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Gharipour M, Mani A, Amini Baghbahadorani M, de Souza Cardoso CK, Jahanfar S, Sarrafzadegan N, de Oliveira C, Silveira EA. How Are Epigenetic Modifications Related to Cardiovascular Disease in Older Adults? Int J Mol Sci 2021; 22:9949. [PMID: 34576113 PMCID: PMC8470616 DOI: 10.3390/ijms22189949] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
The rate of aging has increased globally during recent decades and has led to a rising burden of age-related diseases such as cardiovascular disease (CVD). At the molecular level, epigenetic modifications have been shown recently to alter gene expression during the life course and impair cellular function. In this regard, several CVD risk factors, such as lifestyle and environmental factors, have emerged as key factors in epigenetic modifications within the cardiovascular system. In this study, we attempted to summarized recent evidence related to epigenetic modification, inflammation response, and CVD in older adults as well as the effect of lifestyle modification as a preventive strategy in this age group. Recent evidence showed that lifestyle and environmental factors may affect epigenetic mechanisms, such as DNA methylation, histone acetylation, and miRNA expression. Several substances or nutrients such as selenium, magnesium, curcumin, and caffeine (present in coffee and some teas) could regulate epigenetics. Similarly, physical inactivity, alcohol consumption, air pollutants, psychological stress, and shift working are well-known modifiers of epigenetic patterns. Understanding the exact ways that lifestyle and environmental factors could affect the expression of genes could help to influence the time of incidence and severity of aging-associated diseases. This review highlighted that a healthy lifestyle throughout the life course, such as a healthy diet rich in fibers, vitamins, and essential elements, and specific fatty acids, adequate physical activity and sleep, smoking cessation, and stress control, could be useful tools in preventing epigenetic changes that lead to impaired cardiovascular function.
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Affiliation(s)
- Mojgan Gharipour
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 8158388994, Iran;
| | - Arya Mani
- Cardiovascular Research Center, Department of Internal Medicine, and Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - Mona Amini Baghbahadorani
- Interventional Cardiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 8158388994, Iran;
| | - Camila Kellen de Souza Cardoso
- School of Social Sciences and Health, Nutrition Course, Pontifical Catholic University of Goias, Goiânia 74605-010, Brazil;
| | - Shayesteh Jahanfar
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MI 02111, USA;
| | - Nizal Sarrafzadegan
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan 8158388994, Iran;
- Faculty of Medicine, School of Population and Public Health, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Cesar de Oliveira
- Department of Epidemiology & Public Health, Institute of Epidemiology & Health Care, University College London, London WC1E 6BT, UK;
| | - Erika Aparecida Silveira
- Department of Epidemiology & Public Health, Institute of Epidemiology & Health Care, University College London, London WC1E 6BT, UK;
- Graduate Program in Health Sciences, Faculty of Medicine, Federal University of Goiás, Goiânia 74690-900, Brazil
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2
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Bayraktar R, Ivan C, Bayraktar E, Kanlikilicer P, Kabil NN, Kahraman N, Mokhlis HA, Karakas D, Rodriguez-Aguayo C, Arslan A, Sheng J, Wong S, Lopez-Berestein G, Calin GA, Ozpolat B. Dual Suppressive Effect of miR-34a on the FOXM1/eEF2-Kinase Axis Regulates Triple-Negative Breast Cancer Growth and Invasion. Clin Cancer Res 2018; 24:4225-4241. [PMID: 29748184 DOI: 10.1158/1078-0432.ccr-17-1959] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/30/2017] [Accepted: 05/02/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Recent studies indicated that dysregulation of noncoding RNAs (ncRNA) such as miRNAs is involved in pathogenesis of various human cancers. However, the molecular mechanisms underlying miR-34a are not fully understood in triple-negative breast cancer (TNBC).Experimental Design: We performed in vitro functional assays on TNBC cell lines to investigate the role of miR-34a in FOXM1/eEF2K signaling axis. TNBC tumor xenograft models were used for in vivo therapeutic delivery of miR-34a.Results: In this study, we investigated the role of p53-driven ncRNA miR-34a and found that miR-34a is associated with significantly longer patient survival in TNBC and inversely correlated with levels of proto-oncogenic eEF2K, which was associated with significantly shorter overall patient survival. We showed that miR-34a directly binds to the 3'-untranslated region of eEF2K and FOXM1 mRNAs and suppresses their expression, leading to inhibition of TNBC cell proliferation, motility, and invasion. Notably, restoring miR-34a expression recapitulated the effects of inhibition of eEF2K and FOXM1, the transcription factor for eEF2K and the direct target of p53, in TNBC cell lines, whereas overexpression of eEF2K and FOXM1 rescued the effects and signaling pathways mediated by miR-34a. Moreover, in vivo therapeutic delivery of miR-34a nanoparticles by systemic intravenous administration delayed tumor growth of two different orthotopic TNBC tumor xenograft models by inhibiting eEF2K and FOXM1, intratumoral proliferation and angiogenesis, and inducing apoptosis.Conclusions: Overall, our findings provide new insights into the tumor suppressor role of miR-34a by dual-targeting of FOXM1/eEF2K signaling axis and suggest that miR-34a-based gene therapy may be a potential therapeutic strategy in TNBC. Clin Cancer Res; 24(17); 4225-41. ©2018 AACR.
