - Mercedeh Movassagh
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School Worcester, MA, USA
| | - Yasin Kaymaz
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School Worcester, MA, USA
| | - Kiprotich Chelimo
- Department of Biomedical Sciences and Technology, Maseno University Maseno, Kenya
| | - Juliana Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Ministry of Medical Services Kisumu, Kenya
| | - John M Ong'echa
- Center for Global Health Research, Kenya Medical Research Institute Kisumu, Kenya
| | - Ann M Moormann
- Program in Molecular Medicine, University of Massachusetts Medical School Worcester, MA, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcester, MA, USA; Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical SchoolWorcester, MA, USA
| |
Collapse
|
23
|
Shotorbani BB, Alizadeh E, Salehi R, Barzegar A. Adhesion of mesenchymal stem cells to biomimetic polymers: A review. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 71:1192-1200. [PMID: 27987676 DOI: 10.1016/j.msec.2016.10.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/20/2016] [Accepted: 10/13/2016] [Indexed: 02/07/2023]
Abstract
The mesenchymal stem cells (MSCs) are promising candidates for cell therapy due to the self-renewal, multi-potency, ethically approved state and suitability for autologous transplantation. However, key issue for isolation and manipulation of MSCs is adhesion in ex-vivo culture systems. Biomaterials engineered for mimicking natural extracellular matrix (ECM) conditions which support stem cell adhesion, proliferation and differentiation represent a main area of research in tissue engineering. Some of them successfully enhanced cells adhesion and proliferation because of their biocompatibility, biomimetic texture, and chemistry. However, it is still in its infancy, therefore intensification and optimization of in vitro, in vivo, and preclinical studies is needed to clarify efficacies as well as applicability of those bioengineered constructs. The aim of this review is to discuss mechanisms related to the in-vitro adhesion of MSCs, surfaces biochemical, biophysical, and other factors (of cell's natural and artificial micro-environment) which could affect it and a review of previous research attempting for its bio-chemo-optimization.
Collapse
Affiliation(s)
| | - Effat Alizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Drug Applied Research Center and Faculty of advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran; The Umbilical Cord Stem Cell Research Center (UCSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Roya Salehi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Drug Applied Research Center and Faculty of advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran; The Umbilical Cord Stem Cell Research Center (UCSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran; Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
24
|
Luo W, Liang X, Huang S, Cao X. Molecular cloning, expression analysis and miRNA prediction of vascular endothelial growth factor A (VEGFAa and VEGFAb) in pond loach Misgurnus anguillicaudatus, an air-breathing fish. Comp Biochem Physiol B Biochem Mol Biol 2016; 202:39-47. [PMID: 27513203 DOI: 10.1016/j.cbpb.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/21/2016] [Accepted: 07/30/2016] [Indexed: 01/07/2023]
Abstract
Vascular endothelial growth factor A (VEGFA) is the most studied and the best characterized member of the VEGF family and is a key regulator of angiogenesis via its ability to affect the proliferation, migration, and differentiation of endothelial cells. In this study, the full-length cDNAs encoding VEGFAa and VEGFAb from pond loach, Misgurnus anguillicaudatus, were isolated. The VEGFAa is constituted by an open reading frame (ORF) of 570bp encoding for a peptide of 189 amino acid residues, a 639bp 5'-untranslated region (UTR) and a 2383bp 3' UTR. The VEGFAb is constituted by an ORF of 687bp encoding for a peptide of 228 amino acid residues, a 560bp 5' UTR and a 1268bp 3' UTR. Phylogenetic analysis indicated that the VEGFAa and VEGFAb of pond loach were conserved in vertebrates. Expression levels of VEGFAa and VEGFAb were detected by RT-qPCR at different development stages of pond loach and in different tissues of 6-month-old, 12-month-old and 24-month-old pond loach. Moreover, eight predicted miRNAs (miR-200, miR-29, miR-218, miR-338, miR-103, miR-15, miR-17 and miR-223) targeting VEGFAa and VEGFAb were validated by an intestinal air-breathing inhibition experiment. This study will be of value for further studies into the function of VEGFA and its corresponding miRNAs, which will shed a light on the vascularization and accessory air-breathing process in pond loach.
Collapse
Affiliation(s)
- Weiwei Luo
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 437000, Hubei, People's Republic of China
| | - Xiao Liang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 437000, Hubei, People's Republic of China
| | - Songqian Huang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 437000, Hubei, People's Republic of China
| | - Xiaojuan Cao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 437000, Hubei, People's Republic of China; Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Hubei, People's Republic of China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, People's Republic of China.
| |
Collapse
|
25
|
Wu CW, Biggar KK, Luu BE, Szereszewski KE, Storey KB. Analysis of microRNA expression during the torpor-arousal cycle of a mammalian hibernator, the 13-lined ground squirrel. Physiol Genomics 2016; 48:388-96. [PMID: 27084747 DOI: 10.1152/physiolgenomics.00005.2016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/04/2016] [Indexed: 01/06/2023] Open
Abstract
Hibernation is a highly regulated stress response that is utilized by some mammals to survive harsh winter conditions and involves a complex metabolic reprogramming at the cellular level to maintain tissue protections at low temperature. In this study, we profiled the expression of 117 conserved microRNAs in the heart, muscle, and liver of the 13-lined ground squirrel (Ictidomys tridecemlineatus) across four stages of the torpor-arousal cycle (euthermia, early torpor, late torpor, and interbout arousal) by real-time PCR. We found significant differential regulation of numerous microRNAs that were both tissue specific and torpor stage specific. Among the most significant regulated microRNAs was miR-208b, a positive regulator of muscle development that was found to be upregulated by fivefold in the heart during late torpor (13-fold during arousal), while decreased by 3.7-fold in the skeletal muscle, implicating a potential regulatory role in the development of cardiac hypertrophy and skeletal muscle atrophy in the ground squirrels during torpor. In addition, the insulin resistance marker miR-181a was upregulated by 5.7-fold in the liver during early torpor, which supports previous suggestions of hyperinsulinemia in hibernators during the early stages of the hibernation cycle. Although microRNA expression profiles were largely unique between the three tissues, GO annotation analysis revealed that the putative targets of upregulated microRNAs tend to enrich toward suppression of progrowth-related processes in all three tissues. These findings implicate microRNAs in the regulation of both tissue-specific processes and general suppression of cell growth during hibernation.
Collapse
Affiliation(s)
- Cheng-Wei Wu
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Kyle K Biggar
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Bryan E Luu
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Kama E Szereszewski
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada
| |
Collapse
|
26
|
Kochan DZ, Ilnytskyy Y, Golubov A, Deibel SH, McDonald RJ, Kovalchuk O. Circadian-disruption-induced gene expression changes in rodent mammary tissues. Oncoscience 2016; 3:58-70. [PMID: 27014724 PMCID: PMC4789572 DOI: 10.18632/oncoscience.292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/22/2016] [Indexed: 01/22/2023] Open
Abstract
Evidence is mounting that circadian disruption (CD) is a potential carcinogen in breast cancer development. However, despite the growing concern, to our knowledge, no studies have attempted a genome-wide analysis of CD-induced gene expression changes in mammary tissues. Using a rodent model system, a proven photoperiod-shifting paradigm, varying degrees of CD, and Illumina sequencing, we performed an exploratory genome-wide mRNA analysis in mammary tissues. Even though our analysis did not identify any significant patterns in mRNA levels based on the degree of CD, and the majority of groups did not show changes in gene expression on a large-scale, one group (two-week chronic ZT19) displayed 196 differentially expressed genes, 51 of which have been linked to breast cancer. Through gene-specific pathway analysis, the data illustrate that CD may promote breast cancer development through downregulation of DNA repair and p53 signaling pathways, thus promoting genomic instability and cancer development. Although these results have to be interpreted with caution because only a single group illustrated drastic changes in transcript levels, they indicate that chronic CD may directly induce changes in gene expression on a large-scale with potentially malignant consequences.
