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Lim YJ, Park SA, Wang D, Jin W, Ku WL, Zhang D, Xu J, Patiño LC, Liu N, Chen W, Kazmi R, Zhao K, Zhang YE, Sun L, Chen W. MicroRNA-19b exacerbates systemic sclerosis through promoting Th9 cells. Cell Rep 2024; 43:114565. [PMID: 39083380 DOI: 10.1016/j.celrep.2024.114565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Systemic sclerosis (SSc) is a chronic autoimmune disease characterized by fibrosis of the skin and multiple vital organs, but the immunological pathogenesis of SSc remains unclear. We show here that miR-19b promotes Th9 cells that exacerbate SSc. Specifically, miR-19b and interleukin (IL)-9 increase in CD4+ T cells in experimental SSc in mice induced with bleomycin. Inhibiting miR-19b reduces Th9 cells and ameliorates the disease. Mechanistically, transforming growth factor beta (TGF-β) plus IL-4 activates pSmad3-Ser213 and TRAF6-K63 ubiquitination by suppressing NLRC3. Activated TRAF6 sequentially promotes TGF-β-activated kinase 1 (TAK1) and nuclear factor κB (NF-κB) p65 phosphorylation, leading to the upregulation of miR-19b. Notably, miR-19b activated Il9 gene expression by directly suppressing atypical E2F family member E2f8. In patients with SSc, higher levels of IL9 and MIR-19B correlate with worse disease progression. Our findings reveal miR-19b as a key factor in Th9 cell-mediated SSc pathogenesis and should have clinical implications for patients with SSc.
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Affiliation(s)
- Yun-Ji Lim
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Sang-A Park
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Dandan Wang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Wenwen Jin
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Wai Lim Ku
- Systemic Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Dunfang Zhang
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Junji Xu
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Liliana C Patiño
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Na Liu
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Weiwei Chen
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Rida Kazmi
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA
| | - Keji Zhao
- Systemic Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, 31 Center Drive, Bethesda, MD 20892, USA
| | - Ying E Zhang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Lingyun Sun
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
| | - WanJun Chen
- Mucosal Immunology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, MD 20892, USA.
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Merz MP, Seal SV, Grova N, Mériaux S, Guebels P, Kanli G, Mommaerts E, Nicot N, Kaoma T, Keunen O, Nazarov PV, Turner JD. Early-life influenza A (H1N1) infection independently programs brain connectivity, HPA AXIS and tissue-specific gene expression profiles. Sci Rep 2024; 14:5898. [PMID: 38467724 PMCID: PMC10928197 DOI: 10.1038/s41598-024-56601-5] [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: 09/22/2023] [Accepted: 03/08/2024] [Indexed: 03/13/2024] Open
Abstract
Early-life adversity covers a range of physical, social and environmental stressors. Acute viral infections in early life are a major source of such adversity and have been associated with a broad spectrum of later-life effects outside the immune system or "off-target". These include an altered hypothalamus-pituitary-adrenal (HPA) axis and metabolic reactions. Here, we used a murine post-natal day 14 (PND 14) Influenza A (H1N1) infection model and applied a semi-holistic approach including phenotypic measurements, gene expression arrays and diffusion neuroimaging techniques to investigate HPA axis dysregulation, energy metabolism and brain connectivity. By PND 56 the H1N1 infection had been resolved, and there was no residual gene expression signature of immune cell infiltration into the liver, adrenal gland or brain tissues examined nor of immune-related signalling. A resolved early-life H1N1 infection had sex-specific effects. We observed retarded growth of males and altered pre-stress (baseline) blood glucose and corticosterone levels at PND42 after the infection was resolved. Cerebral MRI scans identified reduced connectivity in the cortex, midbrain and cerebellum that were accompanied by tissue-specific gene expression signatures. Gene set enrichment analysis confirmed that these were tissue-specific changes with few common pathways. Early-life infection independently affected each of the systems and this was independent of HPA axis or immune perturbations.
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Affiliation(s)
- Myriam P Merz
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
- Central Biobank Charité, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Snehaa V Seal
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
| | - Nathalie Grova
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Inserm U1256, NGERE, Nutrition-Génétique Et Exposition Aux Risques Environnementaux, Université de Lorraine, 54000, Nancy, France
| | - Sophie Mériaux
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Pauline Guebels
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Georgia Kanli
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Elise Mommaerts
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Nathalie Nicot
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Olivier Keunen
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Petr V Nazarov
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Jonathan D Turner
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg.
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Talukdar A, Kundu P, Bhattacharjee S, Dey S, Dey A, Biswas JK, Chaudhuri P, Bhattacharya S. Microplastics in mangroves with special reference to Asia: Occurrence, distribution, bioaccumulation and remediation options. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166165. [PMID: 37574065 DOI: 10.1016/j.scitotenv.2023.166165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/15/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
Microplastics (MPs) are a new and lesser-known pollutant that has intrigued the interest of scientists all over the world in recent decades. MP (<5mm in size) can enter marine environments such as mangrove forests in a variety of ways, interfering with the health of the environment and organisms. Mangroves are now getting increasingly exposed to microplastic contamination due to their proximity to human activities and their position as critical transitional zones between land and sea. The present study reviews the status of MPs contamination specifically in mangrove ecosystems situated in Asia. Different sources and characteristics of MPs, subsequent deposition of MPs in mangrove water and sediments, bioaccumulation in different organisms are discussed in this context. MP concentrations in sediments and organisms were higher in mangrove forests exposed to fishing, coastal tourism, urban, and industrial wastewater than in pristine areas. The distribution of MPs varies from organism to organism in mangrove ecosystems, and is significantly influenced by their morphometric characteristics, feeding habits, dwelling environment etc. Mangrove plants can accumulate microplastics in their roots, stem and leaves through absorption, adsorption and entrapment helping in reducing abundance of microplastic in the surrounding environment. Several bacterial and fungal species are reported from these mangrove ecosystems, which are capable of degrading MPs. The bioremediation potential of mangrove plants offers an innovative and sustainable approach to mitigate microplastic pollution. Diverse mechanisms of MP biodegradation by mangrove dwelling organisms are discussed in this context. Biotechnological applications can be utilized to explore the genetic potential of the floral and faunal species found in the Asian mangroves. Detailed studies are required to monitor, control, and evaluate MP pollution in sediments and various organisms in mangrove ecosystems in Asia as well as in other parts of the world.
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Affiliation(s)
| | - Pritha Kundu
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar 803116, India
| | - Shrayan Bhattacharjee
- Ecosystem and Ecology Laboratory, Post-graduate Department of Zoology, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, India
| | - Satarupa Dey
- Department of Botany, Shyampur Siddheswari Mahavidyalaya, Howrah 711301, West Bengal, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Jayanta Kumar Biswas
- Enviromicrobiology, Ecotoxicology & Ecotechnology Research Laboratory (3E-MicroToxTech Lab), Department of Ecological Studies, and International Centre for Ecological Engineering, University of Kalyani, Nadia, West Bengal 741235, India
| | - Punarbasu Chaudhuri
- Department of Environmental Science, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Sayan Bhattacharya
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar 803116, India.
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Willekens J, Mosca P, Burt-Oberecken N, Laugeais E, Kaoma T, Bernardin F, Vallar L, Dimofski P, Renaud M, Lambert L, Leheup B, Guéant JL, Leininger-Muller B, Dreumont N. Cross-Talk between miRNAs from the Dlk1-Dio3 Locus and Histone Methylation to Protect Male Cerebellum from Methyl Donor Deficiency. Mol Nutr Food Res 2023; 67:e2300040. [PMID: 37672803 DOI: 10.1002/mnfr.202300040] [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: 01/24/2023] [Revised: 05/12/2023] [Indexed: 09/08/2023]
Abstract
SCOPE Disruption of the one carbon metabolism during development, i.e., following a gestational vitamin B9 and B12 deficiencies, is involved in birth defects and brain development delay. Using a rat nutritional model, consisting of pups born to dams fed a vitamin B9 and B12 deficient diet (MDD), the study previously reports molecular and cellular alterations in the brain, in a sex dependent manner, with females being more affected than males. The study hypothesizes that epigenetic modifications could participate in the sex differences is observed. METHODS AND RESULTS The study investigates lysine methylation of histones and expression of microRNAs in the cerebellum of MDD male and female pups. The study reports a differential regulation of H3K36Me2 and H4K20Me3 between males and females, in response to MDD. Moreover, distinct regulation of Kmt5b and Kdm2a expression by miR-134-5p and miR-369-5p from the Dlk1-Dio3 locus, contributes to the maintenance of expression of genes involved in synaptic plasticity. CONCLUSION These results could explain the neuroprotection to MDD that male pups display. The work will contribute to the understanding of the consequences of vitamin starvation on brain development, as well as how the epigenome is affected by one carbon metabolism disruption.
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Affiliation(s)
- Jeremy Willekens
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CINJ, Rutgers Cancer Institute of New Jersey, 195 Little Albany St, New Brunswick, NJ 08901, USA
| | - Pauline Mosca
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
| | | | - Edgar Laugeais
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
| | - Tony Kaoma
- Luxembourg Institute of Health, Bioinformatics Platform, 1 A-B, Luxembourg, L-1445, Luxembourg
| | - François Bernardin
- Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, L-1210, Luxembourg
| | - Laurent Vallar
- Luxembourg Institute of Health, Bioinformatics Platform, 1 A-B, Luxembourg, L-1445, Luxembourg
| | | | - Mathilde Renaud
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CHRU Nancy, Hôpital d'enfants, Service de Génétique Clinique, Nancy, F-54000, France
| | - Laetitia Lambert
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CHRU Nancy, Hôpital d'enfants, Service de Génétique Clinique, Nancy, F-54000, France
| | - Bruno Leheup
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CHRU Nancy, Hôpital d'enfants, Service de Génétique Clinique, Nancy, F-54000, France
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Li X, Xu Y, Liao P. Diagnostic performance of microRNA-29a in active pulmonary tuberculosis: a systematic review and meta-analysis. Clinics (Sao Paulo) 2023; 78:100290. [PMID: 37837919 PMCID: PMC10589768 DOI: 10.1016/j.clinsp.2023.100290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/30/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND In recent years, more and more studies have shown that microRNA-29a (miRNA-29a) can be used as a potential biomarker for active tuberculosis, but the results of these studies are not consistent. OBJECTIVE To comprehensively evaluate the value of miRNA-29a in the diagnosis of active tuberculosis by meta-analysis. METHODS The databases of CNKI, WanFang, PubMed, The Cochrane Library, Web of Science and EMBASE were searched for relevant studies. Studies were screened strictly according to inclusion and exclusion criteria. QUADAS-2 scale was used to evaluate the quality of the included studies. Data were extracted and analyzed by Meta-DiSc 1.4 and Stata 16.0 software. RESULTS 13 articles were included, including a total of 1598 subjects, including 872 active tuberculosis patients and 726 controls. The combined sensitivity and specificity of miRNA-29a in the diagnosis of active tuberculosis were 78 % and 76 %, respectively, and the area under the overall summary receiver operating characteristic curve was 0.8564. CONCLUSION miRNA-29a can be used as a biomarker for the diagnosis of active tuberculosis.
