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Zhang J, Xu S, Liu J, Liu T, Fan Z, Zhou Y, Basnet J, Zhang L, Li X, Yang J, Xing X. Construction of a ceRNA network and screening of potential biomarkers and molecular targets in male smokers with chronic obstructive pulmonary disease. Front Genet 2024; 15:1376721. [PMID: 38933922 PMCID: PMC11199688 DOI: 10.3389/fgene.2024.1376721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Background Circular RNAs (circRNAs) play an important role in the occurrence and development of diseases. However, the role of circRNAs in male smokers with chronic obstructive pulmonary disease (COPD) remains unclear. Methods Stable COPD patients and healthy controls were recruited. Peripheral blood mononuclear cells (PBMCs) were extracted. After high-throughput RNA sequencing (RNA-Seq) of PBMCs, a bioinformatics method was used to analyse differentially expressed (DE) circRNAs (DEcircRNAs) and mRNAs (DEmRNAs). Results Total of 114 DEcircRNAs and 58 DEmRNAs were identified. Functional enrichment analysis showed that processes related to COPD include the regulation of interleukin (IL)-18, IL-5 and the NLRP3 inflammasome; differentiation of T helper type 1 (Th1), Th2, and Th17 cells, and the AMPK, Wnt, JAK-STAT, and PI3K-Akt signalling pathways. In the protein-protein interaction (PPI) network, the core genes were MYO16, MYL4, SCN4A, NRCAM, HMCN1, MYOM2, and IQSEC3. Small-molecule prediction results revealed potential drugs for the COPD treatment. Additionally, the circRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) regulatory network was constructed. Conclusion This study identified a set of dysregulated circRNAs and mRNAs and revealed potentially important genes, pathways, new small-molecule drugs and ceRNA regulatory networks in male smokers with COPD. These circRNAs might be prospective biomarkers or potential molecular targets of the ceRNA mechanism for COPD.
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Affiliation(s)
- Jihua Zhang
- Department of Respiratory Medicine, The People’s Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Shuanglan Xu
- Key Laboratory of Respiratory Disease Research of Department of Education of Yunnan Province, Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jie Liu
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Ting Liu
- Key Laboratory of Respiratory Disease Research of Department of Education of Yunnan Province, Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- Graduate School, Kunming Medical University, Kunming, Yunnan, China
| | - Zeqin Fan
- Key Laboratory of Respiratory Disease Research of Department of Education of Yunnan Province, Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yunchun Zhou
- Department of Respiratory Medicine, The People’s Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Jorina Basnet
- Key Laboratory of Respiratory Disease Research of Department of Education of Yunnan Province, Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Liqiong Zhang
- Department of Respiratory Medicine, The People’s Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Xiao Li
- Department of Respiratory Medicine, The People’s Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan, China
| | - Jiao Yang
- First Department of Respiratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Xiqian Xing
- Key Laboratory of Respiratory Disease Research of Department of Education of Yunnan Province, Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People’s Hospital of Yunnan Province, Kunming, Yunnan, China
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Martino E, D’Onofrio N, Balestrieri A, Colloca A, Anastasio C, Sardu C, Marfella R, Campanile G, Balestrieri ML. Dietary Epigenetic Modulators: Unravelling the Still-Controversial Benefits of miRNAs in Nutrition and Disease. Nutrients 2024; 16:160. [PMID: 38201989 PMCID: PMC10780859 DOI: 10.3390/nu16010160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
In the context of nutrient-driven epigenetic alterations, food-derived miRNAs can be absorbed into the circulatory system and organs of recipients, especially humans, and potentially contribute to modulating health and diseases. Evidence suggests that food uptake, by carrying exogenous miRNAs (xenomiRNAs), regulates the individual miRNA profile, modifying the redox homeostasis and inflammatory conditions underlying pathological processes, such as type 2 diabetes mellitus, insulin resistance, metabolic syndrome, and cancer. The capacity of diet to control miRNA levels and the comprehension of the unique characteristics of dietary miRNAs in terms of gene expression regulation show important perspectives as a strategy to control disease susceptibility via epigenetic modifications and refine the clinical outcomes. However, the absorption, stability, availability, and epigenetic roles of dietary miRNAs are intriguing and currently the subject of intense debate; additionally, there is restricted knowledge of their physiological and potential side effects. Within this framework, we provided up-to-date and comprehensive knowledge on dietary miRNAs' potential, discussing the latest advances and controversial issues related to the role of miRNAs in human health and disease as modulators of chronic syndromes.
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Affiliation(s)
- Elisa Martino
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.M.); (A.C.); (C.A.); (M.L.B.)
| | - Nunzia D’Onofrio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.M.); (A.C.); (C.A.); (M.L.B.)
| | - Anna Balestrieri
- Food Safety Department, Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Antonino Colloca
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.M.); (A.C.); (C.A.); (M.L.B.)
| | - Camilla Anastasio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.M.); (A.C.); (C.A.); (M.L.B.)
| | - Celestino Sardu
- Department of Advanced Clinical and Surgical Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (C.S.); (R.M.)
| | - Raffaele Marfella
- Department of Advanced Clinical and Surgical Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (C.S.); (R.M.)
| | - Giuseppe Campanile
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy;
| | - Maria Luisa Balestrieri
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (E.M.); (A.C.); (C.A.); (M.L.B.)