Collapse
Affiliation(s)
- David Z Kochan
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andrey Golubov
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Scott H Deibel
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Robert J McDonald
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| |
Collapse
|
27
|
Tang Z, Yang Y, Wang Z, Zhao S, Mu Y, Li K. Integrated analysis of miRNA and mRNA paired expression profiling of prenatal skeletal muscle development in three genotype pigs. Sci Rep 2015; 5:15544. [PMID: 26496978 PMCID: PMC4620456 DOI: 10.1038/srep15544] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) play a vital role in muscle development by binding to messenger RNAs (mRNAs). Based on prenatal skeletal muscle at 33, 65 and 90 days post-coitus (dpc) from Landrace, Tongcheng and Wuzhishan pigs, we carried out integrated analysis of miRNA and mRNA expression profiling. We identified 33, 18 and 67 differentially expressed miRNAs and 290, 91 and 502 mRNA targets in Landrace, Tongcheng and Wuzhishan pigs, respectively. Subsequently, 12 mRNAs and 3 miRNAs differentially expressed were validated using quantitative real-time PCR (qPCR), and 5 predicted miRNA targets were confirmed via dual luciferase reporter or western blot assays. We identified a set of miRNAs and mRNA genes differentially expressed in muscle development. Gene ontology (GO) enrichment analysis suggests that the miRNA targets are primarily involved in muscle contraction, muscle development and negative regulation of cell proliferation. Our data indicated that more mRNAs are regulated by miRNAs at earlier stages than at later stages of muscle development. Landrace and Tongcheng pigs also had longer phases of myoblast proliferation than Wuzhishan pigs. This study will be helpful to further explore miRNA-mRNA interactions in myogenesis and aid to uncover the molecular mechanisms of muscle development and phenotype variance in pigs.
Collapse
Affiliation(s)
- Zhonglin Tang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yalan Yang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Zishuai Wang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuanping Zhao
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Institute of Animal Science, Anhui Academy of Agricultural Sciences, Hefei, 230031, P. R. China
| | - Yulian Mu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kui Li
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| |
Collapse
|
28
|
Hu Y, Jiang L, Lai W, Qin Y, Zhang T, Wang S, Ye X. MicroRNA-33a disturbs influenza A virus replication by targeting ARCN1 and inhibiting viral ribonucleoprotein activity. J Gen Virol 2015; 97:27-38. [PMID: 26498766 DOI: 10.1099/jgv.0.000311] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In order to explore the roles of microRNA(s) [miRNA(s)] in the influenza A virus life cycle, we compared the miRNA profiles of 293T and HeLa cell lines, as influenza A virus can replicate efficiently in 293T cells but only poorly in HeLa cells. We analysed differentially expressed miRNAs and identified five, including miR-33a, that could disturb influenza A virus replication significantly. Using TargetScan analysis, we found that ARCN1 could be a potential target of miR-33a. To confirm whether miR-33a could truly target ARCN1, we generated a luciferase reporter for the ARCN1 3' untranslated region (UTR) and performed a luciferase assay. The data indicated that miR-33a could suppress the luciferase activity of the reporter for the ARCN1 3' UTR but not a reporter in which the predicted miR-33a targeting sites on ARCN1 3' UTR were mutated. We performed immunoblotting to confirm that miR-33a could downregulate the protein level of ARCN1. Consistently, the level of ARCN1 protein in HeLa cells was significantly lower than that in 293T cells. We also demonstrated that ectopic expression of ARCN1 could partially rescue the inhibitory effect of miR-33a on virus replication. Furthermore, we demonstrated that miR-33a could impede virus replication at the stage of virus internalization, which was similar to the pattern for knockdown of ARCN1, indicating that miR-33a inhibits influenza virus infection by suppressing ARCN1 expression. In addition, we found that miR-33a could also weaken the viral ribonucleoprotein activity in an ARCN1-independent manner. In conclusion, we found that miR-33a is a novel inhibitory factor for influenza A virus replication.
Collapse
Affiliation(s)
- Yi Hu
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, PR China
| | - Liangzhen Jiang
- Graduate University of Chinese Academy of Sciences, , Beijing 100101, PR China
| | - Wenbin Lai
- Graduate University of Chinese Academy of Sciences, , Beijing 100101, PR China
| | - Yujie Qin
- Graduate University of Chinese Academy of Sciences, , Beijing 100101, PR China
| | - Tinghong Zhang
- Graduate University of Chinese Academy of Sciences, , Beijing 100101, PR China
| | - Shixiong Wang
- Graduate University of Chinese Academy of Sciences, , Beijing 100101, PR China
| | - Xin Ye
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, PR China
| |
Collapse
|
29
|
Gene Network Analysis of Glucose Linked Signaling Pathways and Their Role in Human Hepatocellular Carcinoma Cell Growth and Survival in HuH7 and HepG2 Cell Lines. BIOMED RESEARCH INTERNATIONAL 2015; 2015:821761. [PMID: 26380295 PMCID: PMC4561296 DOI: 10.1155/2015/821761] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/06/2015] [Indexed: 12/14/2022]
Abstract
Cancer progression may be affected by metabolism. In this study, we aimed to analyze the effect of glucose on the proliferation and/or survival of human hepatocellular carcinoma (HCC) cells. Human gene datasets regulated by glucose were compared to gene datasets either dysregulated in HCC or regulated by other signaling pathways. Significant numbers of common genes suggested putative involvement in transcriptional regulations by glucose. Real-time proliferation assays using high (4.5 g/L) versus low (1 g/L) glucose on two human HCC cell lines and specific inhibitors of selected pathways were used for experimental validations. High glucose promoted HuH7 cell proliferation but not that of HepG2 cell line. Gene network analyses suggest that gene transcription by glucose could be mediated at 92% through ChREBP in HepG2 cells, compared to 40% in either other human cells or rodent healthy liver, with alteration of LKB1 (serine/threonine kinase 11) and NOX (NADPH oxidases) signaling pathways and loss of transcriptional regulation of PPARGC1A (peroxisome-proliferator activated receptors gamma coactivator 1) target genes by high glucose. Both PPARA and PPARGC1A regulate transcription of genes commonly regulated by glycolysis, by the antidiabetic agent metformin and by NOX, suggesting their major interplay in the control of HCC progression.