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Affiliation(s)
- Xiaoying Li
- Department of Clinical Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, China.
| | - Yuehong Xu
- Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, China
| | - Pu Liao
- Department of Clinical Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou, China; Department of Clinical Laboratory, Chongqing General Hospital, Chongqing, China
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Vázquez-Blomquist D, Hardy-Sosa A, Baez SC, Besada V, Palomares S, Guirola O, Ramos Y, Wiśniewski JR, González LJ, Bello-Rivero I. Proteomics and Phospho-Proteomics Profiling of the Co-Formulation of Type I and II Interferons, HeberFERON, in the Glioblastoma-Derived Cell Line U-87 MG. Cells 2022; 11:4068. [PMID: 36552831 PMCID: PMC9776974 DOI: 10.3390/cells11244068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
HeberFERON, a co-formulation of Interferon (IFN)-α2b and IFN-γ, has effects on skin cancer and other solid tumors. It has antiproliferative effects over glioblastoma multiform (GBM) clones and cultured cell lines, including U-87 MG. Here, we report the first label-free quantitative proteomic and phospho-proteomic analyses to evaluate changes induced by HeberFERON after 72 h incubation of U-87 MG that can explain the effect on cellular proliferation. LC-MS/MS, functional enrichment and networking analysis were performed. We identified 7627 proteins; 122 and 211 were down- and up-regulated by HeberFERON (fold change > 2; p < 0.05), respectively. We identified 23,549 peptides (5692 proteins) and 8900 phospho-peptides; 523 of these phospho-peptides (359 proteins) were differentially modified. Proteomic enrichment showed IFN signaling and its control, direct and indirect antiviral mechanisms were the main modulated processes. Phospho-proteome enrichment displayed the cell cycle as one of the most commonly targeted events together with cytoskeleton organization; translation/RNA splicing, autophagy and DNA repair, as represented biological processes. There is a high interconnection of phosphoproteins in a molecular network; mTOR occupies a centric hub with interactions with translation machinery, cytoskeleton and autophagy components. Novel phosphosites and others with unknown biological functionality in key players in the aforementioned processes were regulated by HeberFERON and involved CDK and ERK kinases. These findings open new experimental hypotheses regarding HeberFERON action. The results obtained contribute to a better understanding of HeberFERON effector mechanisms in the context of GBM treatment.
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Affiliation(s)
- Dania Vázquez-Blomquist
- Pharmacogenomic Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | | | - Saiyet C. Baez
- Département de Neurosciences, Université de Montréal, Montréal, QC H2L0A9, Canada
| | - Vladimir Besada
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Sucel Palomares
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Osmany Guirola
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Yassel Ramos
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Munich, Germany
| | - Luis Javier González
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Iraldo Bello-Rivero
- Clinical Assays Direction, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
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Bilal M, Javaid A, Amjad F, Youssif TA, Afzal S. An overview of prostate cancer (PCa) diagnosis: Potential role of miRNAs. Transl Oncol 2022; 26:101542. [PMID: 36148731 PMCID: PMC9493385 DOI: 10.1016/j.tranon.2022.101542] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/18/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer is the second most frequently diagnosed cancer among men worldwide, with the estimated sixth leading cause of cancer death. Despite major advancements in clinical biology and imaging, digital rectal examination (DRE), prostate-specific antigen (PSA), and biopsies indication remain the keystone for screening. Several kits are used to detect genomic changes and non-coding RNAs in the sample. However, its indication remains controversial for screening purposes. There is an urged need for non-invasive biomarkers to implement precision medicine. Recent research shows that miRNAs have an important role in the diagnostic, prognostic, and therapeutic agents as non-invasive biomarkers. Though prostate cancer data remains controversial in other cancer types, such as breast cancer, miR-21 expression is upregulated. Here, we reported a prolonged revision of miRNAs as prostate cancer prognostic, diagnostic, and predictive tools, including data on androgen receptor (AR) signaling, epithelial-mesenchymal transition (EMT) process, and cancer stem cells (CSCs) regulation. The combined utilization of miRNAs with other tests will help patients and clinicians to select the most appropriate personalized treatment and to avoid overdiagnosis and unnecessary biopsies. Future clinical applications of our reported novel miRNAs have a substantial role in the primary diagnosis of prostate cancer to help treatment decisions.
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Affiliation(s)
- Muhammad Bilal
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan; SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Japan
| | - Aqsa Javaid
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Farhat Amjad
- Quaid-e-Azam Medical College, Bahawalpur, Pakistan
| | | | - Samia Afzal
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
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8
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Tian X, Lu J, Nanding K, Zhang L, Liu Y, Mailisu M, Morigen M, Fan L. The antihyperlipidemic drug potassium piperonate impairs the migration and tumorigenesis of breast cancer cells via the upregulation of miR-31. Front Oncol 2022; 12:828160. [PMID: 36313626 PMCID: PMC9606244 DOI: 10.3389/fonc.2022.828160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 08/26/2022] [Indexed: 09/07/2024] Open
Abstract
Background Breast cancer is the second cause of cancer death in women, and tumor metastasis is the primary cause of mortality. Due to the involvement of many regulatory molecules and signaling pathways, the occurrence and development of metastases needs to be further studied. MicroRNAs (miRNAs) are ubiquitously expressed small non-coding RNAs that have been shown to play an important role in the diagnosis and treatment of many diseases, as well as representing an attractive candidate for metastasis control. In this study, we investigated the mechanism of potassium piperonate (GBK) in impairing breast cancer cell invasion and metastasis by targeting miR-31. Methods Breast cancer cells, either treated with GBK or left untreated, were assessed for migration and invasion capacities using wound healing and transwell assays. GBK-targeted miRNAs were identified and verified using RT-qPCR. Western blotting was used to validate the changes in expression levels of miR-31-targeted genes. Methylation specific PCR was performed to detect the effect of GBK on the methylation levels of the lncRNA LOC554202 host gene. The synergistic effect of GBK and the chemotherapy drug cisplatin (DDP) on breast cancer cells was verified using cell proliferation, colony formation, and RT-qPCR assays in vitro, and the tumor xenograft model in vivo. Results We found that miR-31 was the main target of GBK. GBK treatment affected the epigenetic modification at CpG sites by downregulating DNA methyltransferases. Thus, the CpG-associated methylation levels of lncRNA LOC554202 decreased significantly, and in turn upregulated both miR-31 and its host gene LOC554202 in breast cancer cells. We also observed the significant inhibition of miR-31-targeted genes following GBK treatment, including RHOA, WAVE3, and SATB2, with functions closely related to cancer cell invasion, migration, and proliferation. Furthermore, we revealed that the combination of GBK and DDP had a synergistic effect on inhibiting the proliferation of breast cancer cells in vitro and in vivo, especially in triple negative breast cancer (TNBC). Conclusions This study investigated the target of GBK in the inhibition of breast cancer migration and invasion, and the underlying mechanisms involved, providing theoretical support for the development of GBK as an auxiliary drug for clinical treatment.
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Affiliation(s)
| | | | | | | | | | | | | | - Lifei Fan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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Rabuma T, Gupta OP, Chhokar V. Recent advances and potential applications of cross-kingdom movement of miRNAs in modulating plant's disease response. RNA Biol 2022; 19:519-532. [PMID: 35442163 PMCID: PMC9037536 DOI: 10.1080/15476286.2022.2062172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In the recent past, cross-kingdom movement of miRNAs, small (20–25 bases), and endogenous regulatory RNA molecules has emerged as one of the major research areas to understand the potential implications in modulating the plant’s biotic stress response. The current review discussed the recent developments in the mechanism of cross-kingdom movement (long and short distance) and critical cross-talk between host’s miRNAs in regulating gene function in bacteria, fungi, viruses, insects, and nematodes, and vice-versa during host-pathogen interaction and their potential implications in crop protection. Moreover, cross-kingdom movement during symbiotic interaction, the emerging role of plant’s miRNAs in modulating animal’s gene function, and feasibility of spray-induced gene silencing (SIGS) in combating biotic stresses in plants are also critically evaluated. The current review article analysed the horizontal transfer of miRNAs among plants, animals, and microbes that regulates gene expression in the host or pathogenic organisms, contributing to crop protection. Further, it highlighted the challenges and opportunities to harness the full potential of this emerging approach to mitigate biotic stress efficiently.
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Affiliation(s)
- Tilahun Rabuma
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, INDIA.,Department of Biotechnology, College of Natural and Computational Science, Wolkite University, Wolkite, Ethiopia
| | - Om Prakash Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, INDIA
| | - Vinod Chhokar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, INDIA
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10
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Madhumita M, Paul S. A review on methods for predicting miRNA–mRNA regulatory modules. J Integr Bioinform 2022; 19:jib-2020-0048. [PMID: 35357793 PMCID: PMC9521823 DOI: 10.1515/jib-2020-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/01/2022] [Indexed: 11/15/2022] Open
Abstract
Identification of complex interactions between miRNAs and mRNAs in a regulatory network helps better understand the underlying biological processes. Previously, identification of these interactions was based on sequence-based predicted target binding information. With the advancement in high-throughput omics technologies, miRNA and mRNA expression for the same set of samples are available. This helps develop more efficient and flexible approaches that work by integrating miRNA and mRNA expression profiles with target binding information. Since these integrative approaches of miRNA–mRNA regulatory modules (MRMs) detection is sufficiently able to capture the minute biological details, 26 such algorithms/methods/tools for MRMs identification are comprehensively reviewed in this article. The study covers the significant features underlying every method. Therefore, the methods are classified into eight groups based on mathematical approaches to understand their working and suitability for one’s study. An algorithm could be selected based on the available information with the users and the biological question under investigation.
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Affiliation(s)
- Madhumita Madhumita
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur342037, Rajasthan, India
| | - Sushmita Paul
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur342037, Rajasthan, India
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11
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Meera SP, Bhattacharyya M, Nizam A, Kumar A. A review on microplastic pollution in the mangrove wetlands and microbial strategies for its remediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:4865-4879. [PMID: 34791631 DOI: 10.1007/s11356-021-17451-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Mangroves are one of the most productive ecosystems in the world harboring huge biological diversity. The prime ecological roles of mangroves are prevention of coastal erosion and shoreline protection. Mangroves face varying degrees of threats due to overexploitation, conversion of mangrove habitats for agriculture, settlement and industrial purposes, illegal encroachment, global warming, sea-level rise, El Nino, and pollution. Among them, microplastic (MP) pollution is a major concern threatening not only the mangroves per se but also the rich biodiversity that it shelters. In general, the microbial communities which are paramount to nutrient recycling and ecological dynamics undergo substantial changes upon MP exposure. If the MP pollution in the mangrove habitats continues unabated in the coming decades, there may be serious consequences on the already threatened mangrove ecosystems and the coastal communities. This review article attempts to consolidate MP pollution of mangrove wetlands, its impact on mangroves and associated microbiota, and the microbial solution for its remediation as a sustainable strategy.