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Affiliation(s)
- Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas
| | - Emine Bayraktar
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas
| | - Pinar Kanlikilicer
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas
| | - Nashwa N Kabil
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas
| | - Nermin Kahraman
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas
| | - Hamada A Mokhlis
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, The University of Al-Azhar, Cairo, Egypt
| | - Didem Karakas
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas.,Department of Clinical Biochemistry, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas
| | - Ahmet Arslan
- Department of Medical Genetics, Faculty of Medicine, Namik Kemal University, Tekirdag, Turkey
| | - Jianting Sheng
- Department of Systems Medicine & Bioengineering, Methodist, Houston, Institute for Academic Medicine Research Institute Houston Methodist Weill Cornell Medical College, Houston, Texas
| | - Stephen Wong
- Department of Systems Medicine & Bioengineering, Methodist, Houston, Institute for Academic Medicine Research Institute Houston Methodist Weill Cornell Medical College, Houston, Texas
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas- MD Anderson Cancer Center, Houston, Texas. .,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
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3
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Shukla SK, Shukla S, Chauhan A, Sarvjeet, Khan R, Ahuja A, Singh LV, Sharma N, Prakash C, Singh AV, Panigrahi M. Differential gene expression in Mycobacterium bovis challenged monocyte-derived macrophages of cattle. Microb Pathog 2017; 113:480-489. [PMID: 29170044 DOI: 10.1016/j.micpath.2017.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/14/2017] [Accepted: 11/18/2017] [Indexed: 12/18/2022]
Abstract
A functional genomics approach was used to examine the immune response for transcriptional profiling of PBMC M. bovis infected cattle and healthy control cattle to stimulation with bovine tuberculin (purified protein derivative PPD-b). Total cellular RNA was extracted from non-challenged control and M. bovis challenged MDM for all animals at intervals of 6 h post-challenge, in response to in-vitro challenge with M. bovis (multiplicity of infection 2:1) and prepared for global gene expression analysis using the Agilent Bovine (V2) Gene Expression Microarray, 8 × 60 K. The pattern of expression of these genes in PPD bovine stimulated PBMC provides the first description of an M. bovis specific signature of infection that may provide insights into the molecular basis of the host response to infection. Analysis of these mapped reads showed 2450 genes (1291 up regulated and 1158 down regulated) 462 putative natural antisense transcripts (354 up-regulated and 108 down regulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). The results provided enrichment for genes involved top ten up regulated and down regulated panel of genes, including transcription factors proliferation of T and B lymphocytes. The highest differentially-expressed genes were associated to immune and inflammatory responses, immunity, differentiation, cell growth, apoptosis, cellular trafficking and regulation of lipolysis and thermogenesis. Microarray results were confirmed in infected cattle by RT qPCR to identify potential biomarkers TLR2, CD80, NFKB1, IL8, CXCL6 and ADORA3 of bovine tuberculosis.
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Affiliation(s)
- Sanjeev Kumar Shukla
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India.