Collapse
|
30
|
Saddic LA, Chang TW, Sigurdsson MI, Heydarpour M, Raby BA, Shernan SK, Aranki SF, Body SC, Muehlschlegel JD. Integrated microRNA and mRNA responses to acute human left ventricular ischemia. Physiol Genomics 2015; 47:455-62. [PMID: 26175501 DOI: 10.1152/physiolgenomics.00049.2015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/08/2015] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) play a significant role in ischemic heart disease. Animal models of left ventricular (LV) ischemia demonstrate a unique miRNA profile; however, these models have limitations in describing human disease. In this study, we performed next-generation miRNA and mRNA sequencing on LV tissue from nine patients undergoing cardiac surgery with cardiopulmonary bypass and cardioplegic arrest. Samples were obtained immediately after aortic cross clamping (baseline) and before aortic cross clamp removal (postischemic). Of 1,237 identified miRNAs, 21 were differentially expressed between baseline and postischemic LV samples including the upregulated miRNAs miR-339-5p and miR-483-3p and the downregulated miRNA miR-139-5p. Target prediction analysis of these miRNAs was integrated with mRNA expression from the same LV samples to identify anticorrelated miRNA-mRNA pairs. Gene enrichment studies of candidate mRNA targets demonstrated an association with cardiovascular disease, cell death, and metabolism. Therapeutics that intervene on these miRNAs and their downstream targets may lead to novel mechanisms of mitigating the damage caused by ischemic insults on the human heart.
Collapse
Affiliation(s)
- Louis A Saddic
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tzuu-Wang Chang
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Martin I Sigurdsson
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mahyar Heydarpour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; and
| | - Stanton K Shernan
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sary F Aranki
- Division of Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Simon C Body
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jochen D Muehlschlegel
- Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts;
| |
Collapse
|
31
|
Liu Y, Baker S, Jiang H, Stuart G, Bai Y. Correlating bladder cancer risk genes with their targeting microRNAs using MMiRNA-Tar. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:177-82. [PMID: 26169799 PMCID: PMC4563352 DOI: 10.1016/j.gpb.2015.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/27/2015] [Indexed: 01/05/2023]
Abstract
The Cancer Genome Atlas (TCGA) (http://cancergenome.nih.gov) is a valuable data resource focused on an increasing number of well-characterized cancer genomes. In part, TCGA provides detailed information about cancer-dependent gene expression changes, including changes in the expression of transcription-regulating microRNAs. We developed a web interface tool MMiRNA-Tar (http://bioinf1.indstate.edu/MMiRNA-Tar) that can calculate and plot the correlation of expression for mRNA-microRNA pairs across samples or over a time course for a list of pairs under different prediction confidence cutoff criteria. Prediction confidence was established by requiring that the proposed mRNA-microRNA pair appears in at least one of three target prediction databases: TargetProfiler, TargetScan, or miRanda. We have tested our MMiRNA-Tar tool through analyzing 53 tumor and 11 normal samples of bladder urothelial carcinoma (BLCA) datasets obtained from TCGA and identified 204 microRNAs. These microRNAs were correlated with the mRNAs of five previously-reported bladder cancer risk genes and these selected pairs exhibited correlations in opposite direction between the tumor and normal samples based on the customized cutoff criterion of prediction. Furthermore, we have identified additional 496 genes (830 pairs) potentially targeted by 79 significant microRNAs out of 204 using three cutoff criteria, i.e., false discovery rate (FDR)<0.1, opposite correlation coefficient between the tumor and normal samples, and predicted by at least one of three target prediction databases. Therefore, MMiRNA-Tar provides researchers a convenient tool to visualize the co-relationship between microRNAs and mRNAs and to predict their targeting relationship. We believe that correlating expression profiles for microRNAs and mRNAs offers a complementary approach for elucidating their interactions.
Collapse
Affiliation(s)
- Yang Liu
- Department of Electrical and Computer Engineering, Rose-Hulman Institute of Technology, Terre Haute, IN 47803, USA
| | - Steve Baker
- Department of Math and Computer Science, Indiana State University, Terre Haute, IN 47809, USA
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gary Stuart
- Department of Biology, Indiana State University, Terre Haute, IN 47809, USA; The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA
| | - Yongsheng Bai
- Department of Biology, Indiana State University, Terre Haute, IN 47809, USA; The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA.
| |
Collapse
|
32
|
El Hajj P, Gilot D, Migault M, Theunis A, van Kempen LC, Salés F, Fayyad-Kazan H, Badran B, Larsimont D, Awada A, Bachelot L, Galibert MD, Ghanem G, Journe F. SNPs at miR-155 binding sites of TYRP1 explain discrepancy between mRNA and protein and refine TYRP1 prognostic value in melanoma. Br J Cancer 2015; 113:91-8. [PMID: 26068396 PMCID: PMC4647532 DOI: 10.1038/bjc.2015.194] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/19/2015] [Accepted: 04/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background: We previously demonstrated an inverse correlation between tyrosinase-related protein 1 (TYRP1) mRNA expression in melanoma metastases and patient survival. However, TYRP1 protein was not detected in half of tissues expressing mRNA and did not correlate with survival. Based on a study reporting that 3′ untranslated region (UTR) of TYRP1 mRNA contains two miR-155-5p (named miR-155) binding sites exhibiting single-nucleotide polymorphisms (SNPs) that promote (matched miRNA–mRNA interaction) mRNA decay or not (mismatched), we aimed to investigate the role of miR-155 in the regulation of TYRP1 mRNA expression and protein translation accounting for these SNPs. Methods: The effect of miR-155 on TYRP1 mRNA/protein expression was evaluated in two melanoma cell lines harbouring matched or mismatched miR-155–TYRP1 mRNA interaction after transfection with pre-miR-155. In parallel, 192 skin and lymph node melanoma metastases were examined for TYRP1 mRNA/protein, miR-155 and SNPs and correlated with patient survival. TYRP1 mRNA, SNPs at its 3′UTR and miR-155 were analysed by RT–qPCR, whereas TYRP1 protein was evaluated by western blot in cell lines and by immunohistochemistry in metastatic tissues. Results: The miR-155 induced a dose-dependent TYRP1 mRNA decay and hampered its translation into protein in the line with the ‘match' genotype. In melanoma metastases, TYRP1 mRNA inversely correlated with miR-155 expression but not with TYRP1 protein in the ‘match' group, whereas it positively correlated with protein but not with miR-155 in the ‘mismatch' group. Consequently, in the latter group, TYRP1 protein inversely correlated with survival. Conclusion: Polymorphisms in 3′UTR of TYRP1 mRNA can affect TYRP1 mRNA regulation by miR-155 and its subsequent translation into protein. These SNPs can render TYRP1 mRNA and protein expression nonsusceptible to miR-155 activity and disclose a prognostic value for TYRP1 protein in a subgroup of melanoma patients. These data support the interest in the prognostic value of melanogenic markers and propose TYRP1 to refine prognosis in patients with advanced disease.