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Affiliation(s)
- Suraj Prasannakumari Meera
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Palayad, 670661, Kerala, India
| | - Malini Bhattacharyya
- Department of Plant Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Ashifa Nizam
- Department of Plant Science, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Ajay Kumar
- Department of Plant Science, Central University of Kerala, Kasaragod, 671316, Kerala, India.
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12
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Abstract
Since their first discovery more than 20 years ago, miRNAs have been subject to deliberate research and analysis for revealing their physiological or pathological involvement. Regulatory roles of miRNAs in signal transduction, gene expression, and cellular processes in development, differentiation, proliferation, apoptosis, and homeostasis also imply their critical role in disease pathogenesis. Their roles in cancer, neurodegenerative diseases, and other systemic diseases have been studied broadly. In these regulatory pathways, their mutations and target sequence variations play critical roles to determine their functional repertoire. In this chapter, we summarize studies that investigated the role of mutations, polymorphisms, and other variations of miRNAs in respect to pathological processes.
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13
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Sun Y, Li J, Zheng S. MiR-769-5p, Which Targets HDGF, Inhibits Cell Proliferation and Invasion in Nonsmall Cell Lung Cancer. Cancer Biother Radiopharm 2021. [PMID: 34978893 DOI: 10.1089/cbr.2021.0363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MiR-769-5p regulates tumor correlative genes, which plays a critical role in the progression of various types of tumor. However, the precise regulatory mechanism of miR-769-5p on nonsmall cell lung cancer (NSCLC) is unknown. This study was to discover the role and underlying mechanisms of miR-769-5p in NSCLC. MiR-769-5p expression was shown to be reduced, according to our findings. MiR-769-5p overexpression inhibited NSCLC cell proliferation while promoting NSCLC cell apoptosis. Furthermore, NSCLC cell migration and invasion were reduced when miR-769-5p was overexpressed. Furthermore, HDGF was confirmed as a miR-769-5p target gene that was negatively regulated by miR-769-5p. Furthermore, more research revealed that HDGF overexpression reduced the inhibitory effect of miR-769-5p on NSCLC cell biofunction. Finally, miR-769-5p inhibited NSCLC cell proliferation and invasion by targeting HDGF, indicating that NSCLC could benefit from miR-769-5p as a diagnostic and prognostic biomarker.
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Affiliation(s)
- Yuejun Sun
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Cardiothoracic Surgery, Jiangsu Jiangyin People's Hospital, Jiangyin, China
| | - Jie Li
- Department of Respiratory Medicine, Affiliated Jiangyin Hospital of Southeast University Medical College, Jiangyin, China
| | - Shiying Zheng
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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14
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Taheri-Dehkordi A, Naderi R, Martinelli F, Salami SA. Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining. PLANTA 2021; 254:117. [PMID: 34751821 DOI: 10.1007/s00425-021-03761-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
A robust workflow for the identification of miRNAs and their targets in saffron was developed. MicroRNA-mediated gene regulation in saffron is potentially involved in several biological processes, including the biosynthesis of highly valuable apocarotenoids. Saffron (Crocus sativus L.) is the most expensive spice in the world and a major source of apocarotenoids. Even though miRNAs (20-24 nt non-coding small RNAs) are important regulators of gene expression at transcriptional and post-transcriptional levels, their role in saffron has not been thoroughly investigated. As a result, a workflow for computational identification of miRNAs and their targets can be useful to uncover the regulatory networks underlying biological processes in this valuable plant. The efficiency of several assembly tools such as Trans-ABySS, Trinity, Bridger, rnaSPAdes, and EvidentialGene was evaluated based on both reference-based and reference-free metrics using transcriptome data. A reliable workflow for computational identification of miRNAs and their targets in saffron was described. The EvidentialGene was found to be the most efficient de novo transcriptome assembler for saffron as a complex triploid model, followed by the Trinity. In total, 66 miRNAs from 19 different families that target 2880 genes, including several transcription factors involved in the flowering transition, were identified. Three of the identified targets were involved in the terpenoids backbone biosynthesis. CsCCD and CsUGT genes involved in the apocarotenoids biosynthetic pathway were targeted by csa-miR156g and csa-miR156b-3p, revealing a unique post-transcriptional regulation dynamic in saffron. The identified miRNAs and their targets add to our understanding of the many biological roles of miRNAs in saffron and shed new light on the control of the apocarotenoid biosynthetic pathway in this valuable plant.
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Affiliation(s)
- Ayat Taheri-Dehkordi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | | | - Seyed Alireza Salami
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
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15
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Sun J, Mao S, Ji W. LncRNA H19 activates cell pyroptosis via the miR-22-3p/NLRP3 axis in pneumonia. Am J Transl Res 2021; 13:11384-11398. [PMID: 34786066 PMCID: PMC8581885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Pneumonia is an infectious pulmonary disease with a high morbidity and mortality. It has been reported that multiple long noncoding RNAs (LncRNAs) are involved in the progression of pneumonia, such as LncRNA SNHG16. However, the role and underlying mechanism of LncRNA H19 in the pyroptosis of pneumonia has not been elucidated. The purpose of this research was to explore the mechanism by which LncRNA H19 regulates LPS-induced pneumonia in WI-38 cells. METHODS An LPS induced pneumonia model in WI-38 cells was established. Total RNA extracted from WI-38 cells was analyzed using RT-qPCR, and the total proteins isolated from the WI-38 cells were analyzed using Western blotting. MTT assays, TUNEL staining, bioinformatics, and luciferase reporter assays were subsequently conducted. RESULTS In the LPS induced pneumonia model, LncRNA H19 silences inhibited LPS-induced WL-38 cell pyroptosis, and LncRNA H19 overexpression promotes LPS-induced WL-38 cell pyroptosis. Also, LncRNA H19 acts as a sponge of miR-22-3p, which targets NLRP3, and NLRP3 attenuates the effect of LncRNA H19 silencing on LPS-induced WL-38 cell pyroptosis. CONCLUSION Our data demonstrated the roles and potential mechanisms of LncRNA H19 in the regulation of pneumonia cell pyroptosis, indicating that LncRNA H19 is an efficient predictive and curative target for pneumonia.
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Affiliation(s)
- Jiyang Sun
- Department of Pediatric Pulmonology, Children’s Hospital of Soochow UniversitySuzhou 215003, Jiangsu Province, China
| | - Shun Mao
- Department of Pneumology, The Fifth People’s Hospital of ChangshuChangshu 215500, Jiangsu Province, China
| | - Wei Ji
- Department of Pediatric Pulmonology, Children’s Hospital of Soochow UniversitySuzhou 215003, Jiangsu Province, China
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Simion V, Loussouarn C, Laurent Y, Roncali L, Gosset D, Reverchon F, Rousseau A, Martin F, Midoux P, Pichon C, Garcion E, Baril P. LentiRILES, a miRNA-ON sensor system for monitoring the functionality of miRNA in cancer biology and therapy. RNA Biol 2021; 18:198-214. [PMID: 34570661 DOI: 10.1080/15476286.2021.1978202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A major unresolved challenge in miRNA biology is the capacity to monitor the spatiotemporal activity of miRNAs expressed in animal disease models. We recently reported that the miRNA-ON monitoring system called RILES (RNAi-inducible expression Luciferase system) implanted in lentivirus expression system (LentiRILES) offers unique opportunity to decipher the kinetics of miRNA activity in vitro, in relation with their intracellular trafficking in glioblastoma cells. In this study, we describe in detail the method for the production of LentiRILES stable cell lines and employed it in several applications in the field of miRNA biology and therapy. We show that LentiRILES is a robust, highly specific and sensitive miRNA sensor system that can be used in vitro as a single-cell miRNA monitoring method, cell-based screening platform for miRNA therapeutics and as a tool to analyse the structure-function relationship of the miRNA duplex. Furthermore, we report the kinetics of miRNA activity upon the intracranial delivery of miRNA mimics in an orthotopic animal model of glioblastoma. This information is exploited to evaluate the tumour suppressive function of miRNA-200c as locoregional therapeutic modality to treat glioblastoma. Our data provide evidence that LentiRILES is a robust system, well suited to resolve the activity of endogenous and exogenously expressed miRNAs from basic research to gene and cell therapy.
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Affiliation(s)
- Viorel Simion
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Claire Loussouarn
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Yoan Laurent
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Loris Roncali
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - David Gosset
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Flora Reverchon
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Audrey Rousseau
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Francisco Martin
- GENYO, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Patrick Midoux
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Chantal Pichon
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
| | - Emmanuel Garcion
- Université d'Angers, Université de Nantes, Inserm, CRCINA, Angers, France
| | - Patrick Baril
- Centre De Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Orléans, France
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Bhatia G, Upadhyay SK, Upadhyay A, Singh K. Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection. BMC PLANT BIOLOGY 2021; 21:265. [PMID: 34103007 PMCID: PMC8186045 DOI: 10.1186/s12870-021-03059-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/23/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide. RESULTS Using computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for 'response to stress', 'response to biotic stimulus', 'immune system process', etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism. CONCLUSIONS Overall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.
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Affiliation(s)
- Garima Bhatia
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, 160014, India
| | | | - Anuradha Upadhyay
- National Research Centre for Grapes, Solapur Road, Pune, Maharashtra, 412307, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, BMS Block I, Sector 25, Chandigarh, 160014, India.
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Arrighetti N, Beretta GL. miRNAs as Therapeutic Tools and Biomarkers for Prostate Cancer. Pharmaceutics 2021; 13:380. [PMID: 33805590 PMCID: PMC7999286 DOI: 10.3390/pharmaceutics13030380] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer (PCa) is the fifth cause of tumor-related deaths in man worldwide. Despite the considerable improvement in the clinical management of PCa, several limitations emerged both in the screening for early diagnosis and in the medical treatment. The use of prostate-specific antigen (PSA)-based screening resulted in patients' overtreatment and the standard therapy of patients suffering from locally advanced/metastatic tumors (e.g., radical prostatectomy, radiotherapy, and androgen deprivation therapy) showed time-limited efficacy with patients undergoing progression toward the lethal metastatic castration-resistant PCa (mCRPC). Although valuable alternative therapeutic options have been recently proposed (e.g., docetaxel, cabazitaxel, abiraterone, enzalutamide, and sipuleucel-T), mCRPC remains incurable. Based on this background, there is an urgent need to identify new and more accurate prostate-specific biomarkers for PCa diagnosis and prognosis and to develop innovative medical approaches to counteract mCRPC. In this context, microRNA (miRNAs) emerged as potential biomarkers in prostate tissues and biological fluids and appeared to be promising therapeutic targets/tools for cancer therapy. Here we overview the recent literature and summarize the achievements of using miRNAs as biomarkers and therapeutic targets/tools for fighting PCa.