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Khokhar M, Roy D, Bajpai NK, Bohra GK, Yadav D, Sharma P, Purohit P. Metformin mediates MicroRNA-21 regulated circulating matrix metalloproteinase-9 in diabetic nephropathy: an in-silico and clinical study. Arch Physiol Biochem 2023; 129:1200-1210. [PMID: 34087084 DOI: 10.1080/13813455.2021.1922457] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/22/2021] [Indexed: 01/05/2023]
Abstract
Metformin is commonly used as an oral hypoglycaemic agent in type 2 diabetes mellitus (T2DM). MicroRNA-21 is widely studied in diabetic and diabetic nephropathy (DN) patients. Matrix metalloproteinase-9 (MMP9) is involved in extracellular matrix degradation and tissue repair processes. However, the effect of metformin administration on hsa-miR-21-5p and MMP9 has not been evaluated in T2DM and DN patients. The study subjects were divided into three groups (Healthy controls = 36, T2DM = 38, DN = 35). Anthropometric measurements were taken and biochemical tests were carried out on fasting blood samples. Reverse transcriptase PCR was employed for whole blood gene expression analysis of hsa-miR-21-5p and MMP9. Bioinformatics analyses including drug-gene interaction, protein-protein interaction, functional enrichment analyses and co-expression networks were performed. In the present study, MMP9 and hsa-miR-21-5p levels were downregulated and upregulated respectively in T2DM and DN patients when compared with healthy controls. However, in metformin-treated group, a downregulation of hsa-miR-21-5p and upregulation of MMP9 was observed. In-silico analysis revealed the target genes involved in the miR-21 and MMP9 interaction network. Metformin directly targets miR-21 and regulates MMP9 expression in T2DM patients, influencing the pathogenesis of DN.HighlightsMMP-9 and hsa-miR-21-5p were downregulated and upregulated respectively in T2DM and DN patients in a Western Indian population.The patients treated with metformin showed downregulation of hsa-miR-21-5p and upregulation of MMP9.In-silico analysis revealed MMP-9 as well as PTEN to be targets of hsa-miR-21-5p.Metformin regulates MMP9 expression in T2DM and DN patient populations through hsa-miR-21-5p.
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Affiliation(s)
- Manoj Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005, India
| | - Dipayan Roy
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005, India
| | - Nitin Kumar Bajpai
- Department of Nephrology, All India Institute of Medical Sciences, Jodhpur, 342005, India
| | - Gopal Krishna Bohra
- Department of General Medicine, All India Institute of Medical Sciences, Jodhpur, 342005, India
| | - Dharamveer Yadav
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005, India
| | - Praveen Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005, India
| | - Purvi Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, 342005, India
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Zhou M, He X, Mei C, Ou C. Exosome derived from tumor-associated macrophages: biogenesis, functions, and therapeutic implications in human cancers. Biomark Res 2023; 11:100. [PMID: 37981718 PMCID: PMC10658727 DOI: 10.1186/s40364-023-00538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023] Open
Abstract
Tumor-associated macrophages (TAMs), one of the most abundant immune cell types in the tumor microenvironment (TME), account for approximately 50% of the local hematopoietic cells. TAMs play an important role in tumorigenesis and tumor development through crosstalk between various immune cells and cytokines in the TME. Exosomes are small extracellular vesicles with a diameter of 50-150 nm, that can transfer biological information (e.g., proteins, nucleic acids, and lipids) from secretory cells to recipient cells through the circulatory system, thereby influencing the progression of various human diseases, including cancer. Recent studies have suggested that TAMs-derived exosomes play crucial roles in malignant cell proliferation, invasion, metastasis, angiogenesis, immune responses, drug resistance, and tumor metabolic reprogramming. TAMs-derived exosomes have the potential to be targeted for tumor therapy. In addition, the abnormal expression of non-coding RNAs and proteins in TAMs-derived exosomes is closely related to the clinicopathological features of patients with cancer, and these exosomes are expected to become new liquid biopsy markers for the early diagnosis, prognosis, and monitoring of tumors. In this review, we explored the role of TAMs-derived exosomes in tumorigenesis to provide new diagnostic biomarkers and therapeutic targets for cancer prevention.
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Affiliation(s)
- Manli Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Cheng Mei
- Department of Blood Transfusion, Xiangya Hospital, Clinical Transfusion Research Center, Central South University, Changsha, 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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5
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Ahmadi M, Najari-Hanjani P, Ghaffarnia R, Ghaderian SMH, Mousavi P, Ghafouri-Fard S. The hsa-miR-3613-5p, a potential oncogene correlated with diagnostic and prognostic merits in kidney renal clear cell carcinoma. Pathol Res Pract 2023; 251:154903. [PMID: 37879147 DOI: 10.1016/j.prp.2023.154903] [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: 08/13/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
MicroRNA-3613 (hsa-miR-3613-5p), a biomarker with a dual role as an oncogenic or tumor suppressor, is associated with different types of cancer. This study aimed to determine the correlation between the hsa-miR-3613-5p gene expression and Kidney renal clear cell carcinoma (KIRC). Utilizing several bioinformatics tools, we examined the expression level and clinicopathological value of hsa-miR-3613-5p in patients with KIRC compared to normal tissues. Other bioinformatic measures, including survival analysis, diagnostic merit of hsa-miR-3613-5p, downstream target prediction, potential upstream lncRNAs, network construction, and functional enrichment analysis of hsa-miR-3613-5p, were performed. We observed that overexpression of hsa-miR-3613-5p in KIRC tissues had valuable diagnostic merit and was significantly correlated with the poor overall survival of KIRC patients. We also realized a correlation between abnormal expression of hsa-miR-3613-5p and several clinical parameters such as pathological stage, race, age, and histological grades in patients with KIRC. Moreover, we constructed the most potential regulatory network of hsa-miR-3613-5p in KIRC with 17 different axes, including four pseudogenes, two lncRNAs, and three mRNAs. Besides, we uncovered six variants in the mature form of hsa-miR-3613-5p. Finally, pathway enrichment analysis demonstrated that the top-ranked pathways for hsa-miR-3613-5p are cell cycle, cell adhesion molecules (CAMs), and hepatocellular carcinoma pathways. The present report suggests that the higher expression of hsa-miR-3613-5p is associated with the progression of KIRC. Therefore, it may be considered a valuable indicator for the early detection, risk stratification, and targeted treatment of patients with KIRC.