Collapse
Affiliation(s)
- P El Hajj
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| | - D Gilot
- CNRS UMR 6290, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000 Rennes, France
| | - M Migault
- CNRS UMR 6290, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000 Rennes, France
| | - A Theunis
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| | - L C van Kempen
- Department of Pathology, McGill University and Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, H3T 1E2 Montreal, QC, Canada
| | - F Salés
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| | - H Fayyad-Kazan
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| | - B Badran
- Department of Biochemistry, Lebanese University, Rafic Campus, 1003 Hadath-Beirut, Lebanon
| | - D Larsimont
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| | - A Awada
- Clinic of Medical Oncology, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| | - L Bachelot
- CNRS UMR 6290, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000 Rennes, France
| | - M-D Galibert
- CNRS UMR 6290, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000 Rennes, France
| | - G Ghanem
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| | - F Journe
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles, 1 Rue Heger-Bordet, 1000 Brussels, Belgium
| |
Collapse
|
33
|
Integrated miRNA and mRNA expression profiling in inflamed colon of patients with ulcerative colitis. PLoS One 2014; 9:e116117. [PMID: 25546151 PMCID: PMC4278881 DOI: 10.1371/journal.pone.0116117] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/04/2014] [Indexed: 02/07/2023] Open
Abstract
Background Ulcerative colitis (UC) is associated with differential colonic expression of genes involved in immune response (e.g. IL8) and barrier integrity (e.g. cadherins). MicroRNAs (miRNAs) are regulators of gene expression and are involved in various immune-related diseases. In this study, we investigated (1) if miRNA expression in UC mucosa is altered and (2) if any of these changes correlate with mucosal mRNA expression. Integration of mRNA and miRNA expression profiling may allow the identification of functional links between dysregulated miRNAs and their target mRNA. Methodology Colonic mucosal biopsies were obtained from 17 UC (10 active and 7 inactive) patients and 10 normal controls. Total RNA was used to analyze miRNA and mRNA expression via Affymetrix miRNA 2.0 and Affymetrix Human Gene 1.0ST arrays, respectively. Both miRNA and gene expression profiles were integrated by correlation analysis to identify dysregulated miRNAs with their corresponding predicted target mRNA. Microarray data were validated with qRT-PCR. Regulation of IL8 and CDH11 expression by hsa-miR-200c-3p was determined by luciferase reporter assays. Results When comparing active UC patients vs. controls, 51 miRNAs and 1543 gene probe sets gave significantly different signals. In contrast, in inactive UC vs. controls, no significant miRNA expression differences were found while 155 gene probe sets had significantly different signals. We then identified potential target genes of the significantly dysregulated miRNAs and genes in active UC vs. controls and found a highly significant inverse correlation between hsa-miR-200c-3p and IL8, an inflammatory marker, and between hsa-miR-200c-3p and CDH11, a gene related to intestinal epithelial barrier function. We could demonstrate that hsa-miR-200c-3p directly regulates IL8 and CDH11 expression. Conclusion Differential expression of immune- and barrier-related genes in inflamed UC mucosa may be influenced by altered expression of miRNAs. Integrated analysis of miRNA and mRNA expression profiles revealed hsa-miR-200c-3p for use of miRNA mimics as therapeutics.
Collapse
|
34
|
Sjögren RJO, Egan B, Katayama M, Zierath JR, Krook A. Temporal analysis of reciprocal miRNA-mRNA expression patterns predicts regulatory networks during differentiation in human skeletal muscle cells. Physiol Genomics 2014; 47:45-57. [PMID: 25547110 DOI: 10.1152/physiolgenomics.00037.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
microRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through posttranscriptional repression of target genes. miRNAs exert a fundamental level of control over many developmental processes, but their role in the differentiation and development of skeletal muscle from myogenic progenitor cells in humans remains incompletely understood. Using primary cultures established from human skeletal muscle satellite cells, we performed microarray profiling of miRNA expression during differentiation of myoblasts (day 0) into myotubes at 48 h intervals (day 2, 4, 6, 8, and 10). Based on a time-course analysis, we identified 44 miRNAs with altered expression [false discovery rate (FDR) < 5%, fold change > ±1.2] during differentiation, including the marked upregulation of the canonical myogenic miRNAs miR-1, miR-133a, miR-133b, and miR-206. Microarray profiling of mRNA expression at day 0, 4, and 10 identified 842 and 949 genes differentially expressed (FDR < 10%) at day 4 and 10, respectively. At day 10, 42% of altered transcripts demonstrated reciprocal expression patterns in relation to the directional change of their in silico predicted regulatory miRNAs based on analysis using Ingenuity Pathway Analysis microRNA Target Filter. Bioinformatic analysis predicted networks of regulation during differentiation including myomiRs miR-1/206 and miR-133a/b, miRNAs previously established in differentiation including miR-26 and miR-30, and novel miRNAs regulated during differentiation of human skeletal muscle cells such as miR-138-5p and miR-20a. These reciprocal expression patterns may represent new regulatory nodes in human skeletal muscle cell differentiation. This analysis serves as a reference point for future studies of human skeletal muscle differentiation and development in healthy and disease states.
Collapse
Affiliation(s)
- Rasmus J O Sjögren
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; and
| | - Brendan Egan
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; and
| | - Mutsumi Katayama
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; and Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Krook
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
35
|
Hunting the needle in the haystack: a guide to obtain biologically meaningful microRNA targets. Int J Mol Sci 2014; 15:20266-89. [PMID: 25383673 PMCID: PMC4264166 DOI: 10.3390/ijms151120266] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/22/2014] [Accepted: 10/27/2014] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNAs of ~23 nucleotides in length that form up a novel class of regulatory determinants, with a large set of target mRNAs postulated for every single miRNA. Thousands of miRNAs have been discovered so far, with hundreds of them shown to govern biological processes with impact on disease. However, very little is known about how they specifically interfere with biological pathways and disease mechanisms. To investigate this interaction, the hunt for direct miRNA targets that mediate the miRNA effects—the “needle in the haystack”—is an essential step. In this review we provide a comprehensive workflow of successfully applied methods starting from the identification of putative miRNA-target pairs, followed by validation of direct miRNA–mRNA interactions, and finally presenting methods that dissect the impact of particular miRNA-target pairs on a biological process or disease. This guide allows the way to be paved for obtaining biologically meaningful miRNA targets.
Collapse
|
36
|
Pourrajab F, Babaei Zarch M, BaghiYazdi M, Hekmatimoghaddam S, Zare-Khormizi MR. MicroRNA-based system in stem cell reprogramming; differentiation/dedifferentiation. Int J Biochem Cell Biol 2014; 55:318-28. [PMID: 25150833 DOI: 10.1016/j.biocel.2014.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/09/2014] [Accepted: 08/11/2014] [Indexed: 12/26/2022]
Abstract
Stem cells (SCs) have self-renew ability and give rise to committed progenitors of a single or multiple lineages. Elucidating the genetic circuits that govern SCs to self-renew and to differentiate is essential to understand the roles of SCs and promise of these cells in regenerative medicine. MicroRNAs are widespread agents playing critical roles in regulatory networks of transcriptional expression and have been strongly linked with SCs for simultaneous maintenance of pluripotency properties such as self-renewal. This review aims to provide state-of-the-art presentations on microRNA-dependent molecular mechanisms contribute to the maintenance of pluripotency. Understanding the microRNA signature interactions, in conjunction with cell signaling, is critical for development of improved strategies to reprogram differentiated cells or direct differentiation of pluripotent cells.