| | - Shubhra Shukla
- Department of Biosciences, Integral University, Lucknow, U.P., India
| | - Anuj Chauhan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
| | - Sarvjeet
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
| | - Rehan Khan
- Division of Hematology, Mayo Clinic, Rochester, MN, United States
| | - Anuj Ahuja
- The Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed, Israel
| | - Lakshya Veer Singh
- Tuberculosis Aerosol Challenge Facility Laboratory, ICGEB, Campus, New Delhi, India
| | - Naveen Sharma
- Department of Health Research, IRCS Building, New Delhi, India
| | - Chandan Prakash
- CADRAD, Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
| | - Ajay Vir Singh
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, U.P., India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
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Roden C, Mastriano S, Wang N, Lu J. microRNA Expression Profiling: Technologies, Insights, and Prospects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 888:409-21. [PMID: 26663195 DOI: 10.1007/978-3-319-22671-2_21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Since the early days of microRNA (miRNA) research, miRNA expression profiling technologies have provided important tools toward both better understanding of the biological functions of miRNAs and using miRNA expression as potential diagnostics. Multiple technologies, such as microarrays, next-generation sequencing, bead-based detection system, single-molecule measurements, and quantitative RT-PCR, have enabled accurate quantification of miRNAs and the subsequent derivation of key insights into diverse biological processes. As a class of ~22 nt long small noncoding RNAs, miRNAs present unique challenges in expression profiling that require careful experimental design and data analyses. We will particularly discuss how normalization and the presence of miRNA isoforms can impact data interpretation. We will present one example in which the consideration in data normalization has provided insights that helped to establish the global miRNA expression as a tumor suppressor. Finally, we discuss two future prospects of using miRNA profiling technologies to understand single cell variability and derive new rules for the functions of miRNA isoforms.
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Affiliation(s)
- Christine Roden
- Department of Genetics, Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, 10 Amistad Street, Rm 237C, New Haven, CT, 06520-8005, USA
| | - Stephen Mastriano
- Department of Genetics, Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, 10 Amistad Street, Rm 237C, New Haven, CT, 06520-8005, USA
| | - Nayi Wang
- The Biomedical Engineering Graduate Program, New Haven, CT, 06520, USA
| | - Jun Lu
- Department of Genetics, Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, 10 Amistad Street, Rm 237C, New Haven, CT, 06520-8005, USA. .,Yale Center for RNA Science and Medicine, New Haven, CT, 06520, USA.
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5
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Momose F, Seo N, Akahori Y, Sawada SI, Harada N, Ogura T, Akiyoshi K, Shiku H. Guanine-Rich Sequences Are a Dominant Feature of Exosomal microRNAs across the Mammalian Species and Cell Types. PLoS One 2016; 11:e0154134. [PMID: 27101102 PMCID: PMC4839687 DOI: 10.1371/journal.pone.0154134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/08/2016] [Indexed: 12/19/2022] Open
Abstract
Exosome is an extracellular vesicle released from multivesicular endosomes and contains micro (mi) RNAs and functional proteins derived from the donor cells. Exosomal miRNAs act as an effector during communication with appropriate recipient cells, this can aid in the utilization of the exosomes in a drug delivery system for various disorders including malignancies. Differences in the miRNA distribution pattern between exosomes and donor cells indicate the active translocation of miRNAs into the exosome cargos in a miRNA sequence-dependent manner, although the molecular mechanism is little known. In this study, we statistically analyzed the miRNA microarray data and revealed that the guanine (G)-rich sequence is a dominant feature of exosome-dominant miRNAs, across the mammalian species-specificity and the cell types. Our results provide important information regarding the potential use of exosome cargos to develop miRNA-based drugs for the treatment of human diseases.
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Affiliation(s)
- Fumiyasu Momose
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Edobashi, Tsu, Mie 514–8507, Japan
- ERATO Bio-Nanotransporter Project, Japan Science and Technology Agency (JST), Tokyo 102–0076, Japan
| | - Naohiro Seo
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Edobashi, Tsu, Mie 514–8507, Japan
- ERATO Bio-Nanotransporter Project, Japan Science and Technology Agency (JST), Tokyo 102–0076, Japan
- * E-mail: (NS); (HS)
| | - Yasushi Akahori
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Edobashi, Tsu, Mie 514–8507, Japan
- ERATO Bio-Nanotransporter Project, Japan Science and Technology Agency (JST), Tokyo 102–0076, Japan
| | - Shin-ichi Sawada
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615–8510, Japan
- ERATO Bio-Nanotransporter Project, Japan Science and Technology Agency (JST), Tokyo 102–0076, Japan
| | - Naozumi Harada
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Edobashi, Tsu, Mie 514–8507, Japan
- ERATO Bio-Nanotransporter Project, Japan Science and Technology Agency (JST), Tokyo 102–0076, Japan