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Affiliation(s)
- Mohsen Ahmadi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parisa Najari-Hanjani
- Department of Genetics, Faculty of Advanced Technologies in Medicine, Golestan University of Medical Science, Gorgan, Iran
| | - Roya Ghaffarnia
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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6
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DeSouza NR, Quaranto D, Carnazza M, Jarboe T, Tiwari RK, Geliebter J. Interactome of Long Non-Coding RNAs: Transcriptomic Expression Patterns and Shaping Cancer Cell Phenotypes. Int J Mol Sci 2023; 24:9914. [PMID: 37373059 DOI: 10.3390/ijms24129914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
RNA biology has gained extensive recognition in the last two decades due to the identification of novel transcriptomic elements and molecular functions. Cancer arises, in part, due to the accumulation of mutations that greatly contribute to genomic instability. However, the identification of differential gene expression patterns of wild-type loci has exceeded the boundaries of mutational study and has significantly contributed to the identification of molecular mechanisms that drive carcinogenic transformation. Non-coding RNA molecules have provided a novel avenue of exploration, providing additional routes for evaluating genomic and epigenomic regulation. Of particular focus, long non-coding RNA molecule expression has been demonstrated to govern and direct cellular activity, thus evidencing a correlation between aberrant long non-coding RNA expression and the pathological transformation of cells. lncRNA classification, structure, function, and therapeutic utilization have expanded cancer studies and molecular targeting, and understanding the lncRNA interactome aids in defining the unique transcriptomic signatures of cancer cell phenotypes.
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Affiliation(s)
- Nicole R DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Michelle Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
| | - Raj K Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10591, USA
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Abstract
MicroRNAs exert their effects in the context of gene regulatory networks. The recent development of high-throughput experimental approaches and the growing availability of gene expression data have permitted comprehensive functional studies of miRNAs. However, the data interpretation is often challenging due to the fact that miRNAs not only act cooperatively with other miRNAs but also participate in complex networks by interacting with other functional elements, including non-coding RNAs or transcription factors that often have extensive effects on cell biology. This chapter provides detailed practical procedures on how to use miRNet 2.0 ( https://www.mirnet.ca ) to perform miRNA regulatory network analytics to gain functional insights.
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Affiliation(s)
- Le Chang
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jianguo Xia
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Institute of Parasitology, McGill University, Montreal, QC, Canada.
- Department of Animal Science, McGill University, Montreal, QC, Canada.
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Schmitz U. Overview of Computational and Experimental Methods to Identify Tissue-Specific MicroRNA Targets. Methods Mol Biol 2023; 2630:155-177. [PMID: 36689183 DOI: 10.1007/978-1-0716-2982-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As ubiquitous posttranscriptional regulators of gene expression, microRNAs (miRNAs) play key roles in cell physiology and function across taxa. In the last two decades, we have gained a good understanding about miRNA biogenesis pathways, modes of action, and consequences of miRNA-mediated gene regulation. More recently, research has focused on exploring causes for miRNA dysregulation, miRNA-mediated crosstalk between genes and signaling pathways, and the role of miRNAs in disease.This chapter discusses methods for the identification of miRNA-target interactions and causes for tissue-specific miRNA-target regulation. Computational approaches for predicting miRNA target sites and assessing tissue-specific target regulation are discussed. Moreover, there is an emphasis on features that affect miRNA target recognition and how high-throughput sequencing protocols can help in assessing miRNA-mediated gene regulation on a genome-wide scale. In addition, this chapter introduces some experimental approaches for the validation of miRNA targets as well as web-based resources sharing predicted and validated miRNA-target interactions.
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Affiliation(s)
- Ulf Schmitz
- Department of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
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Network analysis of long non-coding RNA expression profiles in common warts. Heliyon 2022; 8:e11790. [DOI: 10.1016/j.heliyon.2022.e11790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 04/15/2022] [Accepted: 11/14/2022] [Indexed: 11/20/2022] Open
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Danggui Buxue Decoction Ameliorates Idiopathic Pulmonary Fibrosis through MicroRNA and Messenger RNA Regulatory Network. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3439656. [PMID: 35518349 PMCID: PMC9064538 DOI: 10.1155/2022/3439656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/25/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To develop a putative microRNA (miRNA) and messenger RNA (mRNA) regulatory network of Danggui Buxue decoction's (DGBXD) amelioration of idiopathic pulmonary fibrosis (IPF). METHODS The Gene Expression Omnibus (GEO) database was used to identify differentially expressed miRNAs (DE-miRNAs) and differentially expressed mRNAs (DE-mRNAs). Using miRNet, the predicted target genes of identified DE-miRNAs were estimated, and then the target genes of DE-miRNAs in IPF were comprehensively examined. The Enrichr database was used to conduct functional enrichment and pathway enrichment. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was employed to obtain the target genes of DGBXD as well as active compounds. A putative miRNA-mRNA regulatory network of DGBXD acting on IPF was developed by intersecting the target genes of DGBXD with the DE-miRNA target genes in IPF. A bleomycin-induced mouse model was established and used to perform histopathology as well as real-time quantitative polymerase chain reaction (qRT-PCR) analyses of some miRNA-mRNA pairs. RESULTS Fourteen upmodulated DE-miRNAs and six downmodulated DE-miRNAs were screened. The downstream target genes of upmodulated and downmodulated DE-miRNAs were predicted. Subsequently, 1160 upmodulated DE-mRNAs and 1427 downmodulated DE-mRNAs were identified. Then, target genes of DE-miRNAs comprising 49 downmodulated and 53 upmodulated target genes were further screened to perform functional enrichment and pathway enrichment analyses. Subsequently, 196 target genes of DGBXD were obtained from TCMSP, with six downregulated target genes and six upregulated target genes of DGBXD acting on IPF being identified. A promising miRNA-mRNA regulatory network of DGBXD acting on IPF was developed in this study. Moreover, mir-493 together with its target gene Olr1 and mir-338 together with Hif1a were further validated by qRT-PCR. CONCLUSION This study proposed detailed possible processes of miRNA-mRNA modulatory axis in IPF and constructed a prospective IPF-related miRNA-mRNA modulatory network with the aim of alleviating IPF with DGBXD.