Collapse
Affiliation(s)
- Fatemeh Pourrajab
- School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran; Department of Clinical Biochemistry and Molecular Biology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | | | - Mohammad BaghiYazdi
- School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | |
Collapse
|
37
|
Ni Y, Lempp FA, Mehrle S, Nkongolo S, Kaufman C, Fälth M, Stindt J, Königer C, Nassal M, Kubitz R, Sültmann H, Urban S. Hepatitis B and D viruses exploit sodium taurocholate co-transporting polypeptide for species-specific entry into hepatocytes. Gastroenterology 2014; 146:1070-83. [PMID: 24361467 DOI: 10.1053/j.gastro.2013.12.024] [Citation(s) in RCA: 615] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 12/04/2013] [Accepted: 12/07/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Hepatitis B and D viruses (HBV and HDV) are human pathogens with restricted host ranges and high selectivity for hepatocytes; the HBV L-envelope protein interacts specifically with a receptor on these cells. We aimed to identify this receptor and analyze whether it is the recently described sodium-taurocholate co-transporter polypeptide (NTCP), encoded by the SLC10A1 gene. METHODS To identify receptor candidates, we compared gene expression patterns between differentiated HepaRG cells, which express the receptor, and naïve cells, which do not. Receptor candidates were evaluated by small hairpin RNA silencing in HepaRG cells; the ability of receptor expression to confer binding and infection were tested in transduced hepatoma cell lines. We used interspecies domain swapping to identify motifs for receptor-mediated host discrimination of HBV and HDV binding and infection. RESULTS Bioinformatic analyses of comparative expression arrays confirmed that NTCP, which was previously identified through a biochemical approach is a bona fide receptor for HBV and HDV. NTCPs from rat, mouse, and human bound Myrcludex B, a peptide ligand derived from the HBV L-protein. Myrcludex B blocked NTCP transport of bile salts; small hairpin RNA-mediated knockdown of NTCP in HepaRG cells prevented their infection by HBV or HDV. Expression of human but not mouse NTCP in HepG2 and HuH7 cells conferred a limited cell-type-related and virus-dependent susceptibility to infection; these limitations were overcome when cells were cultured with dimethyl sulfoxide. We identified 2 short-sequence motifs in human NTCP that were required for species-specific binding and infection by HBV and HDV. CONCLUSIONS Human NTCP is a specific receptor for HBV and HDV. NTCP-expressing cell lines can be efficiently infected with these viruses, and might be used in basic research and high-throughput screening studies. Mapping of motifs in NTCPs have increased our understanding of the species specificities of HBV and HDV, and could lead to small animal models for studies of viral infection and replication.
Collapse
Affiliation(s)
- Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Florian A Lempp
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Mehrle
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Shirin Nkongolo
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christina Kaufman
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Maria Fälth
- German Cancer Research Center and National Center for Tumor Diseases, Unit Cancer Genome Research, Heidelberg, Germany
| | - Jan Stindt
- Clinic for Gastroenterology, Hepatology and Infectiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Christian Königer
- Department of Internal Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Michael Nassal
- Department of Internal Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Ralf Kubitz
- Clinic for Gastroenterology, Hepatology and Infectiology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Holger Sültmann
- German Cancer Research Center and National Center for Tumor Diseases, Unit Cancer Genome Research, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany.
| |
Collapse
|
38
|
Li J, Li C, Han J, Zhang C, Shang D, Yao Q, Zhang Y, Xu Y, Liu W, Zhou M, Yang H, Su F, Li X. The detection of risk pathways, regulated by miRNAs, via the integration of sample-matched miRNA-mRNA profiles and pathway structure. J Biomed Inform 2014; 49:187-97. [PMID: 24561483 DOI: 10.1016/j.jbi.2014.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/17/2013] [Accepted: 02/03/2014] [Indexed: 11/26/2022]
Abstract
The use of genome-wide, sample-matched miRNA (miRNAs)-mRNA expression data provides a powerful tool for the investigation of miRNAs and genes involved in diseases. The identification of miRNA-regulated pathways has been crucial for analysis of the role of miRNAs. However, the classical identification method fails to consider the structural information of pathways and the regulation of miRNAs simultaneously. We proposed a method that simultaneously integrated the change in gene expression and structural information in order to identify pathways. Our method used fold changes in miRNAs and gene products, along with the quantification of the regulatory effect on target genes, to measure the change in gene expression. Topological characteristics were investigated to measure the influence of gene products on entire pathways. Through the analysis of multiple myeloma and prostate cancer expression data, our method was proven to be effective and reliable in identifying disease risk pathways that are regulated by miRNAs. Further analysis showed that the structure of a pathway plays a crucial role in the recognition of the pathway as a factor in disease risk.
Collapse
Affiliation(s)
- Jing Li
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China; Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, PR China
| | - Chunquan Li
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Junwei Han
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Desi Shang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Qianlan Yao
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Wei Liu
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Meng Zhou
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Fei Su
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China
| | - Xia Li
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, PR China.
| |
Collapse
|
39
|
Kim M, Chen X, Chin LJ, Paranjape T, Speed WC, Kidd KK, Zhao H, Weidhaas JB, Slack FJ. Extensive sequence variation in the 3' untranslated region of the KRAS gene in lung and ovarian cancer cases. Cell Cycle 2014; 13:1030-40. [PMID: 24552817 DOI: 10.4161/cc.27941] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While cancer is a serious health issue, there are very few genetic biomarkers that predict predisposition, prognosis, diagnosis, and treatment response. Recently, sequence variations that disrupt microRNA (miRNA)-mediated regulation of genes have been shown to be associated with many human diseases, including cancer. In an early example, a variant at one particular single nucleotide polymorphism (SNP) in a let-7 miRNA complementary site in the 3' untranslated region (3' UTR) of the KRAS gene was associated with risk and outcome of various cancers. The KRAS oncogene is an important regulator of cellular proliferation, and is frequently mutated in cancers. To discover additional sequence variants in the 3' UTR of KRAS with the potential as genetic biomarkers, we resequenced the complete region of the 3' UTR of KRAS in multiple non-small cell lung cancer and epithelial ovarian cancer cases either by Sanger sequencing or capture enrichment followed by high-throughput sequencing. Here we report a comprehensive list of sequence variations identified in cases, with some potentially dysregulating expression of KRAS by altering putative miRNA complementary sites. Notably, rs712, rs9266, and one novel variant may have a functional role in regulation of KRAS by disrupting complementary sites of various miRNAs, including let-7 and miR-181.