| | - Toru Ogura
- Clinical Research Support Center, Mie University Hospital, Tsu Mie 514–8507, Japan
| | - Kazunari Akiyoshi
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615–8510, Japan
- ERATO Bio-Nanotransporter Project, Japan Science and Technology Agency (JST), Tokyo 102–0076, Japan
| | - Hiroshi Shiku
- Department of Immuno-Gene Therapy, Mie University Graduate School of Medicine, Edobashi, Tsu, Mie 514–8507, Japan
- ERATO Bio-Nanotransporter Project, Japan Science and Technology Agency (JST), Tokyo 102–0076, Japan
- * E-mail: (NS); (HS)
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6
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miR-16-5p Is a Stably-Expressed Housekeeping MicroRNA in Breast Cancer Tissues from Primary Tumors and from Metastatic Sites. Int J Mol Sci 2016; 17:ijms17020156. [PMID: 26821018 PMCID: PMC4783890 DOI: 10.3390/ijms17020156] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 01/24/2023] Open
Abstract
For quantitative microRNA analyses in formalin-fixed paraffin-embedded (FFPE) tissue, expression levels have to be normalized to endogenous controls. To investigate the most stably-expressed microRNAs in breast cancer and its surrounding tissue, we used tumor samples from primary tumors and from metastatic sites. MiRNA profiling using TaqMan(®) Array Human MicroRNA Cards, enabling quantification of 754 unique human miRNAs, was performed in FFPE specimens from 58 patients with metastatic breast cancer. Forty-two (72%) samples were collected from primary tumors and 16 (28%) from metastases. In a cross-platform analysis of a validation cohort of 32 FFPE samples from patients with early breast cancer genome-wide microRNA expression analysis using SurePrintG3 miRNA (8 × 60 K)(®) microarrays from Agilent(®) was performed. Eleven microRNAs could be detected in all samples analyzed. Based on NormFinder and geNorm stability values and the high correlation (rho ≥ 0.8) with the median of all measured microRNAs, miR-16-5p, miR-29a-3p, miR-126-3p, and miR-222-3p are suitable single gene housekeeper candidates. In the cross-platform validation, 29 human microRNAs were strongly expressed (mean log2-intensity > 10) and 21 of these microRNAs including miR-16-5p and miR-29a-3p were also stably expressed (CV < 5%). Thus, miR-16-5p and miR-29a-3p are both strong housekeeper candidates. Their Normfinder stability values calculated across the primary tumor and metastases subgroup indicate that miR-29a-3p can be considered as the strongest housekeeper in a cohort with mainly samples from primary tumors, whereas miR-16-5p might perform better in a metastatic sample enriched cohort.
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Abstract
MicroRNAs (miRNAs) are small, highly conserved noncoding RNA molecules involved in the regulation of gene expression. Since each miRNA regulates the expression of hundreds of target mRNAs, miRNAs could function as master coordinators, efficiently regulating fundamental cellular processes, including proliferation, apoptosis, and development. Furthermore, miRNAs may provide useful diagnostic and therapeutic targets in a variety of diseases. However, miRNA expression profiling is essential for the investigation of the biological functions and clinical applications of miRNAs. Therefore, in this chapter, we review and discuss commonly used techniques for miRNAs profiling, as well as their advantages and restrictions.
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Affiliation(s)
- Lu Gao
- Department of Pathology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 7th Floor, Baltimore, MD, 21201-1192, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 7th Floor, Baltimore, MD, 21201-1192, USA.
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8
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Kebschull M, Papapanou PN. Mini but mighty: microRNAs in the pathobiology of periodontal disease. Periodontol 2000 2015; 69:201-20. [PMID: 26252410 PMCID: PMC4530521 DOI: 10.1111/prd.12095] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2015] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are a family of small, noncoding RNA molecules that negatively regulate protein expression either by inhibiting initiation of the translation of mRNA or by inducing the degradation of mRNA molecules. Accumulating evidence suggests that miRNA-mediated repression of protein expression is of paramount importance in a broad range of physiologic and pathologic conditions. In particular, miRNA-induced dysregulation of molecular processes involved in inflammatory pathways has been shown to contribute to the development of chronic inflammatory diseases. In this review, first of all we provide an overview of miRNA biogenesis, the main mechanisms of action and the miRNA profiling tools currently available. Then, we summarize the available evidence supporting a specific role for miRNAs in the pathobiology of periodontitis. Based on a review of available data on the differential expression of miRNAs in gingival tissues in states of periodontal health and disease, we address specific roles for miRNAs in molecular and cellular pathways causally linked to periodontitis. Our review points to several lines of evidence suggesting the involvement of miRNAs in periodontal tissue homeostasis and pathology. Although the intricate regulatory networks affected by miRNA function are still incompletely mapped, further utilization of systems biology tools is expected to enhance our understanding of the pathobiology of periodontitis.