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11
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Liu XS, Kui XY, Gao Y, Chen XQ, Zeng J, Liu XY, Zhang Y, Zhang YH, Pei ZJ. Comprehensive Analysis of YTHDF1 Immune Infiltrates and ceRNA in Human Esophageal Carcinoma. Front Genet 2022; 13:835265. [PMID: 35401696 PMCID: PMC8983832 DOI: 10.3389/fgene.2022.835265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/21/2022] [Indexed: 12/13/2022] Open
Abstract
Background: YTHDF1 is highly expressed in multiple tumors and affects tumor progression. However, there are only a few comprehensive studies on the analysis of YTHDF1 in esophageal cancer.Methods: We analyzed YTHDF1 expression in pan-cancer by comparing both the GEPIA and TCGA cohorts, and further verified the differences in YTHDF1 expression between the ESCA and normal groups by the GEO ESCA cohort and in vitro experiments. The correlation of YTHDF1 expression and the clinical characteristics of ESCA patients was analyzed using the TCGA ESCA clinical data. The GO and KEGG enrichment analyses of the YTHDF1 coexpressed genes were completed by bioinformatics analysis, and the GGI and PPI were constructed for the YTHDF1, respectively. The relationship between YTHDF1 expression and the infiltration of ESCA immune cells was analyzed by using the TIMER database and the TCGA ESCA cohort. The relationships between YTHDF1 expression levels and glycolysis and ferroptosis-related genes were analyzed using the TCGA and GEPIA ESCA cohorts. Finally, the ceRNA network that may be involved in YTHDF1 in ESCA was predicted and constructed through a variety of databases.Results: YTHDF1 was overexpressed in various cancers, and in vitro experiments confirmed that YTHDF1 expression was higher in ESCA samples than in normal samples. The expression of YTHDF1 has some accuracy in predicting the tumor outcome. Expression of YTHDF1 was significantly associated with multiple clinical features in ESCA patients. GO and KEGG enrichment analyses indicated that YTHDF1 coexpressed genes involved multiple biological functions. There is a potential association between YTHDF1 expression and multiple immune cell infiltration, glycolysis, and ferroptosis-related genes in ESCA. YTHDF1 may be involved in multiple ceRNA regulatory networks in ESCA, including PAXIP1-AS1/hsa-miR-376c-3p/YTHDF1 axis, THUMPD3-AS1/hsa-miR-655-3p/YTHDF1 axis, and SNHG20/hsa-miR-655-3p/YTHDF1 axis, respectively.Conclusion: YTHDF1 can serve as a biomarker of ESCA, related to the immune cell infiltration of ESCA, regulation of glycolysis and ferroptosis, and the ceRNA regulatory network.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Xu-Sheng Liu, ; Zhi-Jun Pei,
| | - Xue-Yan Kui
- Postgraduate Training Basement of Jinzhou Medical University, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yan Gao
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | | | - Jing Zeng
- Department of Infection Control, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Xiao-Yu Liu
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yu Zhang
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yao-Hua Zhang
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- Hubei Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Xu-Sheng Liu, ; Zhi-Jun Pei,
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Zhang Y, Jiang W, Xia Q, Lin J, Xu J, Zhang S, Tian L, Han X. Construction of a potential microRNA and messenger RNA regulatory network of acute lung injury in mice. Sci Rep 2022; 12:777. [PMID: 35039607 PMCID: PMC8763866 DOI: 10.1038/s41598-022-04800-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/03/2022] [Indexed: 12/23/2022] Open
Abstract
Acute lung injury (ALI) is a life-threatening clinical condition associated with critically ill patients, and the construction of potential microRNA (miRNA) and messenger RNA (mRNA) regulatory networks will help to fully elucidate its underlying molecular mechanisms. First, we screened fifteen upregulated differentially expressed miRNAs (DE-miRNAs) and six downregulated DE-miRNAs from the Gene Expression Omnibus (GEO) database. Then, the predicted target genes of the upregulated and downregulated DE-miRNAs were identified from the miRNet database. Subsequently, differentially expressed mRNAs (DE-mRNAs) were identified from the GEO database and subjected to combined analysis with the predicted DE-miRNA target genes. Eleven target genes of the upregulated DE-miRNAs and one target gene of the downregulated DE-miRNAs were screened out. To further validate the prediction results, we randomly selected a dataset for subsequent analysis and found some accurate potential miRNA-mRNA regulatory axes, including mmu-mir-7b-5p-Gria1, mmu-mir-486a-5p-Shc4 and mmu-mir-486b-5p-Shc4 pairs. Finally, mir-7b and its target gene Gria1 and mir-486b and its target gene Shc4 were further validated in a bleomycin-induced ALI mouse model. We established a potential miRNA-mRNA regulatory network of ALI in mice, which may provide a basis for basic and clinical research on ALI and advance the available treatment options.
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Affiliation(s)
- Yufeng Zhang
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, 214400, China
| | - Weilong Jiang
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, 214400, China
| | - Qingqing Xia
- Department of Respiratory Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, 214400, China
| | - Jinfeng Lin
- Department of Critical Care Medicine, Nantong Third People's Hospital, Nantong University, Nantong, 226001, China
| | - Junxian Xu
- Department of Critical Care Medicine, Nantong Third People's Hospital, Nantong University, Nantong, 226001, China
| | - Suyan Zhang
- Department of Critical Care Medicine, Nantong Third People's Hospital, Nantong University, Nantong, 226001, China
| | - Lijun Tian
- Department of Critical Care Medicine, Nantong Third People's Hospital, Nantong University, Nantong, 226001, China.
| | - Xudong Han
- Department of Critical Care Medicine, Nantong Third People's Hospital, Nantong University, Nantong, 226001, China.