Collapse
Affiliation(s)
- Minlee Kim
- Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA
| | - Xiaowei Chen
- Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA; Program in Computational Biology and Bioinformatics; Yale University School of Medicine; New Haven, CT USA
| | - Lena J Chin
- Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA
| | - Trupti Paranjape
- Department of Therapeutic Radiology; Yale University School of Medicine; New Haven, CT USA
| | - William C Speed
- Department of Genetics; Yale University School of Medicine; New Haven, CT USA
| | - Kenneth K Kidd
- Department of Genetics; Yale University School of Medicine; New Haven, CT USA
| | - Hongyu Zhao
- Program in Computational Biology and Bioinformatics; Yale University School of Medicine; New Haven, CT USA; Department of Genetics; Yale University School of Medicine; New Haven, CT USA
| | - Joanne B Weidhaas
- Department of Therapeutic Radiology; Yale University School of Medicine; New Haven, CT USA
| | - Frank J Slack
- Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven, CT USA
| |
Collapse
|
40
|
Radfar H, Wong W, Morris Q. BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles. BMC Genomics 2013; 14:592. [PMID: 24001276 PMCID: PMC3933272 DOI: 10.1186/1471-2164-14-592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background Popular miRNA target prediction techniques use sequence features to determine the functional miRNA target sites. These techniques commonly ignore the cellular conditions in which miRNAs interact with their targets in vivo. Gene expression data are rich resources that can complement sequence features to take into account the context dependency of miRNAs. Results We introduce BayMiR, a new computational method, that predicts the functionality of potential miRNA target sites using the activity level of the miRNAs inferred from genome-wide mRNA expression profiles. We also found that mRNA expression variation can be used as another predictor of functional miRNA targets. We benchmarked BayMiR, the expression variation, Cometa, and the TargetScan “context scores” on two tasks: predicting independently validated miRNA targets and predicting the decrease in mRNA abundance in miRNA overexpression assays. BayMiR performed better than all other methods in both benchmarks and, surprisingly, the variation index performed better than Cometa and some individual determinants of the TargetScan context scores. Furthermore, BayMiR predicted miRNA target sets are more consistently annotated with GO and KEGG terms than similar sized random subsets of genes with conserved miRNA seed regions. BayMiR gives higher scores to target sites residing near the poly(A) tail which strongly favors mRNA degradation using poly(A) shortening. Our work also suggests that modeling multiplicative interactions among miRNAs is important to predict endogenous mRNA targets. Conclusions We develop a new computational method for predicting the target mRNAs of miRNAs. BayMiR applies a large number of mRNA expression profiles and successfully identifies the mRNA targets and miRNA activities without using miRNA expression data. The BayMiR package is publicly available and can be readily applied to any mRNA expression data sets.
Collapse
Affiliation(s)
| | | | - Quaid Morris
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
41
|
Mao Y, Chen H, Lin Y, Xu X, Hu Z, Zhu Y, Wu J, Xu X, Zheng X, Xie L. microRNA-330 inhibits cell motility by downregulating Sp1 in prostate cancer cells. Oncol Rep 2013; 30:327-33. [PMID: 23670210 DOI: 10.3892/or.2013.2452] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/16/2013] [Indexed: 12/26/2022] Open
Abstract
microRNAs (miRNAs), small non-coding RNAs, have emerged as key regulators of a large number of genes. The present study aimed to explore novel biological functions of miR-330 in the human prostate cancer cell lines DU145 and PC3. We confirmed that miR-330 was downregulated and inversely correlated with specificity protein 1 (Sp1) expression. Overexpression of miR-330 by transfection of a chemically synthesized miR-330 mimic induced a reduction in expression levels of the Sp1 protein, accompanied by significant suppression of cellular migration and invasion capability. In addition, the Sp1-knockdown experiments presented similar phenomena. Finally, the luciferase reporter assay validated Sp1 as the direct target of miR-330. These findings indicate that miR-330 acts as an anti-metastatic miRNA in prostate cancer.
Collapse
Affiliation(s)
- Yeqing Mao
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Dmitriev P, Barat A, Polesskaya A, O'Connell MJ, Robert T, Dessen P, Walsh TA, Lazar V, Turki A, Carnac G, Laoudj-Chenivesse D, Lipinski M, Vassetzky YS. Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes. BMC Genomics 2013; 14:265. [PMID: 23597168 PMCID: PMC3639941 DOI: 10.1186/1471-2164-14-265] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/26/2013] [Indexed: 01/10/2023] Open
Abstract
Background miRNA profiling performed in myogenic cells and biopsies from skeletal muscles has previously identified miRNAs involved in myogenesis. Results Here, we have performed miRNA transcriptome profiling in human affinity-purified CD56+ myoblasts induced to differentiate in vitro. In total, we have identified 60 miRNAs differentially expressed during myogenic differentiation. Many were not known for being differentially expressed during myogenic differentiation. Of these, 14 (miR-23b, miR-28, miR-98, miR-103, miR-107, miR-193a, miR-210, miR-324-5p, miR-324-3p, miR-331, miR-374, miR-432, miR-502, and miR-660) were upregulated and 6 (miR-31, miR-451, miR-452, miR-565, miR-594 and miR-659) were downregulated. mRNA transcriptome profiling performed in parallel resulted in identification of 6,616 genes differentially expressed during myogenic differentiation. Conclusions This simultaneous miRNA/mRNA transcriptome profiling allowed us to predict with high accuracy target genes of myogenesis-related microRNAs and to deduce their functions.
Collapse
Affiliation(s)
- Petr Dmitriev
- UMR 8126, Univ. Paris-Sud 11, CNRS, Institut de Cancérologie Gustave-Roussy, 39, rue Camille-Desmoulins, Villejuif 94805, France
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Kitano J, Yoshida K, Suzuki Y. RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks. BMC Genomics 2013; 14:214. [PMID: 23547919 PMCID: PMC3637797 DOI: 10.1186/1471-2164-14-214] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/20/2013] [Indexed: 01/01/2023] Open
Abstract
Background Non-coding small RNAs, ranging from 20 to 30 nucleotides in length, mediate the regulation of gene expression and play important roles in many biological processes. One class of small RNAs, microRNAs (miRNAs), are highly conserved across taxa and mediate the regulation of the chromatin state and the post-transcriptional regulation of messenger RNA (mRNA). Another class of small RNAs is the Piwi-interacting RNAs, which play important roles in the silencing of transposons and other functional genes. Although the biological functions of the different small RNAs have been elucidated in several laboratory animals, little is known regarding naturally occurring variation in small RNA transcriptomes among closely related species. Results We employed next-generation sequencing technology to compare the expression profiles of brain small RNAs between sympatric species of the Japanese threespine stickleback (Gasterosteus aculeatus). We identified several small RNAs that were differentially expressed between sympatric Pacific Ocean and Japan Sea sticklebacks. Potential targets of several small RNAs were identified as repetitive sequences. Female-biased miRNA expression from the old X chromosome was also observed, and it was attributed to the degeneration of the Y chromosome. Conclusions Our results suggest that expression patterns of small RNA can differ between incipient species and may be a potential mechanism underlying differential mRNA expression and transposon activity.
Collapse
Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, Japan.
| | | | | |
Collapse
|
44
|
Szabó PM, Butz H, Igaz P, Rácz K, Hunyady L, Patócs A. Minireview: miRomics in endocrinology: a novel approach for modeling endocrine diseases. Mol Endocrinol 2013; 27:573-85. [PMID: 23349525 PMCID: PMC5416806 DOI: 10.1210/me.2012-1220] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 12/31/2012] [Indexed: 01/26/2023] Open
Abstract
MicroRNAs (miRNAs) are small (16-24 nucleotides) noncoding RNAs that negatively regulate gene expression. Growing evidence demonstrates that miRNAs participate in the regulation of numerous physiological and pathological processes. The clinical utility of the cell-type-specific miRNA expression profile (miRomics) has been directly demonstrated in molecular classification of tumor samples and in prediction of prognosis or therapeutic responsiveness. Identification of the relevant miRNAs and their targets requires both in silico and molecular biological methods. In this review, we summarize the methodological arsenal used in miRNA-related research, and through our own data on adrenal tumors, we present how miRNA could be integrated into omics-based networks. The expanding knowledge obtained from miRNA research may lead to the development of novel diagnostic and treatment modalities in future.