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Affiliation(s)
- Moritz Kebschull
- Associate Professor of Dental Medicine, Consultant, Department of Periodontology, Operative and Preventive Dentistry, University of Bonn, Welschnonnenstr. 17, 53111 Bonn, Germany, Tel: +49-228-28722-007,
| | - Panos N. Papapanou
- Professor of Dental Medicine, Director, Division of Periodontics, Chair, Section of Oral and Diagnostic Sciences, Columbia University College of Dental Medicine, 630 West 168 Street, PH-7E-110, New York, NY 10032, USA, Tel: +1-212-342-3008, Fax: +1-212-305-9313,
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9
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Abstract
Molecular diagnostics comprises a main analytical division in clinical laboratory diagnostics. The analysis of RNA or DNA helps to diagnose infectious diseases and identify genetic determined disorders or even cancer. Starting from mono-parametric tests within the last years, technologies have evolved that allow for the detection of many parameters in parallel, e.g., by using multiplex nucleic acid amplification techniques, microarrays, or next-generation sequencing technologies. The introduction of closed-tube systems as well as lab-on-a-chip devices further resulted in a higher automation degree with a reduced contamination risk. These applications complement or even stepwise replace classical methods in clinical microbiology like virus cultures, resistance determination, microscopic and metabolic analyses, as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel biomarkers. This article provides an overview of microarrays as diagnostics devices and research tools. Introduced in 1995 for transcription analysis, microarrays are used today to detect several different biomolecules like DNA, RNA, miRNA, and proteins among others. Mainly used in research, some microarrays also found their way to clinical diagnostics. Further, closed lab-on-a-chip devices that use DNA microarrays as detection tools are discussed, and additionally, an outlook toward applications of next-generation sequencing tools in diagnostics will be given.
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Affiliation(s)
- Volker A. Erdmann
- Free University of Berlin Institute of Chemistry/Biochemistry, Thielallee 63, Berlin Germany
| | - Stefan Jurga
- Nanobiomedical Center, Adam Mickiewicz University, Umultowska 85 Poznań, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Z. Noskowskiego 12/14 Poznań, Poland
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10
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MicroRNA expression profiling of PPD-B stimulated PBMC from M. bovis-challenged unvaccinated and BCG vaccinated cattle. Vaccine 2014; 32:5839-44. [DOI: 10.1016/j.vaccine.2014.07.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/09/2014] [Accepted: 07/09/2014] [Indexed: 12/13/2022]
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11
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Differential expression of miR-139, miR-486 and miR-21 in breast cancer patients sub-classified according to lymph node status. Cell Oncol (Dordr) 2014; 37:215-27. [DOI: 10.1007/s13402-014-0176-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2014] [Indexed: 12/31/2022] Open
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12
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Li H, Xie S, Liu M, Chen Z, Liu X, Wang L, Li D, Zhou Y. The clinical significance of downregulation of mir-124-3p, mir-146a-5p, mir-155-5p and mir-335-5p in gastric cancer tumorigenesis. Int J Oncol 2014; 45:197-208. [PMID: 24805774 DOI: 10.3892/ijo.2014.2415] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/31/2014] [Indexed: 12/26/2022] Open
Abstract
Dysregulated miRNAs in gastric cancer are usually screened by miRNA microarray from clinical samples, however, reports have indicated that results of each miRNA microarray screening are considerably different, and dysregulated miRNAs, especially downregulated miRNAs were contradictory. In view of this, the Human Cancer Pathway Finder miRNA PCR array was applied to compare 7 gastric cancer cell lines AGS, SGC-7901, MKN-45, MKN-28, MGC-803, BCG-823, and HGC-27 with an immortalized normal gastric cell line, GES-1 in cancer pathway-related miRNA expression profile, followed by qPCR verification, the clinical significance of downregulated miRNAs and the Enriched KEGG pathways and GO terms of their target genes were analyzed. Thirty-eight miRNAs were upregulated, and four miRNAs were downregulated in gastric cancer cell lines. Clinical significance of 4 miRNAs including mir-124-3p, mir-146a-5p, mir-155-5p and mir-335-5p in gastric cancer tissue compared with adjacent non-tumor tissues of 58 patients indicated that the low-expression group of mir-124-3p, mir-146a-5p, mir-155-5p and mir-335-5p showed more extensive lymph node metastasis, lymphatic invasion, venous invasion, high-stage Borrmann type, lymphatic invasion and poor differentiation than that of the high-expression groups, respectively (P<0.05; χ² test). Enriched KEGG pathway analyses showed that most of the targeted genes of the 4 miRNAs concentrated on 37 signaling pathways, and were involved in the same pathways related to cancer. Enriched GO terms showed that targeted genes of the 4 miRNAs concentrated on 339 terms, 24 of 339 terms are associated with cancer tumorigenesis. The Human Cancer Pathway Finder miRNA PCR array could be used to screen dysregulated miRNAs effectively, and 4 screened miRNAs, mir-124-3p, mir-146a-5p, mir-155-5p and mir-335-5p were found to be downregulated in gastric cancer. Clinical significance and bioinformatic analysis on the target genes of these 4 miRNAs indicated that they were deeply involved in tumorigenesis, suggesting roles such as miRNA tumor suppressors in gastric cancer tumorigenesis which could be applied in gastric cancer diagnosis and prognosis.