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13
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Cione E, Cannataro R, Gallelli L, De Sarro G, Caroleo MC. Exosome microRNAs in Metabolic Syndrome as Tools for the Early Monitoring of Diabetes and Possible Therapeutic Options. Pharmaceuticals (Basel) 2021; 14:ph14121257. [PMID: 34959658 PMCID: PMC8706321 DOI: 10.3390/ph14121257] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Exosomes are nano-sized extracellular vesicles produced and released by almost all cell types. They play an essential role in cell-cell communications by delivering cellular bioactive compounds such as functional proteins, metabolites, and nucleic acids, including microRNA, to recipient cells. Thus, they are involved in various physio-pathological conditions. Exosome-miRNAs are associated with numerous diseases, including type 2 diabetes, a complex multifactorial metabolic disorder linked to obesity. In addition, exosome-miRNAs are emerging as essential regulators in the progression of diabetes, principally for pancreatic β-cell injury and insulin resistance. Here, we have clustered the recent findings concerning exosome-miRNAs associated with β-cell dysfunction to provide a novel approach for the early diagnosis and therapy of diabetes.
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Affiliation(s)
- Erika Cione
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Ed. Polifunzionale, Arcavacata di Rende, 87036 Rende, CS, Italy;
- GalaScreen Laboratories, University of Calabria, Ed. Polifunzionale, Arcavacata di Rende, 87036 Rende, CS, Italy;
- Correspondence:
| | - Roberto Cannataro
- GalaScreen Laboratories, University of Calabria, Ed. Polifunzionale, Arcavacata di Rende, 87036 Rende, CS, Italy;
| | - Luca Gallelli
- Department of Health Science, University of Catanzaro and Operative Unit of Clinical Pharmacology and Pharmacovigilance, Mater Domini Hospital, 88100 Catanzaro, CZ, Italy; (L.G.); (G.D.S.)
| | - Giovambattista De Sarro
- Department of Health Science, University of Catanzaro and Operative Unit of Clinical Pharmacology and Pharmacovigilance, Mater Domini Hospital, 88100 Catanzaro, CZ, Italy; (L.G.); (G.D.S.)
| | - Maria Cristina Caroleo
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Ed. Polifunzionale, Arcavacata di Rende, 87036 Rende, CS, Italy;
- GalaScreen Laboratories, University of Calabria, Ed. Polifunzionale, Arcavacata di Rende, 87036 Rende, CS, Italy;
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14
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Sharma C, Purohit P, Khokhar M, Modi A, Singh P, Shekhar S, Sharma S, Gothwal M, Sharma P. A clinical and in-silico study exploring the association of CASP-3, NF-kB, miR-187, and miR-146 in pre-eclampsia. Hypertens Pregnancy 2021; 40:288-302. [PMID: 34727826 DOI: 10.1080/10641955.2021.1983592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Apoptosis is involved in pathogenesis of Pre-eclampsia (PE), further research is needed to determine its molecular mechanism. METHODS The study recruited two groups (controls; 09, PE; 11). Biochemical tests, RT-PCR and ELISA were employed for analysis of genes and MicroRNAs (miRNA). Bioinformatics tools were employed for interactomics analysis. RESULTS There was increased apoptosis in maternal placental tissue (MPT) and Maternal Blood Cells (MBC) as demonstrated by expression of CASP3 and NF-κB1. miR-146-5p and 187-5p were downregulated in MBC and MPT but upregulated in fetal placental tissue (FPT).. DISCUSSION An increased apoptosis in MBC and MPT is a significant contributory factor for PE in pregnancy, while FPT is immune to the aforementioned effects.
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Affiliation(s)
- Charu Sharma
- Department of Obstetrics & Gynecology, AIIMS Jodhpur, Jodhpur, India
| | - Purvi Purohit
- Department of Biochemistry, AIIMS Jodhpur, Jodhpur, India
| | - Manoj Khokhar
- Department of Biochemistry, AIIMS Jodhpur, Jodhpur, India
| | - Anupama Modi
- Department of Biochemistry, AIIMS Jodhpur, Jodhpur, India
| | - Pratibha Singh
- Department of Obstetrics & Gynecology, AIIMS Jodhpur, Jodhpur, India
| | - Shashank Shekhar
- Department of Obstetrics & Gynecology, AIIMS Jodhpur, Jodhpur, India
| | - Shailja Sharma
- Department of Biochemistry, AIIMS Jodhpur, Jodhpur, India
| | - Meenakshi Gothwal
- Department of Obstetrics & Gynecology, AIIMS Jodhpur, Jodhpur, India
| | - Praveen Sharma
- Department of Biochemistry, AIIMS Jodhpur, Jodhpur, India
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15
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Dragomir MP, Knutsen E, Calin GA. Classical and noncanonical functions of miRNAs in cancers. Trends Genet 2021; 38:379-394. [PMID: 34728089 DOI: 10.1016/j.tig.2021.10.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Alterations in microRNAs (miRNAs) expression are causative in the initiation and progression of human cancers. The molecular events responsible for the widespread differential expression of miRNAs in malignancy are exemplified by their location in cancer-associated genomic regions, epigenetic mechanisms, transcriptional dysregulation, chemical modifications and editing, and alterations in miRNA biogenesis proteins. The classical miRNA function is synonymous with post-transcriptional repression of target protein genes. However, several studies have reported miRNAs functioning outside this paradigm and some of these novel modes of regulation of gene expression have been implicated in cancers. Here, we summarize key aspects of miRNA involvement in cancer, with a special focus on these lesser-studied mechanisms of action.