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Affiliation(s)
| | - Giovanni Luca Beretta
- Molecular Pharmacology Unit, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
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19
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Nazarov PV, Kreis S. Integrative approaches for analysis of mRNA and microRNA high-throughput data. Comput Struct Biotechnol J 2021; 19:1154-1162. [PMID: 33680358 PMCID: PMC7895676 DOI: 10.1016/j.csbj.2021.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Review on tools and databases linking miRNA and its mRNA targetome. Databases show little overlap in miRNA targetome predictions suggesting strong contextual effects. Deconvolution and deep learning approaches are promising new approaches to improve miRNA targetome predictions.
Advanced sequencing technologies such as RNASeq provide the means for production of massive amounts of data, including transcriptome-wide expression levels of coding RNAs (mRNAs) and non-coding RNAs such as miRNAs, lncRNAs, piRNAs and many other RNA species. In silico analysis of datasets, representing only one RNA species is well established and a variety of tools and pipelines are available. However, attaining a more systematic view of how different players come together to regulate the expression of a gene or a group of genes requires a more intricate approach to data analysis. To fully understand complex transcriptional networks, datasets representing different RNA species need to be integrated. In this review, we will focus on miRNAs as key post-transcriptional regulators summarizing current computational approaches for miRNA:target gene prediction as well as new data-driven methods to tackle the problem of comprehensively and accurately dissecting miRNome-targetome interactions.
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Key Words
- CCA, canonical correlation analysis
- CDS, coding sequence
- CLASH, cross-linking, ligation and sequencing of hybrids
- CLIP, cross-linking immunoprecipitation
- CNN, convolutional neural network
- Data integration
- GO, gene ontology
- ICA, independent component analysis
- Matrix factorization
- NGS, next-generation sequencing
- NMF, non-negative matrix factorization
- PCA, principal component analysis
- RNASeq, high-throughput RNA sequencing
- TDMD, target RNA-directed miRNA degradation
- TF, transcription factors
- Target prediction
- Transcriptomics
- circRNA, circular RNA
- lncRNA, long non-coding RNA
- mRNA, messenger RNA
- miRNA, microRNA
- microRNA
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Affiliation(s)
- Petr V Nazarov
- Multiomics Data Science Research Group, Department of Oncology & Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Strassen L-1445, Luxembourg
| | - Stephanie Kreis
- Signal Transduction Group, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
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20
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Feng H, Zhang YB, Gui JF, Lemon SM, Yamane D. Interferon regulatory factor 1 (IRF1) and anti-pathogen innate immune responses. PLoS Pathog 2021; 17:e1009220. [PMID: 33476326 PMCID: PMC7819612 DOI: 10.1371/journal.ppat.1009220] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The eponymous member of the interferon regulatory factor (IRF) family, IRF1, was originally identified as a nuclear factor that binds and activates the promoters of type I interferon genes. However, subsequent studies using genetic knockouts or RNAi-mediated depletion of IRF1 provide a much broader view, linking IRF1 to a wide range of functions in protection against invading pathogens. Conserved throughout vertebrate evolution, IRF1 has been shown in recent years to mediate constitutive as well as inducible host defenses against a variety of viruses. Fine-tuning of these ancient IRF1-mediated host defenses, and countering strategies by pathogens to disarm IRF1, play crucial roles in pathogenesis and determining the outcome of infection.
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Affiliation(s)
- Hui Feng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Hebei Province Cangzhou Hospital of Integrated Traditional Chinese and Western Medicine, Cangzhou, Hebei, China
| | - Yi-Bing Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Stanley M. Lemon
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology & Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (SML); (DY)
| | - Daisuke Yamane
- Department of Diseases and Infection, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
- * E-mail: (SML); (DY)
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21
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Volovat SR, Volovat C, Hordila I, Hordila DA, Mirestean CC, Miron OT, Lungulescu C, Scripcariu DV, Stolniceanu CR, Konsoulova-Kirova AA, Grigorescu C, Stefanescu C, Volovat CC, Augustin I. MiRNA and LncRNA as Potential Biomarkers in Triple-Negative Breast Cancer: A Review. Front Oncol 2020; 10:526850. [PMID: 33330019 PMCID: PMC7716774 DOI: 10.3389/fonc.2020.526850] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Noncoding RNAs (ncRNAs) include a diverse range of RNA species, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). MiRNAs, ncRNAs of approximately 19-25 nucleotides in length, are involved in gene expression regulation either via degradation or silencing of the messenger RNAs (mRNAs) and have roles in multiple biological processes, including cell proliferation, differentiation, migration, angiogenesis, and apoptosis. LncRNAs, which are longer than 200 nucleotides, comprise one of the largest and most heterogeneous RNA families. LncRNAs can activate or repress gene expression through various mechanisms, acting alone or in combination with miRNAs and other molecules as part of various pathways. Until recently, most research has focused on individual lncRNA and miRNA functions as regulators, and there is limited available data on ncRNA interactions relating to the tumor growth, metastasis, and therapy of cancer, acting either on mRNA alone or as competing endogenous RNA (ceRNA) networks. Triple-negative breast cancer (TNBC) represents approximately 10%-20% of all breast cancers (BCs) and is highly heterogenous and more aggressive than other types of BC, for which current targeted treatment options include hormonotherapy, PARP inhibitors, and immunotherapy; however, no targeted therapies for TNBC are available, partly because of a lack of predictive biomarkers. With advances in proteomics, new evidence has emerged demonstrating the implications of dysregulation of ncRNAs in TNBC etiology. Here, we review the roles of lncRNAs and miRNAs implicated in TNBC, including their interactions and regulatory networks. Our synthesis provides insight into the mechanisms involved in TNBC progression and has potential to aid the discovery of new diagnostic and therapeutic strategies.
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Affiliation(s)
- Simona Ruxandra Volovat
- Department of Medical Oncology-Radiotherapy, Grigore T Popa University of Medicine and Pharmacy, Iași, Romania
| | - Constantin Volovat
- Department of Medical Oncology-Radiotherapy, Grigore T Popa University of Medicine and Pharmacy, Iași, Romania.,Center of Oncology Euroclinic, Iași, Romania
| | | | | | | | | | - Cristian Lungulescu
- Department of Medical Oncology, University of Medicine and Pharmacy, Craiova, Romania
| | | | - Cati Raluca Stolniceanu
- Department of Biophysics and Medical Physics-Nuclear Medicine, University of Medicine and Pharmacy Gr. T. Popa Iasi, Iași, Romania
| | | | - Cristina Grigorescu
- Department of Surgery, Grigore T Popa University of Medicine and Pharmacy, Iași, Romania
| | - Cipriana Stefanescu
- Department of Biophysics and Medical Physics-Nuclear Medicine, University of Medicine and Pharmacy Gr. T. Popa Iasi, Iași, Romania
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22
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Kirchmeyer M, Servais F, Ginolhac A, Nazarov PV, Margue C, Philippidou D, Nicot N, Behrmann I, Haan C, Kreis S. Systematic Transcriptional Profiling of Responses to STAT1- and STAT3-Activating Cytokines in Different Cancer Types. J Mol Biol 2020; 432:5902-5919. [PMID: 32950480 DOI: 10.1016/j.jmb.2020.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Cytokines orchestrate responses to pathogens and in inflammatory processes, but they also play an important role in cancer by shaping the expression levels of cytokine response genes. Here, we conducted a large profiling study comparing miRNome and mRNA transcriptome data generated following different cytokine stimulations. Transcriptomic responses to STAT1- (IFNγ, IL-27) and STAT3-activating cytokines (IL6, OSM) were systematically compared in nine cancerous and non-neoplastic cell lines of different tissue origins (skin, liver and colon). The largest variation in our datasets was seen between cell lines of the three different tissues rather than stimuli. Notably, the variability in miRNome datasets was a lot more pronounced than in mRNA data. Our data also revealed that cells of skin, liver and colon tissues respond very differently to cytokines and that the cell signaling networks activated or silenced in response to STAT1- or STAT3-activating cytokines are specific to the tissue and the type of cytokine. However, globally, STAT1-activating cytokines had stronger effects than STAT3-inducing cytokines with most significant responses in liver cells, showing more genes upregulated and with higher fold change. A more detailed analysis of gene regulations upon cytokine stimulation in these cells provided insights into STAT1- versus STAT3-driven processes in hepatocarcinogenesis. Finally, independent component analysis revealed interconnected transcriptional networks distinct between cancer cells and their healthy counterparts.
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Affiliation(s)
- Mélanie Kirchmeyer
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Florence Servais
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Aurélien Ginolhac
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1AB rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Christiane Margue
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Demetra Philippidou
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, 1AB rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Iris Behrmann
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Claude Haan
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Stephanie Kreis
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg.
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Taherian-Esfahani Z, Ghafouri-Fard S. A bioinformatics approach for identification lncRNA-miRNA-protein interactions for SNHG1 and SNHG5. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Jin W, Fei X, Wang X, Song Y, Chen F. Detection and Prognosis of Prostate Cancer Using Blood-Based Biomarkers. Mediators Inflamm 2020; 2020:8730608. [PMID: 32454797 PMCID: PMC7218965 DOI: 10.1155/2020/8730608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/24/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PCa) is second only to lung cancer as a cause of death. Clinical assessment of patients and treatment efficiency therefore depend on the disease being diagnosed as early as possible. However, due to issues regarding the use of prostate-specific antigen (PSA) for screening purposes, PCa management is among the most contentious of healthcare matters. PSA screening is problematic primarily because of diagnosis difficulties and the high rate of false-positive biopsies. Novel PCa biomarkers, such as the Prostate Health Index (PHI) and the 4Kscore, have been proposed in recent times to improve PSA prediction accuracy and have shown higher performance by preventing redundant biopsies. The 4Kscore also shows high precision in determining the risk of developing high-grade PCa, whereas elevated PHI levels suggest that the tumor is aggressive. Some evidence also supports the effectiveness of miRNAs as biomarkers for distinguishing PCa from benign prostatic hyperplasia and for assessing the aggressiveness of the disease. A number of miRNAs that possibly act as tumor inhibitors or oncogenes are impaired in PCa. These new biomarkers are comprehensively reviewed in the present study in terms of their potential use in diagnosing and treating PCa.