Collapse
Affiliation(s)
- Péter M Szabó
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Second Department of Medicine, Semmelweis University, 46 Szentkirályi Street, Budapest, Hungary H-1088
| | | | | | | | | | | |
Collapse
|
45
|
Weng CW, Lee SC, Lee YL, Ng KL. Analysis of the NCI-60 dataset for cancer-related microRNA and mRNA using expression profiles. Comput Biol Chem 2013; 44:15-21. [PMID: 23499870 DOI: 10.1016/j.compbiolchem.2013.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
BACKGROUND Recent studies have indicated that microRNA (miRNA) may play an oncogenic or tumor suppressor role in human cancer. To study the regulatory role of miRNAs in tumorigenesis, an integrated platform has been set up to provide a user friendly interface for query. The main advantage of the present platform is that all the miRNA target genes' information and disease records are drawn from experimentally verified or high confidence records. RESULTS MiRNA target gene results are annotated with reference to the disease gene as well as the pathway database. The correlation strength between miRNA and target gene expression profile is quantified by computing the correlation coefficient using the NCI-60 expression profiling data. Comprehensive analysis of the NCI-60 data found that the cumulative percentage of negative correlation coefficients for cleavage regulation is slightly higher than its positive counterpart; which indicated that the mRNA degradation mechanism is slightly dominant. In addition, the RNAHybrid and TargetScans scores are computed which potentially served as quantitative estimators for miRNA-mRNA binding events. Three scores are defined for each miRNA-mRNA pair, which are based on the disease gene and pathway information. These three scores allow user to sort out high confidence cancer-related miRNA-mRNA pairs. Statistical tests were applied to investigate the relations of three chromosomal features, i.e., CpG island, fragile site, and miRNA cluster, with cancer-related miRNAs. A web-based interface has been set up for query, which can be accessed at: http://ppi.bioinfo.asia.edu.tw/mirna_target/ CONCLUSIONS The main advantage of the present platform on miRNA-mRNA targeting information is that all the target genes' information and disease records are experimentally verified. Although this may limit the number of miRNA-mRNA relationships, the results provided here are more solid and have fewer false positive events. Certain novel cancer-related miRNA-mRNA pairs are identified and confirmed in the literature. Fisher's exact test suggests that CpG island and fragile site associated miRNAs tend to associate with cancer formation. In summary, the present platform provides an easy means of investigating cancer-related miRNAs.
Collapse
Affiliation(s)
- Chia-Wei Weng
- Department of Biomedical Informatics, Asia University, 500 Lioufeng Road, Wufeng Shiang, Taichung 41354, Taiwan.
| | | | | | | |
Collapse
|
46
|
Li Y, Zhu X, Xu W, Wang D, Yan J. miR-330 regulates the proliferation of colorectal cancer cells by targeting Cdc42. Biochem Biophys Res Commun 2013; 431:560-5. [PMID: 23337504 DOI: 10.1016/j.bbrc.2013.01.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 01/04/2013] [Indexed: 12/25/2022]
Abstract
MicroRNAs are small non-coding RNA molecules that play important roles in the multistep process of colorectal carcinoma (CRC) development. However, the miRNA-mRNA regulatory network is far from being fully understood. The objective of this study was to investigate the expression and the biological roles of miR-330 in colorectal cancer cells. Cdc42, one of the best characterized members of the Rho GTPase family, was found to be up-regulated in several types of human tumors including CRC and has been implicated in cancer initiation and progression. In the present study, we identified miR-330, as a potential regulator of Cdc42, was found to be inversely correlated with Cdc42 expression in colorectal cancer cell lines. Ectopic expression of miR-330 down-regulated Cdc42 expression at both protein and mRNA level, mimicked the effect of Cdc42 knockdown in inhibiting proliferation, inducing G1 cell cycle arrest and apoptosis of the colorectal cancer cells, whereas restoration of Cdc42 could partially attenuate the effects of miR-330. In addition, elevated expression of miR-330 could suppress the immediate downstream effectors of Cdc42 and inhibit the growth of colorectal cancer cells in vivo. To sum up, our results establish a role of miR-330 in negatively regulating Cdc42 expression and colorectal cancer cell proliferation. They suggest that manipulating the expression level of Cdc42 by miR-330 has the potential to influence colorectal cancer progression.
Collapse
Affiliation(s)
- Yuefeng Li
- The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | | | | | | | | |
Collapse
|
47
|
Wu W, Hu Z, Qin Y, Dong J, Dai J, Lu C, Zhang W, Shen H, Xia Y, Wang X. Seminal plasma microRNAs: potential biomarkers for spermatogenesis status. Mol Hum Reprod 2012; 18:489-497. [PMID: 22675043 DOI: 10.1093/molehr/gas022] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (18-25 nt), playing important regulatory roles via interaction with cellular messenger RNAs. The altered expression of miRNAs in specific tissues has been associated with diseases such as cancer and diabetes. We examined the presence of two selected miRNAs (miR-19b and let-7a) in human seminal plasma from fertile men and idiopathic infertile patients with oligozoospermia and non-obstructive azoospermia (NOA) using quantitative real-time PCR. We detected miRNAs in the seminal plasma of humans. The levels of miRNAs in the seminal plasma were reproducible in repeat samples from the same individuals. In addition, we examined the expression patterns of two selected miRNAs in 96 idiopathic infertile males (48 oligozoospermia and 48 NOA) and 48 fertile controls. Another 48 individuals of each group were used for verification. Our data showed that the expression levels of these two miRNAs in the seminal plasma significantly increased in idiopathic infertile males with NOA compared with fertile controls, whereas the expression levels were similar between idiopathic infertile males with oligozoospermia and fertile controls. In conclusion our results indicate that the expression of miR-19b and let-7a in the seminal plasma are reproducible and stable. Aberrant over-expression levels of miR-19b and let-7a may be an indicator of spermatogenic failure.