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Affiliation(s)
- Mihnea P Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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16
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Luo Y, Li H, Huang H, Xue L, Li H, Liu L, Fu H. Integrated analysis of ceRNA network in hepatocellular carcinoma using bioinformatics analysis. Medicine (Baltimore) 2021; 100:e26194. [PMID: 34087888 PMCID: PMC8183720 DOI: 10.1097/md.0000000000026194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 05/13/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) can work as microRNA (miRNA) sponges through a competitive endogenous RNA (ceRNA) mechanism. LncRNAs and miRNAs are important components of competitive endogenous binding, and their expression imbalance in hepatocellular carcinoma (HCC) is closely related to tumor development, diagnosis, and prognosis. This study explored the potential impact of the ceRNA regulatory network in HCC on the prognosis of HCC patients. METHODS We thoroughly researched the differential expression profiles of lncRNAs, miRNAs, and mRNAs from 2 HCC Gene Expression Omnibus datasets (GSE98269 and GSE60502). Then, a dysregulated ceRNA network was constructed by bioinformatics. In addition, hub genes in the ceRNA network were screened by Cytoscape, these hub genes functional analysis was performed by gene set enrichment analysis, and the expression of these hub genes in tumors and their correlation with patient prognosis were verified with Gene Expression Profiling Interactive Analysis. RESULTS A ceRNA network was successfully constructed in this study including 4 differentially expressed (DE) lncRNAs, 7 DEmiRNAs, and 166 DEmRNAs. Importantly, 4 core genes (CCNA2, CHEK1, FOXM1, and MCM2) that were significantly associated with HCC prognosis were identified. CONCLUSIONS Our study provides comprehensive and meaningful insights into HCC tumorigenesis and the underlying molecular mechanisms of ceRNA. Furthermore, the specific ceRNAs can be further used as potential therapeutic targets and prognostic biomarkers for HCC.
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Affiliation(s)
| | | | | | | | | | - Li Liu
- Department of Liver Disease, The 3rd People's Hospital of Kunming, Kunming, Yunnan, China
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17
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He X, Kuang G, Wu Y, Ou C. Emerging roles of exosomal miRNAs in diabetes mellitus. Clin Transl Med 2021; 11:e468. [PMID: 34185424 PMCID: PMC8236118 DOI: 10.1002/ctm2.468] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Exosomes are small extracellular vesicles 40-160 nm in diameter that are secreted by almost all cell types. Exosomes can carry diverse cargo including RNA, DNA, lipids, proteins, and metabolites. Exosomes transfer substances and information between cells by circulating in body fluids and are thus involved in diverse physiological and pathological processes in the human body. Recent studies have closely associated exosomal microRNAs (miRNAs) with various human diseases, including diabetes mellitus (DM), which is a complex multifactorial metabolic disorder disease. Exosomal miRNAs are emerging as pivotal regulators in the progression of DM, mainly in terms of pancreatic β-cell injury and insulin resistance. Exosomal miRNAs are closely associated with DM-associated complications, such as diabetic retinopathy (DR), diabetic nephropathy (DN), and diabetic cardiomyopathy (DCM), etc. Further investigations of the mechanisms of action of exosomal miRNAs and their role in DM will be valuable for the thorough understanding of the physiopathological process of DM. Here, we have summarized recent findings regarding exosomal miRNAs associated with DM to provide a new strategy for identifying potential diagnostic biomarkers and drug targets for the early diagnosis and treatment, respectively, of DM.
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Affiliation(s)
- Xiaoyun He
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunan410008China
- Departments of Ultrasound Imaging, Xiangya HospitalCentral South UniversityChangshaHunan410008China
| | - Gaoyan Kuang
- Department of OrthopedicsThe First Affiliated Hospital of Hunan University of Chinese MedicineChangshaHunan410007China
- Postdoctoral Research WorkstationHinye Pharmaceutical Co. LtdChangshaHunan410331China
| | - Yongrong Wu
- Hunan university of Chinese MedicineChangshaHunan410208China
| | - Chunlin Ou
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunan410008China
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18
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Heinson AI, Woo J, Mukim A, White CH, Moesker B, Bosque A, Spina CA, Woelk CH, Macarthur BD, Beliakova-Bethell N. Micro RNA Targets in HIV Latency: Insights into Novel Layers of Latency Control. AIDS Res Hum Retroviruses 2021; 37:109-121. [PMID: 33045840 PMCID: PMC7876363 DOI: 10.1089/aid.2020.0150] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite the considerable progress that has been made in identifying cellular factors and pathways that contribute to establishment and maintenance of the latent HIV reservoir, it remains the major obstacle to eradicating this virus. Most recently, noncoding genes have been implicated in regulation of HIV expression. In this study, small RNA sequencing was used to profile expression of microRNAs (miRNAs) in a primary CD4+ T cell in vitro model of HIV latency. Previously, we have shown that protein-coding genes dysregulated in this model were enriched for the p53 signaling pathway, which was confirmed experimentally. We further found a link between p53 signaling and dysregulated long noncoding RNAs. In this study, we hypothesized that miRNAs may provide an additional level of regulation of the p53 signaling pathway during HIV latency. Twenty-six miRNAs were identified to be dysregulated in our latency model. A subset of these miRNAs was validated by real-time quantitative polymerase chain reaction. Predicted messenger RNA (mRNA) targets and cellular pathways enriched for mRNA targets were identified using several analytical methods. Our analyses showed that many protein-coding genes and pathways targeted by dysregulated miRNAs have relevance to regulation of HIV expression or establishment of HIV latency. The p53 signaling pathway was found among pathways that were targeted by dysregulated miRNAs at a greater level than expected by chance. This study provides a mechanistic insight into regulation of the p53 pathway through miRNAs that may contribute to the establishment of latency.