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Affiliation(s)
- Wei Jin
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiang Fei
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yan Song
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Fangjie Chen
- Department of Medical Genetics, School of Life Sciences, China Medical University, Shenyang, Liaoning, China
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25
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Li J, Lv H, Che Y. microRNA-381-3p Confers Protection Against Ischemic Stroke Through Promoting Angiogenesis and Inhibiting Inflammation by Suppressing Cebpb and Map3k8. Cell Mol Neurobiol 2020; 40:1307-1319. [PMID: 32297103 DOI: 10.1007/s10571-020-00815-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/16/2020] [Indexed: 11/27/2022]
Abstract
Ischemic stroke is a serious disease with limited prevention methods, and various genes and microRNAs (miRNAs) have been found to be dysregulated in the pathogenesis of this disease. This study aims to explore the potential role of miR-381-3p in ischemic stroke, along with its underlying mechanism. A mouse model of ischemic stroke was developed using middle cerebral artery occlusion. Next, the expression of mitogen-activated protein kinase kinase kinase 8 (Map3k8) and CCAAT enhancer binding protein beta (Cebpb) was determined by RT-qPCR. Gain- and loss-of-function approaches were applied to analyze the effects of miR-381-3p, Cebpb and Map3k8 on the biological functions of endothelial progenitor cells (EPCs) with the involvement of the tumor necrosis factor-α (TNF-α) signaling pathway. In addition, dual luciferase reporter gene assay was performed for the analysis of the relationship among miR-381-3p, Map3k8 and Cebpb. Further, rescue experiment was performed with the help of JNK/p38 specific agonist, Anisomycin. Map3k8 and Cebpb were highly expressed in ischemic stroke. Loss-of-function of Map3k8 or Cebpb in EPCs contributed to accelerated proliferation, migration and angiogenesis of EPCs. Next, miR-381-3p downregulated the expression of its two target genes, Map3k8 and Cebpb. miR-381-3p overexpression promoted angiogenesis of EPCs, and inhibited inflammation, which could be reversed by restoration of Map3k8 or Cebpb. Additionally, silencing Map3k8 or Cebpb inhibited the activation of TNF-α signaling pathway. Furthermore, Anisomycin treatment could enhance inflammation and inhibit angiogenesis. Taken together, miR-381-3p downregulates Map3k8 and Cebpb to protect against ischemic stroke, broadening our understanding of the pathogenesis of ischemic stroke.
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Affiliation(s)
- Jie Li
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, No. 4, Chongshan East Road, Huanggu District, Shenyang, 110032, Liaoning, People's Republic of China
| | - Hui Lv
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, No. 4, Chongshan East Road, Huanggu District, Shenyang, 110032, Liaoning, People's Republic of China
| | - Yuqin Che
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, No. 4, Chongshan East Road, Huanggu District, Shenyang, 110032, Liaoning, People's Republic of China.
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26
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Dong K, Du Q, Cui X, Wan P, Kaltenmeier C, Luo J, Yan B, Yan Y, Geller DA. MicroRNA-301a (miR-301a) is induced in hepatocellular carcinoma (HCC) and down- regulates the expression of interferon regulatory factor-1. Biochem Biophys Res Commun 2020; 524:273-279. [PMID: 31987500 PMCID: PMC7857543 DOI: 10.1016/j.bbrc.2020.01.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/05/2020] [Indexed: 12/21/2022]
Abstract
Hepatocellular carcinoma (HCC) tumors evade death in part by downregulating expression of the tumor suppressor gene Interferon regulatory factor-1 (IRF-1). However, the molecular mechanisms accounting for IRF-1 suppression in HCC have not been well described. In this study, we identified a novel microRNA-301a (miR-301a) binding site in the 3'-untranslated region (3'- UTR) of the human IRF-1 gene and hypothesized a functional role for miR-301a in regulating HCC growth. We show that miR-301a is markedly upregulated in primary HCC tumors and HCC cell lines, while IRF-1 is down-regulated in a post-transcriptional manner. MiR-301a regulates basal and inducible IRF-1 expression in HCC cells with an inverse relationship between miR-301a and IRF-1 expression in HCC cells. Chronic hypoxia induces miR-301a in HCC in vitro and decreases IRF-1 expression. Finally, miR-301a inhibition increases apoptosis and decreases HCC cell proliferation. These findings suggest that targeting of IRF-1 by miR-301a contributes to the molecular basis for IRF-1 downregulation in HCC and provides new insight into the regulation of HCC by miRNAs.
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Affiliation(s)
- Kun Dong
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Qiang Du
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Xiao Cui
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Peiqi Wan
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | | | - Jing Luo
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Bing Yan
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Yihe Yan
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - David A Geller
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
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27
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Zhang M, Wang Y, Matyunina LV, Akbar A, McDonald JF. The ability of miRNAs to induce mesenchymal-to-epithelial transition (MET) in cancer cells is highly dependent upon genetic background. Cancer Lett 2020; 480:15-23. [PMID: 32234315 DOI: 10.1016/j.canlet.2020.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/30/2022]
Abstract
Understanding of the molecular basis of host cell-miRNA interactions is prerequisite to the successful application of miRNAs as potential therapeutic agents. We studied the morphological and molecular consequences of over expression of three sequence divergent miRNAs previously implicated in the mesenchymal-to-epithelial transition process (MET) in three distinct mesenchymal-like cancer cell lines. The ability of miRNAs to induce morphological changes characteristic of MET positively correlated with induced changes in the expression of genes previously implicated in the process. Variability in the responses of different mesenchymal-like cells to over expression of the same miRNAs was attributable to inherent differences in trans-regulatory profiles pre-disposing these cells to miRNA-induced MET. Collectively our results indicate that miRNA-mediated regulation of MET is a highly integrated process that is significantly modulated by the molecular background of individual cells.
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Affiliation(s)
- Mengnan Zhang
- School of Biological Sciences and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA.
| | - Yuehua Wang
- School of Biological Sciences and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA.
| | - Lilya V Matyunina
- School of Biological Sciences and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA.
| | - Amber Akbar
- School of Biological Sciences and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA.
| | - John F McDonald
- School of Biological Sciences and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA; Integrated Cancer Research Center, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA, 30332, USA.
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28
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Zhao D. Single nucleotide alterations in MicroRNAs and human cancer-A not fully explored field. Noncoding RNA Res 2020; 5:27-31. [PMID: 32128468 PMCID: PMC7044681 DOI: 10.1016/j.ncrna.2020.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are ~20 nt long small noncoding RNAs that are processed from stem-looped precursors and function mainly as posttranscriptional regulators of protein coding genes through binding to 3'-untranslated regions of messenger RNAs to inhibit the translation or cause RNA degradation. It is predicted microRNAs could regulate up to half of all human genes and are proved to play important roles in human diseases including cancer. They bind to target mRNAs based on complementary binding which is dominated by the so-called "seed" region which are the 5' 2-8 bases of the microRNA. Due to the small size in nature, even a single nucleotide variation in the precursor region especially those located in the seed regions could show big influence. Here, I summarized and reviewed the current knowledge of these single nucleotide alterations in microRNAs in human cancer including (i) common SNPs in the precursor region, (ii) isomiRs, (iii) somatic mutations of microRNAs. Briefly, this is an underexploited field and clearly, warrants further studies to reveal their biological and clinical significances. I believe they will be key to advancing personalized medicine.
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Affiliation(s)
- Dan Zhao
- Department of Genetics and Cell Biology, Nankai University School of Life Sciences, Tianjin, 300071, China
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29
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Shi H, Sun H, Li J, Bai Z, Wu J, Li X, Lv Y, Zhang G. Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarction. Aging (Albany NY) 2020; 12:945-964. [PMID: 31927529 PMCID: PMC6977700 DOI: 10.18632/aging.102667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/24/2019] [Indexed: 12/14/2022]
Abstract
Analyses of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) implicated in myocardial infarction (MI) have increased our understanding of gene regulatory mechanisms in MI. However, it is not known how their expression fluctuates over the different stages of MI progression. In this study, we used time-series gene expression data to examine global lncRNA and miRNA expression patterns during the acute phase of MI and at three different time points thereafter. We observed that the largest expression peak for mRNAs, lncRNAs, and miRNAs occurred during the acute phase of MI and involved mainly protein-coding, rather than non-coding RNAs. Functional analysis indicated that the lncRNAs and miRNAs most sensitive to MI and most unstable during MI progression were usually related to fewer biological functions. Additionally, we developed a novel computational method for identifying dysregulated competing endogenous lncRNA-miRNA-mRNA triplets (LmiRM-CTs) during MI onset and progression. As a result, a new panel of candidate diagnostic biomarkers defined by seven lncRNAs was suggested to have high classification performance for patients with or without MI, and a new panel of prognostic biomarkers defined by two lncRNAs evidenced high discriminatory capability for MI patients who developed heart failure from those who did not.
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Affiliation(s)
- Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Haoran Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jiayao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ziyi Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiuhong Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Guangde Zhang
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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30
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Li J, Liu X, Wang W, Li C. miR-133a-3p promotes apoptosis and induces cell cycle arrest by targeting CREB1 in retinoblastoma. Arch Med Sci 2020; 16:941-956. [PMID: 32542098 PMCID: PMC7286343 DOI: 10.5114/aoms.2019.86901] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/25/2018] [Indexed: 12/29/2022] Open
Abstract
INTRODUCTION Retinoblastoma (RB) is a malignant tumor that is derived from photoreceptors. It is common in children under 3 years old with a family genetic predisposition. MicroRNA-133a-3p (miR-133a-3p) is one of the tumor-related miRNAs that interprets a critical function in the genesis and development of various tumors. This study investigated the effects and underlying mechanisms of miR-133a-3p in RB. MATERIAL AND METHODS Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis was used to assess the miR-133a-3p expression in RB tissues and a cell model. MTT assay, western blot, flow cytometry and luciferase reporter assay were performed to evaluate the effect of miR-133a-3p on cell viability, apoptosis and the cell cycle. An RB xenograft model was established to assess the in vivo influence of miR-133a-3p on RB growth. RESULTS MiR-133a-3p level was reduced in RB tissues and the cell model (p < 0.01 or p < 0.001). Addition of miR-133a-3p reduced cell viability, and increased apoptosis and cell cycle arrest (p < 0.001). Additionally, CREB1 was identified to be the target of miR-133a-3p in RB cell lines (p < 0.001). Cell viability reduction, apoptosis and cell cycle arrest increases mediated by miR-133a-3p were attenuated by CREB1 overexpression (p < 0.001). MiR-133a-3p inhibited tumor growth of RB in vivo (p < 0.001). CONCLUSIONS Our results reveal that miR-133a-3p exhibits anti-cancer effects by targeting CREB1 in RB. This study provides a new direction for effective targeted treatment of this disease.