Collapse
Affiliation(s)
- Wei Wu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, 140 Hanzhong Road, Nanjing 210029, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Belleannée C, Calvo E, Thimon V, Cyr DG, Légaré C, Garneau L, Sullivan R. Role of microRNAs in controlling gene expression in different segments of the human epididymis. PLoS One 2012; 7:e34996. [PMID: 22511979 PMCID: PMC3325285 DOI: 10.1371/journal.pone.0034996] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 03/08/2012] [Indexed: 12/01/2022] Open
Abstract
Background The molecular mechanisms implicated in regionalized gene expression in the human epididymis have not yet been fully elucidated. Interestingly, more than 200 microRNAs (miRNAs) have been identified in the human epididymis and could be involved in the regulation of mRNA stability and post-transcriptional expression in this organ. Methods Using a miRNA microarray approach, we investigated the correlation between miRNA signatures and gene expression profiles found in three distinct regions (caput, corpus and cauda) of human epididymides from 3 donors. In silico prediction of transcript miRNA targets was performed using TargetScan and Miranda software's. FHCE1 immortalized epididymal cell lines were cotransfected with mimic microRNAs and plasmid constructs containing the 3′UTR of predicted target genes downstream of the luciferase gene. Results We identified 35 miRNAs differentially expressed in the distinct segments of the epididymis (fold change ≥2, P-value≤0.01). Among these miRNAs, miR-890, miR-892a, miR-892b, miR-891a, miR-891b belonging to the same epididymis-enriched cluster located on the X chromosome, are significantly more expressed in the corpus and cauda regions than in the caput. Interestingly, a strong negative correlation (r = −0,89, P-value≤0.001) was found between the pattern of expression of miR-892b and its potential mRNA target Esrrg (Estrogen Related Receptor Gamma) and with miR-145 and Cldn10 mRNA (r = −0,92, P-value≤0.001). We confirmed that miR-145 and miR-892b inhibit the expression of the luciferase reporter via Cldn10 and Esrrg 3′ UTRs, respectively. Conclusion Our study shows that the expression of miRNAs is segmented along the human epididymis and correlates with the pattern of target gene expression in different regions. Therefore, epididymal miRNAs may be in control of the maintenance of gene expression profile in the epididymis, which dictates segment-specific secretion of proteins and establishes physiological compartments that directly or indirectly affect sperm maturation and fertility.
Collapse
Affiliation(s)
- Clémence Belleannée
- Centre de Recherche du CHUQ and Département d'Obstétrique-Gynécologie, Faculté de Médecine, Université Laval, Québec, Canada
- * E-mail: (RS); (CB)
| | - Ezéquiel Calvo
- Laboratory of Endocrinology and Genomics, CHUL Research Center and Department of Molecular Medicine, Université Laval, Québec, Canada
| | - Véronique Thimon
- Département de Biologie, Université de la Martinique, Martinique, France
| | - Daniel G. Cyr
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - Christine Légaré
- Centre de Recherche du CHUQ and Département d'Obstétrique-Gynécologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Louis Garneau
- Centre de Recherche du CHUQ and Département d'Obstétrique-Gynécologie, Faculté de Médecine, Université Laval, Québec, Canada
| | - Robert Sullivan
- Centre de Recherche du CHUQ and Département d'Obstétrique-Gynécologie, Faculté de Médecine, Université Laval, Québec, Canada
- Laboratory of Endocrinology and Genomics, CHUL Research Center and Department of Molecular Medicine, Université Laval, Québec, Canada
- * E-mail: (RS); (CB)
| |
Collapse
|
49
|
Muniategui A, Nogales-Cadenas R, Vázquez M, L. Aranguren X, Agirre X, Luttun A, Prosper F, Pascual-Montano A, Rubio A. Quantification of miRNA-mRNA interactions. PLoS One 2012; 7:e30766. [PMID: 22348024 PMCID: PMC3279346 DOI: 10.1371/journal.pone.0030766] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/21/2011] [Indexed: 02/07/2023] Open
Abstract
miRNAs are small RNA molecules (′ 22nt) that interact with their corresponding target mRNAs inhibiting the translation of the mRNA into proteins and cleaving the target mRNA. This second effect diminishes the overall expression of the target mRNA. Several miRNA-mRNA relationship databases have been deployed, most of them based on sequence complementarities. However, the number of false positives in these databases is large and they do not overlap completely. Recently, it has been proposed to combine expression measurement from both miRNA and mRNA and sequence based predictions to achieve more accurate relationships. In our work, we use LASSO regression with non-positive constraints to integrate both sources of information. LASSO enforces the sparseness of the solution and the non-positive constraints restrict the search of miRNA targets to those with down-regulation effects on the mRNA expression. We named this method TaLasso (miRNA-Target LASSO). We used TaLasso on two public datasets that have paired expression levels of human miRNAs and mRNAs. The top ranked interactions recovered by TaLasso are especially enriched (more than using any other algorithm) in experimentally validated targets. The functions of the genes with mRNA transcripts in the top-ranked interactions are meaningful. This is not the case using other algorithms. TaLasso is available as Matlab or R code. There is also a web-based tool for human miRNAs at http://talasso.cnb.csic.es/.
Collapse
Affiliation(s)
- Ander Muniategui
- Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebastian, Spain
| | | | - Miguél Vázquez
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Xabier L. Aranguren
- Center for Molecular and Vascular Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Xabier Agirre
- Hematology Department and Area of Cell Therapy, Clínica Universidad de Navarra, Foundation for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Aernout Luttun
- Center for Molecular and Vascular Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Felipe Prosper
- Hematology Department and Area of Cell Therapy, Clínica Universidad de Navarra, Foundation for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Angel Rubio
- Group of Bioinformatics, CEIT and TECNUN, University of Navarra, San Sebastian, Spain
- * E-mail:
| |
Collapse
|
50
|
Kuo TY, Hsi E, Yang IP, Tsai PC, Wang JY, Juo SHH. Computational analysis of mRNA expression profiles identifies microRNA-29a/c as predictor of colorectal cancer early recurrence. PLoS One 2012; 7:e31587. [PMID: 22348113 PMCID: PMC3278467 DOI: 10.1371/journal.pone.0031587] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 01/09/2012] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is one of the leading malignant cancers with a rapid increase in incidence and mortality. The recurrences of CRC after curative resection are sometimes unavoidable and often take place within the first year after surgery. MicroRNAs may serve as biomarkers to predict early recurrence of CRC, but identifying them from over 1,400 known human microRNAs is challenging and costly. An alternative approach is to analyze existing expression data of messenger RNAs (mRNAs) because generally speaking the expression levels of microRNAs and their target mRNAs are inversely correlated. In this study, we extracted six mRNA expression data of CRC in four studies (GSE12032, GSE17538, GSE4526 and GSE17181) from the gene expression omnibus (GEO). We inferred microRNA expression profiles and performed computational analysis to identify microRNAs associated with CRC recurrence using the IMRE method based on the MicroCosm database that includes 568,071 microRNA-target connections between 711 microRNAs and 20,884 gene targets. Two microRNAs, miR-29a and miR-29c, were disclosed and further meta-analysis of the six mRNA expression datasets showed that these two microRNAs were highly significant based on the Fisher p-value combination (p = 9.14 × 10(-9) for miR-29a and p = 1.14 × 10(-6) for miR-29c). Furthermore, these two microRNAs were experimentally tested in 78 human CRC samples to validate their effect on early recurrence. Our empirical results showed that the two microRNAs were significantly down-regulated (p = 0.007 for miR-29a and p = 0.007 for miR-29c) in the early-recurrence patients. This study shows the feasibility of using mRNA profiles to indicate microRNAs. We also shows miR-29a/c could be potential biomarkers for CRC early recurrence.
Collapse
Affiliation(s)
- Tai-Yue Kuo
- Department of Medical Genetics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Edward Hsi
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - I-Ping Yang
- Department of Medical Genetics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Nursing, Shu Zen College of Medicine and Management, Kaohsiung, Taiwan
| | - Pei-Chien Tsai
- Department of Medical Genetics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jaw-Yuan Wang
- Department of Medical Genetics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Suh-Hang Hank Juo
- Department of Medical Genetics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| |
Collapse
|