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Affiliation(s)
- Ashley I. Heinson
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jeongmin Woo
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Amey Mukim
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California, USA
| | - Cory H. White
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Bastiaan Moesker
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Alberto Bosque
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, District of Columbia, USA
| | - Celsa A. Spina
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California, USA
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | | | - Ben D. Macarthur
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nadejda Beliakova-Bethell
- VA San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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19
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Xu SL, Deng YS, Liu J, Xu SY, Zhao FY, Wei L, Tian YC, Yu CE, Cao B, Huang XX, Yang M, He XH, Bai M, Huang YC, Xing XQ, Yang J. Regulation of circular RNAs act as ceRNA in a hypoxic pulmonary hypertension rat model. Genomics 2020; 113:11-19. [PMID: 33249173 DOI: 10.1016/j.ygeno.2020.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/24/2020] [Accepted: 11/22/2020] [Indexed: 02/05/2023]
Abstract
To explore potential critical genes and identify circular RNAs (circRNAs) that act as the competitive endogenous RNA (ceRNA) in a hypoxic pulmonary hypertension (HPH) rat model. Constructed rat model, and a bioinformatics method was used to analyse differentially expressed (DE) genes and construct a circRNA-miRNA-mRNA ceRNA regulatory network. Then, qRT-PCR was used to verify. The significant DEcircRNAs/DEmiRNAs/DEmRNAs was showed, and a ceRNA network with 8 DEcircRNAs, 9 DEmiRNAs and 46 DEmRNAs were constructed. The functional enrichment suggested the inflammatory response, NF-κB signalling, MAPK cascade and Toll-like receptor were associated with HPH. Further assessment confirmed that circ_002723, circ_008021, circ_016925 and circ_020581 could have a potential ceRNA mechanism by sponging miR-23a or miR-21 to control downstream target gene and be involved in the pathophysiology of HPH. The qRT-PCR validation results were consistent with the RNA-Seq results. This study revealed potentially important genes, pathways and ceRNA regulatory networks in HPH.
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Affiliation(s)
- Shuang-Lan Xu
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Yi-Shu Deng
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Jie Liu
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Shuang-Yan Xu
- Department of Dermatology, The People's Hospital of Yuxi City, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi 653100, Yunan, China
| | - Fang-Yun Zhao
- Department of Pharmacy, Yan'an Hospital Affiliated to Kunming Medical University, Kunming 650051, Yunnan, China
| | - Li Wei
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Ying-Chun Tian
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Cai-E Yu
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Bing Cao
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Xiao-Xian Huang
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Mei Yang
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Xiao-Hua He
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Min Bai
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Yun-Chao Huang
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China
| | - Xi-Qian Xing
- Department of Respiratory Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming 650021, Yunnan, China.
| | - Jiao Yang
- First Department of Respiratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China.
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20
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Chang L, Zhou G, Soufan O, Xia J. miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology. Nucleic Acids Res 2020; 48:W244-W251. [PMID: 32484539 PMCID: PMC7319552 DOI: 10.1093/nar/gkaa467] [Citation(s) in RCA: 419] [Impact Index Per Article: 104.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/27/2020] [Accepted: 05/21/2020] [Indexed: 12/11/2022] Open
Abstract
miRNet is an easy-to-use, web-based platform designed to help elucidate microRNA (miRNA) functions by integrating users' data with existing knowledge via network-based visual analytics. Since its first release in 2016, miRNet has been accessed by >20 000 researchers worldwide, with ∼100 users on a daily basis. While version 1.0 was focused primarily on miRNA-target gene interactions, it has become clear that in order to obtain a global view of miRNA functions, it is necessary to bring other important players into the context during analysis. Driven by this concept, in miRNet version 2.0, we have (i) added support for transcription factors (TFs) and single nucleotide polymorphisms (SNPs) that affect miRNAs, miRNA-binding sites or target genes, whilst also greatly increased (>5-fold) the underlying knowledgebases of miRNAs, ncRNAs and disease associations; (ii) implemented new functions to allow creation and visual exploration of multipartite networks, with enhanced support for in situ functional analysis and (iii) revamped the web interface, optimized the workflow, and introduced microservices and web application programming interface (API) to sustain high-performance, real-time data analysis. The underlying R package is also released in tandem with version 2.0 to allow more flexible data analysis for R programmers. The miRNet 2.0 website is freely available at https://www.mirnet.ca.
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Affiliation(s)
- Le Chang
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Othman Soufan
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Institute of Parasitology, McGill University, Montreal, Quebec, Canada.,Department of Animal Science, McGill University, Montreal, Quebec, Canada
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21
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Nutrition and microRNAs: Novel Insights to Fight Sarcopenia. Antioxidants (Basel) 2020; 9:antiox9100951. [PMID: 33023202 PMCID: PMC7601022 DOI: 10.3390/antiox9100951] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022] Open
Abstract
Sarcopenia is a progressive age-related loss of skeletal muscle mass and strength, which may result in increased physical frailty and a higher risk of adverse events. Low-grade systemic inflammation, loss of muscle protein homeostasis, mitochondrial dysfunction, and reduced number and function of satellite cells seem to be the key points for the induction of muscle wasting, contributing to the pathophysiological mechanisms of sarcopenia. While a range of genetic, hormonal, and environmental factors has been reported to contribute to the onset of sarcopenia, dietary interventions targeting protein or antioxidant intake may have a positive effect in increasing muscle mass and strength, regulating protein homeostasis, oxidative reaction, and cell autophagy, thus providing a cellular lifespan extension. MicroRNAs (miRNAs) are endogenous small non-coding RNAs, which control gene expression in different tissues. In skeletal muscle, a range of miRNAs, named myomiRNAs, are involved in many physiological processes, such as growth, development, and maintenance of muscle mass and function. This review aims to present and to discuss some of the most relevant molecular mechanisms related to the pathophysiological effect of sarcopenia. Besides, we explored the role of nutrition as a possible way to counteract the loss of muscle mass and function associated with ageing, with special attention paid to nutrient-dependent miRNAs regulation. This review will provide important information to better understand sarcopenia and, thus, to facilitate research and therapeutic strategies to counteract the pathophysiological effect of ageing.
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Abstract
Small RNAs (sRNAs), including microRNAs (miRNAs), are noncoding RNA (ncRNA) molecules involved in gene regulation. sRNAs play important roles in development; however, their significance in nutritional control and as metabolic modulators is still emerging. The mechanisms by which diet impacts metabolic genes through miRNAs remain an important area of inquiry. Recent work has established how miRNAs are transported in body fluids often within exosomes, which are small cell-derived vesicles that function in intercellular communication. The abundance of other recently identified ncRNAs and new insights regarding ncRNAs as dietary bioactive compounds could remodel our understanding about how foods impact gene expression. Although controversial, some groups have shown that dietary RNAs from plants and animals (i.e., milk) are functional in consumers. In the future, regulating sRNAs either directly through dietary delivery or indirectly by altered expression of endogenous sRNA may be part of nutritional interventions for regulating metabolism.