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Affiliation(s)
| | - Xiuming Liu
- Corresponding author: Xiuming Liu, Department of Ophthalmology the Affiliated Huai’an, No. 1 People’s Hospital of Nanjing Medical University, 1 Huanghe Road West, Huaiyin District, Huai’an, Jiangsu, 223300, China, Phone: +86 0517 80872120, Fax: +86 0517 80872120, E-mail:
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31
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Gan WZ, Ramachandran V, Lim CSY, Koh RY. Omics-based biomarkers in the diagnosis of diabetes. J Basic Clin Physiol Pharmacol 2019; 31:/j/jbcpp.ahead-of-print/jbcpp-2019-0120/jbcpp-2019-0120.xml. [PMID: 31730525 DOI: 10.1515/jbcpp-2019-0120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023]
Abstract
Diabetes mellitus (DM) is a group of metabolic diseases related to the dysfunction of insulin, causing hyperglycaemia and life-threatening complications. Current early screening and diagnostic tests for DM are based on changes in glucose levels and autoantibody detection. This review evaluates recent studies on biomarker candidates in diagnosing type 1, type 2 and gestational DM based on omics classification, whilst highlighting the relationship of these biomarkers with the development of diabetes, diagnostic accuracy, challenges and future prospects. In addition, it also focuses on possible non-invasive biomarker candidates besides common blood biomarkers.
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Affiliation(s)
- Wei Zien Gan
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - Valsala Ramachandran
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - Crystale Siew Ying Lim
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University Kuala Lumpur, 56000 Kuala Lumpur, Malaysia
| | - Rhun Yian Koh
- Division of Applied Biomedical Science and Biotechnology, School of Health Sciences, International Medical University, 57000 Kuala Lumpur, Malaysia, Phone: +60327317207
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32
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Wang S, Huang M, Wang Z, Wang W, Zhang Z, Qu S, Liu C. MicroRNA‑133b targets TGFβ receptor I to inhibit TGF‑β‑induced epithelial‑to‑mesenchymal transition and metastasis by suppressing the TGF‑β/SMAD pathway in breast cancer. Int J Oncol 2019; 55:1097-1109. [PMID: 31545407 PMCID: PMC6776189 DOI: 10.3892/ijo.2019.4879] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/04/2019] [Indexed: 01/01/2023] Open
Abstract
Breast cancer (BC) is one of the most common types of cancer and the leading cause of cancer-associated mortality among women worldwide. Accumulating evidence indicates that microRNA (miR)-133b inhibits the proliferation and invasion of cancer cells. Considering that transforming growth factor (TGF)-β signaling plays a key role in cellular epithelial-to-mesenchymal transition (EMT) and cancer metastasis, it is crucial to explore the roles and underlying molecular mechanisms of miR-133b in regulating TGF-β-induced EMT during progression of BC. In the present study, an inverse correlation was observed between the expression of miR-133b and TGFβ receptor I (TGFβR1) mRNA in BC cells and tissues. Furthermore, miR-133b expression was found to be decreased in the BC tissues of patients with lymph node metastasis and advanced tumor-node-metastasis stage, while the expression of TGFβR1 was upregulated. Overexpression of miR-133b significantly decreased the expression of TGFβR1, an indispensable receptor of TGF-β/SMAD signaling, and suppressed TGF-β-induced EMT and BC cell invasion in vitro, whereas miR-133b knockdown exerted the opposite effects. Mechanistically, TGFβR1 was verified as a direct target of miR-133b as determined by bioinformatics analysis and a dual-luciferase reporter assay. In addition, small interfering RNA-mediated knockdown of TGFβR1 mimicked the phenotype of miR-133b overexpression in BC cells. Furthermore, miR-133b overexpression suppressed BC cell invasion in vivo. Collectively, the findings of the present study indicated that miR-133b acts as a tumor suppressor, inhibiting TGF-β-induced EMT and metastasis by directly targeting TGFβR1, and suppressing the TGF-β/SMAD pathway. Therefore, miR-133b may be of value as a diagnostic biomarker of BC.
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Affiliation(s)
- Shengjie Wang
- Laboratory Animal Center of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Mingliang Huang
- Medical College of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Zichen Wang
- Medical College of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Wan Wang
- Medical College of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Zhiyuan Zhang
- Medical College of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Shuting Qu
- Medical College of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Chun Liu
- Laboratory Animal Center of Nantong University, Nantong, Jiangsu 226000, P.R. China
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33
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Nazarov PV, Wienecke-Baldacchino AK, Zinovyev A, Czerwińska U, Muller A, Nashan D, Dittmar G, Azuaje F, Kreis S. Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients. BMC Med Genomics 2019; 12:132. [PMID: 31533822 PMCID: PMC6751789 DOI: 10.1186/s12920-019-0578-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The amount of publicly available cancer-related "omics" data is constantly growing and can potentially be used to gain insights into the tumour biology of new cancer patients, their diagnosis and suitable treatment options. However, the integration of different datasets is not straightforward and requires specialized approaches to deal with heterogeneity at technical and biological levels. METHODS Here we present a method that can overcome technical biases, predict clinically relevant outcomes and identify tumour-related biological processes in patients using previously collected large discovery datasets. The approach is based on independent component analysis (ICA) - an unsupervised method of signal deconvolution. We developed parallel consensus ICA that robustly decomposes transcriptomics datasets into expression profiles with minimal mutual dependency. RESULTS By applying the method to a small cohort of primary melanoma and control samples combined with a large discovery melanoma dataset, we demonstrate that our method distinguishes cell-type specific signals from technical biases and allows to predict clinically relevant patient characteristics. We showed the potential of the method to predict cancer subtypes and estimate the activity of key tumour-related processes such as immune response, angiogenesis and cell proliferation. ICA-based risk score was proposed and its connection to patient survival was validated with an independent cohort of patients. Additionally, through integration of components identified for mRNA and miRNA data, the proposed method helped deducing biological functions of miRNAs, which would otherwise not be possible. CONCLUSIONS We present a method that can be used to map new transcriptomic data from cancer patient samples onto large discovery datasets. The method corrects technical biases, helps characterizing activity of biological processes or cell types in the new samples and provides the prognosis of patient survival.
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Affiliation(s)
- Petr V. Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Anke K. Wienecke-Baldacchino
- Life Sciences Research Unit (LSRU), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Epidemiology and Microbial Genomics Unit, Department of Microbiology, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Andrei Zinovyev
- INSERM, U900, F-75005 Paris, France
- MINES ParisTech, PSL Research University, F-75006 Paris, France
| | - Urszula Czerwińska
- INSERM, U900, F-75005 Paris, France
- MINES ParisTech, PSL Research University, F-75006 Paris, France
- Centre de Recherches Interdisciplinaires, Université Paris Descartes, Paris, France
| | - Arnaud Muller
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | | | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Francisco Azuaje
- Quantitative Biology Unit, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Stephanie Kreis
- Life Sciences Research Unit (LSRU), University of Luxembourg, L-4367 Belvaux, Luxembourg
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p73-Governed miRNA Networks: Translating Bioinformatics Approaches to Therapeutic Solutions for Cancer Metastasis. Methods Mol Biol 2019; 1912:33-52. [PMID: 30635889 DOI: 10.1007/978-1-4939-8982-9_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The transcription factor p73 synthesizes a large number of isoforms and presents high structural and functional homology with p53, a well-known tumor suppressor and a famous "Holy Grail" of anticancer targeting. p73 has attracted increasing attention mainly because (a) unlike p53, p73 is rarely mutated in cancer, (b) some p73 isoforms can inhibit all hallmarks of cancer, and (c) it has the ability to mimic oncosuppressive functions of p53, even in p53-mutated cells. These attributes render p73 and its downstream pathways appealing for therapeutic targeting, especially in mutant p53-driven cancers. p73 functions are, at least partly, mediated by microRNAs (miRNAs), which constitute nodal components of p73-governed networks. p73 not only regulates transcription of crucial miRNA genes, but is also predicted to affect miRNA populations in a transcription-independent manner by developing protein-protein interactions with components of the miRNA processing machinery. This combined effect of p73, both in miRNA transcription and maturation, appears to be isoform-dependent and can result in a systemic switch of cell miRNomes toward either an anti-oncogenic or oncogenic outcome. In this review, we combine literature search with bioinformatics approaches to reconstruct the p73-governed miRNA network and discuss how these crosstalks may be exploited to develop next-generation therapeutics.
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35
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Kang H, Ahn H, Jo K, Oh M, Kim S. mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering. Bioinformatics 2019; 37:1544-1553. [PMID: 31070735 DOI: 10.1093/bioinformatics/btz306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/23/2019] [Accepted: 04/25/2019] [Indexed: 01/27/2023] Open
Abstract
Abstract
Background
MicroRNAs, small noncoding RNAs, are conserved in many species, and they are key regulators that mediate post-transcriptional gene silencing. Since biologists cannot perform experiments for each of target genes of thousands of microRNAs in numerous specific conditions, prediction on microRNA target genes has been extensively investigated. A general framework is a two-step process of selecting target candidates based on sequence and binding energy features and then predicting targets based on negative correlation of microRNAs and their targets. However, there are few methods that are designed for target predictions using time-series gene expression data.
Results
In this article, we propose a new pipeline, mirTime, that predicts microRNA targets by integrating sequence features and time-series expression profiles in a specific experimental condition. The most important feature of mirTime is that it uses the Gaussian process regression model to measure data at unobserved or unpaired time points. In experiments with two datasets in different experimental conditions and cell types, condition-specific target modules reported in the original papers were successfully predicted with our pipeline. The context specificity of target modules was assessed with three (correlation-based, target gene-based and network-based) evaluation criteria. mirTime showed better performance than existing expression-based microRNA target prediction methods in all three criteria.