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Affiliation(s)
- Hailong Li
- Division of Gastroenterology and Hepatology, First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Shoupin Xie
- First People's Hospital of Lanzhou, Lanzhou, Gansu 730050, P.R. China
| | - Min Liu
- Division of Gastroenterology and Hepatology, First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Zhaofeng Chen
- Division of Gastroenterology and Hepatology, First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Xiaojun Liu
- Division of Gastroenterology and Hepatology, First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Li Wang
- Division of Gastroenterology and Hepatology, First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Dayan Li
- Division of Gastroenterology and Hepatology, First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Yongning Zhou
- Division of Gastroenterology and Hepatology, First Hospital of Lanzhou University, Lanzhou, Gansu 730000, P.R. China
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Abstract
As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in miRNA-related research demands global miRNA expression profiling on large numbers of samples. We describe here a robust protocol that supports high-throughput sample labeling and detection on hundreds of samples simultaneously. This method employs 96-well-based miRNA capturing from total RNA samples and on-site biochemical reactions, coupled with bead-based detection in 96-well format for hundreds of miRNAs per sample. With low-cost, high-throughput, high detection specificity, and flexibility to profile both small and large numbers of samples, this protocol can be adapted in a wide range of laboratory settings.
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Affiliation(s)
- Yanwen Guo
- Department of Genetics, Yale Stem Cell Center, Yale University, 10 Amistad Street, New Haven, CT, 06520-8005, USA
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The application of high-throughput analyses to cancer diagnosis and prognosis. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Alvarez-Mora MI, Rodriguez-Revenga L, Madrigal I, Torres-Silva F, Mateu-Huertas E, Lizano E, Friedländer MR, Martí E, Estivill X, Milà M. MicroRNA expression profiling in blood from fragile X-associated tremor/ataxia syndrome patients. GENES BRAIN AND BEHAVIOR 2013; 12:595-603. [PMID: 23790110 DOI: 10.1111/gbb.12061] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 06/12/2013] [Accepted: 06/21/2013] [Indexed: 01/05/2023]
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder associated with FMR1 gene premutation alleles (55-200 CGG repeats). Fragile X-associated tremor/ataxia syndrome clinical core features include action tremor, gait ataxia, cognitive deficits progressing to dementia, and frequently parkinsonism. Although the pathogenic molecular mechanism of FXTAS is not completely understood, the restriction of the phenotype to the FMR1 premutation range has given rise to a model based on a RNA toxic gain-of-function. Since the identification of the first microRNAs (miRNAs) and their role in normal development, several studies have associated them with neurodegenerative diseases such as Parkinson, Alzheimer and Huntington diseases, suggesting that they play a key role in brain development, as well as in its morphogenesis. Herein, we present the characterization of miRNA expression profiles in FXTAS male patients using deep sequencing-based technologies and microarray technology. Deep sequencing analysis evidenced 83 miRNAs that were significantly deregulated whereas microarray analysis showed 31. When comparing these results, 14 miRNAs were found deregulated in FXTAS patients. MiR-424 and miR-574-3p showed significant fold change adjusted P-values in both platforms in FXTAS patients. MiR-424 has been founded substantially and specifically enriched in human cerebral cortical white matter of Alzheimer disease patients, which, together with cerebral atrophy, is a prominent imaging finding in individuals with FXTAS. The study provides the first systematic evidence of differential miRNA expression changes in FXTAS blood samples. Although further studies are necessary to better characterize the miRNA function in FXTAS disorder, our results suggest that they might contribute to its pathogenesis.
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Affiliation(s)
- M I Alvarez-Mora
- Biochemistry and Molecular Genetics Department, Hospital Clínic, Barcelona, Spain
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