Availability and implementation
mirTime is available at https://github.com/mirTime/mirtime.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hyejin Kang
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Hongryul Ahn
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyuri Jo
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Minsik Oh
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea
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Zhang P, Yang X, Wang L, Zhang D, Luo Q, Wang B. Overexpressing miR‑335 inhibits DU145 cell proliferation by targeting early growth response 3 in prostate cancer. Int J Oncol 2019; 54:1981-1994. [PMID: 31081063 PMCID: PMC6521937 DOI: 10.3892/ijo.2019.4778] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/18/2019] [Indexed: 12/25/2022] Open
Abstract
MicroRNA-335 (miR-335) was reported to suppress cell proliferation in prostate cancer (PC), a common malignancy in males. The expression of early growth response 3 (EGR3) was determined to be elevated in human PC tissues; however, the possible effects and underlying mechanism of miR-335 on PC remains unknown. In the present study, miR-335 mimics and miR-335 inhibitors were respectively transfected into DU145 cells. Stable silencing of EGR3 was observed in DU145 cells following transfection with small interfering RNA. We also used Cell Counting Kit-8 and in vitro angiogenesis assays to determine the viability and revascularization potential of DU145 cells. The expression levels of EGR and caspase-3 activity were analyzed by immunohistochemistry and immunocytochemistry, respectively. We predicted the target of miR-335 by bioinformatics analysis and a dual-luciferase reporter gene assay. Western blot and quantitative real-time polymerase chain reaction analyses were performed to determine the protein and mRNA expression of molecules. miR-335 expression was downregulated in PC tissues and cell lines. Overexpression of miR-335 significantly reduced the viability and the formation of regenerative tubes of DU145 cells, and inhibited the expression of inflammatory factors. EGR3 was proposed as a possible target of miR-335, and was negatively regulated by miR-335. Silencing EGR3 suppressed the viability and angiogenesis of DU145 cells, and reduced the activity of caspase-3 and inflammatory factor expression. miR-335 inhibition along with EGR3 silencing EGR3 inhibited the cell proliferation. Furthermore, miR-335 inhibited the formation of a PC solid tumor xenograft in vivo. Thus, miR-335 may exert an antitumor effect on DU145 cells by regulating the expression of EGR3. The findings of the present study may provide insight into a novel therapeutic strategy for the treatment of prostatic carcinoma.
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Affiliation(s)
- Peng Zhang
- Department of Urinary Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710004, P.R. China
| | - Xiaojie Yang
- Department of Urinary Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710004, P.R. China
| | - Li Wang
- Department of Urinary Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710004, P.R. China
| | - Dong Zhang
- Department of Urinary Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710004, P.R. China
| | - Qidong Luo
- Department of Urinary Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710004, P.R. China
| | - Binxian Wang
- Department of Urinary Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710004, P.R. China
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37
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Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine. Sci Rep 2019; 9:3552. [PMID: 30837504 PMCID: PMC6401051 DOI: 10.1038/s41598-019-38989-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes–i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like ‘photosynthesis’ and ‘oxidative phosphorylation’. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.
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Hua Y, Zhang C, Shi W, Chen H. High-throughput sequencing reveals microRNAs and their targets in response to drought stress in wheat (Triticum aestivum L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1586586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Ye Hua
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
| | - Cheng Zhang
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
| | - Wanxi Shi
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
| | - Hong Chen
- Department of Longdong Winter Wheat Engineering and Technology Research, College of Agriculture and Forestry, Longdong University, Qingyang, PR China
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39
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Grabowski P, Rappsilber J. A Primer on Data Analytics in Functional Genomics: How to Move from Data to Insight? Trends Biochem Sci 2019; 44:21-32. [PMID: 30522862 PMCID: PMC6318833 DOI: 10.1016/j.tibs.2018.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023]
Abstract
High-throughput methodologies and machine learning have been central in developing systems-level perspectives in molecular biology. Unfortunately, performing such integrative analyses has traditionally been reserved for bioinformaticians. This is now changing with the appearance of resources to help bench-side biologists become skilled at computational data analysis and handling large omics data sets. Here, we show an entry route into the field of omics data analytics. We provide information about easily accessible data sources and suggest some first steps for aspiring computational data analysts. Moreover, we highlight how machine learning is transforming the field and how it can help make sense of biological data. Finally, we suggest good starting points for self-learning and hope to convince readers that computational data analysis and programming are not intimidating.
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Affiliation(s)
- Piotr Grabowski
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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40
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Loss of DNA methylation is related to increased expression of miR-21 and miR-146b in papillary thyroid carcinoma. Clin Epigenetics 2018; 10:144. [PMID: 30454026 PMCID: PMC6245861 DOI: 10.1186/s13148-018-0579-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/06/2018] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation in miRNA genes has been reported as a mechanism that may cause dysregulation of mature miRNAs and consequently impact the gene expression. This mechanism is largely unstudied in papillary thyroid carcinomas (PTC). Methods To identify differentially methylated miRNA-encoding genes, we performed global methylation analysis (Illumina 450 K), integrative analysis (TCGA database), data confirmation (pyrosequencing and RT-qPCR), and functional assays. Results Methylation analysis revealed 27 differentially methylated miRNA genes. The integrative analyses pointed out miR-21 and miR-146b as potentially regulated by methylation (hypomethylation and increased expression). DNA methylation and expression patterns of miR-21 and miR-146b were confirmed as altered, as well as seven of 452 mRNAs targets were down-expressed. The combined methylation and expression levels of miR-21 and miR-146b showed potential to discriminate malignant from benign lesions (91–96% sensitivity and 96–97% specificity). An increased expression of miR-146b due to methylation loss was detected in the TPC1 cell line. The miRNA mimic transfection highlighted putative target mRNAs. Conclusions The increased expression of miR-21 and miR-146b due to loss of DNA methylation in PTC resulted in the disruption of the transcription machinery and biological pathways. These miRNAs are potential diagnostic biomarkers, and these findings provide support for future development of targeted therapies. Electronic supplementary material The online version of this article (10.1186/s13148-018-0579-8) contains supplementary material, which is available to authorized users.
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41
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Jike W, Sablok G, Bertorelle G, Li M, Varotto C. In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L. Sci Rep 2018; 8:16667. [PMID: 30420632 PMCID: PMC6232160 DOI: 10.1038/s41598-018-34982-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5′-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.
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Affiliation(s)
- Wuhe Jike
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.,Università degli Studi di Ferrara, Dipartimento di Scienze della Vita e Biotecnologie, Ferrara, Italy
| | - Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.,Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Giorgio Bertorelle
- Università degli Studi di Ferrara, Dipartimento di Scienze della Vita e Biotecnologie, Ferrara, Italy
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
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42
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Hao S, Li S, Wang J, Zhao L, Zhang C, Huang W, Wang C. Phycocyanin Reduces Proliferation of Melanoma Cells through Downregulating GRB2/ERK Signaling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10921-10929. [PMID: 30253646 DOI: 10.1021/acs.jafc.8b03495] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
As a type of functional food additive, phycocyanin is shown to have a potential antineoplastic property. However, its underlying anticancer mechanism in melanoma cells remains unknown. We previously reported a 35S in vivo/vitro labeling analysis for dynamic proteomic (SiLAD) technology. It could exclusively detect protein synthesis rates via pulse labeling of newly expressed proteins by 35S, providing a high time-resolution method for analysis of protein variations. In the present study, we performed a time course analysis in A375 melanoma cells after phycocyanin treatment using SiLAD. Protein expression velocities were specifically visualized and their regulation modes were dynamically traced. Strikingly, novel protein synthesis patterns were discovered in the early phase of phycocyanin treatment, suggesting a possible mechanism of phycocyanin regulation. Furthermore, network analysis and phenotype experiments demonstrated that GRB2-ERK1/2 pathway was involved in phycocyanin-mediated regulation process and responsible for the proliferation suppression of melanoma cell, which could be a therapeutic target for malignant melanoma.
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Affiliation(s)
- Shuai Hao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives , Beijing Technology and Business University , Beijing 100048 , China
| | - Shuang Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives , Beijing Technology and Business University , Beijing 100048 , China
| | - Jing Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives , Beijing Technology and Business University , Beijing 100048 , China
| | - Lei Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives , Beijing Technology and Business University , Beijing 100048 , China
| | - Chan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives , Beijing Technology and Business University , Beijing 100048 , China
| | - Weiwei Huang
- Genetron Health (Beijing) Co. Ltd, Beijing 102208 , China
| | - Chengtao Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives , Beijing Technology and Business University , Beijing 100048 , China
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43
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Cytokine-mediated modulation of the hepatic miRNome: miR-146b-5p is an IL-6-inducible miRNA with multiple targets. J Leukoc Biol 2018; 104:987-1002. [DOI: 10.1002/jlb.ma1217-499rr] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 12/14/2022] Open
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44
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Rainer J, Meraviglia V, Blankenburg H, Piubelli C, Pramstaller PP, Paolin A, Cogliati E, Pompilio G, Sommariva E, Domingues FS, Rossini A. The arrhythmogenic cardiomyopathy-specific coding and non-coding transcriptome in human cardiac stromal cells. BMC Genomics 2018; 19:491. [PMID: 29940860 PMCID: PMC6019788 DOI: 10.1186/s12864-018-4876-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/18/2018] [Indexed: 01/05/2023] Open
Abstract
Background Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recently described, cardiac stromal cells (CStCs). In the present study, we aim to identify ACM-specific expression profiles of human CStCs derived from endomyocardial biopsies of ACM patients and healthy individuals employing TaqMan Low Density Arrays for miRNA expression profiling, and high throughput sequencing for gene expression quantification. Results We identified 3 miRNAs and 272 genes as significantly differentially expressed at a 5% false discovery rate. Both the differentially expressed genes as well as the target genes of the ACM-specific miRNAs were found to be enriched in cell adhesion-related biological processes. Functional similarity and protein interaction-based network analyses performed on the identified deregulated genes, miRNA targets and known ACM-causative genes revealed clusters of highly related genes involved in cell adhesion, extracellular matrix organization, lipid transport and ephrin receptor signaling. Conclusions We determined for the first time the coding and non-coding transcriptome characteristic of ACM cardiac stromal cells, finding evidence for a potential contribution of miRNAs, specifically miR-29b-3p, to ACM pathogenesis or phenotype maintenance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4876-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy.
| | - Viviana Meraviglia
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy.
| | - Hagen Blankenburg
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Chiara Piubelli
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Adolfo Paolin
- Treviso Tissue Bank Foundation, Piazzalo Ospedale 1, 31100, Treviso, Italy
| | - Elisa Cogliati
- Treviso Tissue Bank Foundation, Piazzalo Ospedale 1, 31100, Treviso, Italy
| | - Giulio Pompilio
- Vascular Biology and Regenerative Medicine Unit, Centro Cardiologico Monzino IRCCS, via Parea 4, 20138, Milan, Italy
| | - Elena Sommariva
- Vascular Biology and Regenerative Medicine Unit, Centro Cardiologico Monzino IRCCS, via Parea 4, 20138, Milan, Italy
| | - Francisco S Domingues
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
| | - Alessandra Rossini
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Viale Druso 1, 39100, Bolzano, Italy
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45
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Lin P, Zhu L, Sun W, Yang Z, Sun H, Li D, Cui R, Zheng X, Yu X. Prostate cancer cell proliferation is suppressed by microRNA-3160-5p via targeting of F-box and WD repeat domain containing 8. Oncol Lett 2018; 15:9436-9442. [PMID: 29805667 DOI: 10.3892/ol.2018.8505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 12/15/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs/miRs), which are endogenous non-coding single-stranded RNAs 19-25 nucleotides in length, regulate gene expression by blocking translation or transcription repression. The present study revealed that miR-3160-5p was widely expressed in prostate cancer cells by reverse transcription-quantitative polymerase chain reaction. There was a negative association between the expression of miR-3160-5p and F-box and WD repeat domain containing 8 (Fbxw8) in prostate cancer DU145 cells. A luciferase activity assay was used to verify that Fbxw8 is the target of miR-3160-5p. In the present study, using MTT assay and cell cycle analysis, it was demonstrated that DU145 cell proliferation was repressed and the cell cycle was arrested in the G2/M cell cycle phase with upregulation of miR-3160-5p. Subsequent studies demonstrated that miR-3160-5p regulated the progression of the cell cycle in DU145 prostate cancer cells when the expression levels of phosphorylated cell division cycle (CDC)2, CDC25C and cyclin B1 were directly inhibited. Taken together, these findings revealed the mechanism underlying the role of miR-3160-5p in regulating the proliferation of DU145 cells and indicated that miR-3160-5p may serve as a promising novel therapeutic tool for prostate cancer.
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Affiliation(s)
- Ping Lin
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Lijuan Zhu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Wenjing Sun
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Zhengkai Yang
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Hui Sun
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Dong Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Rongjun Cui
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Xiulan Zheng
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Ultrasonography and Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Xiaoguang Yu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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46
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Dubey R, Malhotra SS, Gupta SK. Forskolin-mediated BeWo cell fusion involves down-regulation of miR-92a-1-5p that targets dysferlin and protein kinase cAMP-activated catalytic subunit alpha. Am J Reprod Immunol 2018; 79:e12834. [PMID: 29484758 DOI: 10.1111/aji.12834] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/04/2018] [Indexed: 12/16/2022] Open
Abstract
PROBLEM To study the role of miRNA(s) during trophoblastic BeWo cell fusion. METHOD OF STUDY Changes in miRNA(s) profile of BeWo cells treated with forskolin were analyzed using Affymetrix miRNA microarray platform. Down-regulated miRNA, miR-92a-1-5p, was overexpressed in BeWo cells followed by forskolin treatment to understand its relevance in the process of BeWo cell fusion by desmoplakin I+II staining and hCG secretion by ELISA. Predicted targets of miR-92a-1-5p were also confirmed by qRT-PCR/Western blotting. RESULTS The miRNA profiling of BeWo cells after forskolin (25 μmol/L) treatment identified miR-92a-1-5p as the most significantly down-regulated miRNA both at 24 and 48 hours time points. Overexpression of miR-92a-1-5p in these cells led to a significant decrease in forskolin-mediated cell fusion and hCG secretion. miRNA target prediction software, TargetScan, revealed dysferlin (DYSF) and protein kinase cAMP-activated catalytic subunit alpha (PRKACA), as target genes of miR-92a-1-5p. Overexpression of miR-92a-1-5p in BeWo cells showed reduction in forskolin-induced transcripts for DYSF and PRKACA. Further, reduction in DYSF (~2.6-fold) at protein level and PRKACA-encoded protein kinase A catalytic subunit alpha (PKAC-α; ~1.6-fold) were also observed. CONCLUSION These observations suggest that miR-92a-1-5p regulates forskolin-mediated BeWo cell fusion and hCG secretion by regulating PKA signaling pathway and dysferlin expression.
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Affiliation(s)
- Richa Dubey
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Sudha S Malhotra
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | - Satish K Gupta
- Reproductive Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
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47
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Salamo O, Mortaz E, Mirsaeidi M. Noncoding RNAs: New Players in Pulmonary Medicine and Sarcoidosis. Am J Respir Cell Mol Biol 2018; 58:147-156. [DOI: 10.1165/rcmb.2017-0196tr] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Oriana Salamo
- Division of Pulmonary and Critical Care, University of Miami, Miami, Florida
| | - Esmaeil Mortaz
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands; and
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, Florida
- Section of Pulmonary Medicine, Miami Veterans Affairs Healthcare System, Miami, Florida
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48
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Mullany LE, Herrick JS, Wolff RK, Stevens JR, Samowitz W, Slattery ML. MicroRNA-transcription factor interactions and their combined effect on target gene expression in colon cancer cases. Genes Chromosomes Cancer 2017; 57:192-202. [PMID: 29226599 PMCID: PMC5807123 DOI: 10.1002/gcc.22520] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/11/2022] Open
Abstract
Transcription factors (TFs) and microRNAs (miRNAs) regulate gene expression: TFs by influencing messenger RNA (mRNA) transcription and miRNAs by influencing mRNA translation and transcript degradation. Additionally, miRNAs and TFs alter each other's expression, making it difficult to ascertain the effect either one has on target gene (TG) expression. In this investigation, we use a two‐way interaction model with the TF and miRNA as independent variables to investigate whether miRNAs and TFs work together to influence TG expression levels in colon cancer subjects. We used known TF binding sites and validated miRNA targets to determine potential miRNA‐TF‐TG interactions, restricting interactions to those with a TF previously associated with altered risk of colorectal cancer death. We analyzed interactions using normal colonic mucosa expression as well as differential expression, which is measured as colonic carcinoma expression minus normal colonic mucosa expression. We analyzed 3518 miRNA‐TF‐TG triplets using normal mucosa expression and 617 triplets using differential expression. Normal colonic RNA‐Seq data were available for 168 individuals; of these, 159 also had carcinoma RNA‐Seq data. Thirteen unique miRNA‐TF‐TG interactions, comprising six miRNAs, four TFs, and 11 TGs, were statistically significant after adjustment for multiple comparisons in normal colonic mucosa, and 14 unique miRNA‐TF‐TG interactions, comprising two miRNAs, two TFs, and 13 TGs, were found for carcinoma‐normal differential expression. Our results show that TG expression is influenced by both miRNAs as well as TFs, and the influence of one regulator impacts the effect of the other on the shared TG expression.
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Affiliation(s)
- Lila E Mullany
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Division of Epidemiology, University of Utah, Salt Lake City, Utah
| | - Jennifer S Herrick
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Division of Epidemiology, University of Utah, Salt Lake City, Utah
| | - Roger K Wolff
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Division of Epidemiology, University of Utah, Salt Lake City, Utah
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, Utah
| | - Wade Samowitz
- Department of Pathology, University of Utah School, Salt Lake City, Utah
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Division of Epidemiology, University of Utah, Salt Lake City, Utah
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Comparative analysis of cytokine/chemokine regulatory networks in patients with hippocampal sclerosis (HS) and focal cortical dysplasia (FCD). Sci Rep 2017; 7:15904. [PMID: 29162878 PMCID: PMC5698416 DOI: 10.1038/s41598-017-16041-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/06/2017] [Indexed: 01/22/2023] Open
Abstract
Experimental and clinical evidence have demonstrated aberrant expression of cytokines/chemokines and their receptors in patients with hippocampal sclerosis (HS) and focal cortical dysplasia (FCD). However, there is limited information regarding the modulation of cytokine/chemokine-regulatory networks, suggesting contribution of miRNAs and downstream transcription factors/receptors in these pathologies. Hence, we studied the levels of multiple inflammatory mediators (IL1β, IL1Ra, IL6, IL10, CCL3, CCL4, TNFα and VEGF) along with transcriptional changes of nine related miRNAs and mRNA levels of downstream effectors of significantly altered cytokines/chemokines in brain tissues obtained from patients with HS (n = 26) and FCD (n = 26). Up regulation of IL1β, IL6, CCL3, CCL4, STAT-3, C-JUN and CCR5, and down regulation of IL 10 were observed in both HS and FCD cases (p < 0.05). CCR5 was significantly up regulated in FCD as compared to HS (p < 0.001). Both, HS and FCD presented decreased miR-223-3p, miR-21-5p, miR-204-5p and let-7a-5p and increased miR-155-5p expression (p < 0.05). As compared to HS, miR-204-5p (upstream to CCR5 and IL1β) and miR-195-5p (upstream to CCL4) were significantly decreased in FCD patients (p < 0.01). Our results suggest differential alteration of cytokine/chemokine regulatory networks in HS and FCD and provide a rationale for developing pathology specific therapy.
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Iskandar AR, Martinez Y, Martin F, Schlage WK, Leroy P, Sewer A, Torres LO, Majeed S, Merg C, Trivedi K, Guedj E, Frentzel S, Mathis C, Ivanov NV, Peitsch MC, Hoeng J. Comparative effects of a candidate modified-risk tobacco product Aerosol and cigarette smoke on human organotypic small airway cultures: a systems toxicology approach. Toxicol Res (Camb) 2017; 6:930-946. [PMID: 30090554 PMCID: PMC6062162 DOI: 10.1039/c7tx00152e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/27/2017] [Indexed: 12/22/2022] Open
Abstract
Using an in vitro human small airway epithelium model, we assessed the biological impact of an aerosol from a candidate modified-risk tobacco product, the tobacco heating system (THS) 2.2, to investigate the potential reduced risk of THS2.2 aerosol exposure compared with cigarette smoke. Following the recommendations of the Institute of Medicine and the Tobacco Product Assessment Consortium, in which modified-risk tobacco products assessment should be performed in comparison with standard conventional products, the effects of the THS2.2 aerosol exposure on the small airway cultures were compared with those of 3R4F cigarette smoke. We used a systems toxicology approach whereby elucidation of toxic effects is derived not only from functional assay readouts but also from omics technologies. Cytotoxicity, ciliary beating function, secretion of pro-inflammatory mediators and histological assessment represented functional assays. The omics data included transcriptomic and miRNA profiles. Exposure-induced perturbations of causal biological networks were computed from the transcriptomic data. The results showed that THS2.2 aerosol exposure at the tested doses elicited lower cytotoxicity levels and lower changes in the secreted pro-inflammatory mediators than 3R4F smoke. Although THS2.2 exposure elicited alterations in the gene expression, a higher transcriptome-induced biological impact was observed following 3R4F smoke: The effects of THS2.2 aerosol exposure, if observed, were mostly transient and diminished more rapidly after exposure than those of 3R4F smoke. The study demonstrated that the systems toxicology approach can reveal changes at the cellular level that would be otherwise not detected from functional assays, thus increasing the sensitivity to detect potential toxicity of a treatment/exposure.
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Affiliation(s)
- Anita R Iskandar
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Yannick Martinez
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Florian Martin
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Walter K Schlage
- Biology consultant , Max-Baermann-Str. 21 , 51429 Bergisch Gladbach , Germany
| | - Patrice Leroy
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Alain Sewer
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Laura Ortega Torres
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Shoaib Majeed
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Celine Merg
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Keyur Trivedi
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Emmanuel Guedj
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Stefan Frentzel
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Carole Mathis
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Nikolai V Ivanov
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Manuel C Peitsch
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
| | - Julia Hoeng
- PMI R&D , Philip Morris Products S.A. (Part of Philip Morris International group of companies) , Quai Jeanrenaud 5 , CH-2000 Neuchâtel , Switzerland . ; ; Tel: +41 (58)242 2214
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