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Affiliation(s)
- Elizabeth M McNeill
- Department of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011, USA
| | - Kendal D Hirschi
- Departments of Pediatrics and Human and Molecular Genetics, Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas 77030, USA;
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23
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A novel serum miRNA-pair classifier for diagnosis of sarcoma. PLoS One 2020; 15:e0236097. [PMID: 32673360 PMCID: PMC7365454 DOI: 10.1371/journal.pone.0236097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/30/2020] [Indexed: 11/19/2022] Open
Abstract
Soft tissue sarcomas (STS) is a set of rare malignant tumor originated from mesoderm. For the prognosis of sarcoma, early diagnosis is important, however, currently no mature and non-invasive method for diagnosis exists. MicroRNAs (miRNAs) are a class of noncoding RNAs and their expression varies greatly, especially during tumor activity. The purpose of this study was to construct a predictive model for the diagnosis of sarcomas based on the relative expression level of miRNA in serum. miRNA array expression data of 677 samples including 402 malignant sarcoma samples and 275 healthy samples was used to construct the prediction model. Based on 6 gene pairs, random generalized linear model (RGLM) was constructed, with an accuracy of 100% in the internal test dataset and of 74.3% in the merged external dataset in prediction whether a serum sample was obtained from a sarcoma patient, with a specificity of 100% in the internal test dataset and 90.5% in the external dataset. In conclusion, our serum miRNA-pair classifier has the potential to be used for the screening of sarcoma with high accuracy and specificity.
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24
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Cui J, Shu J. Circulating microRNA trafficking and regulation: computational principles and practice. Brief Bioinform 2020; 21:1313-1326. [PMID: 31504144 PMCID: PMC7412956 DOI: 10.1093/bib/bbz079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 01/18/2023] Open
Abstract
Rapid advances in genomics discovery tools and a growing realization of microRNA's implication in intercellular communication have led to a proliferation of studies of circulating microRNA sorting and regulation across cells and different species. Although sometimes, reaching controversial scientific discoveries and conclusions, these studies have yielded new insights in the functional roles of circulating microRNA and a plethora of analytical methods and tools. Here, we consider this body of work in light of key computational principles underpinning discovery of circulating microRNAs in terms of their sorting and targeting, with the goal of providing practical guidance for applications that is focused on the design and analysis of circulating microRNAs and their context-dependent regulation. We survey a broad range of informatics methods and tools that are available to the researcher, discuss their key features, applications and various unsolved problems and close this review with prospects and broader implication of this field.
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Affiliation(s)
- Juan Cui
- Systems Biology and Biomedical Informatics Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jiang Shu
- Systems Biology and Biomedical Informatics Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
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25
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Expression profile of microRNAs in the testes of patients with Klinefelter syndrome. Sci Rep 2020; 10:11470. [PMID: 32651451 PMCID: PMC7351945 DOI: 10.1038/s41598-020-68294-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/18/2020] [Indexed: 02/07/2023] Open
Abstract
Klinefelter syndrome (KS) is the most common sex chromosome aneuploidy. A distinctive characteristic of KS is oligozoospermia. Despite multiple studies that have described the natural history of the degenerative process of germ cells in patients with KS, the molecular mechanisms that initiate this process are not well characterized. MicroRNA (miRNA)-mediated post-transcriptional control mechanisms have been increasingly recognized as important regulators of spermatogenesis; however, only a few studies have evaluated the role of miRNAs in the gonadal failure of these patients. Here, we describe a differential expression profile for the miRNAs in testicular tissue samples taken from KS patients. We analysed testicular tissue samples from 4 KS patients and 5 control patients (obstructive azoospermia) through next-generation sequencing, which can provide information about the mechanisms involved in the degeneration of germ cells. A distinctive differential expression profile was identified for 166 miRNAs in the KS patients: 66 were upregulated, and 100 were downregulated. An interactome analysis was performed for 7 of the upregulated and the 20 downregulated miRNAs. The results showed that the target genes are involved in the development, proliferation, and differentiation processes of spermatogenesis, which may explain their role in the development of infertility. This is the first report of a miRNA expression profile generated from testicular tissue samples of KS patients.
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26
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Reckoning the Dearth of Bioinformatics in the Arena of Diabetic Nephropathy (DN)—Need to Improvise. Processes (Basel) 2020. [DOI: 10.3390/pr8070808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Diabetic nephropathy (DN) is a recent rising concern amongst diabetics and diabetologist. Characterized by abnormal renal function and ending in total loss of kidney function, this is becoming a lurking danger for the ever increasing population of diabetics. This review touches upon the intensity of this complication and briefly reviews the role of bioinformatics in the area of diabetes. The advances made in the area of DN using proteomic approaches are presented. Compared to the enumerable inputs observed through the use of bioinformatics resources in the area of proteomics and even diabetes, the existing scenario of skeletal application of bioinformatics advances to DN is highlighted and the reasons behind this discussed. As this review highlights, almost none of the well-established tools that have brought breakthroughs in proteomic research have been applied into DN. Laborious, voluminous, cost expensive and time-consuming methodologies and advances in diagnostics and biomarker discovery promised through beckoning bioinformatics mechanistic approaches to improvise DN research and achieve breakthroughs. This review is expected to sensitize the researchers to fill in this gap, exploiting the available inputs from bioinformatics resources.
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27
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Inferring the Disease-Associated miRNAs Based on Network Representation Learning and Convolutional Neural Networks. Int J Mol Sci 2019; 20:ijms20153648. [PMID: 31349729 PMCID: PMC6696449 DOI: 10.3390/ijms20153648] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 02/06/2023] Open
Abstract
Identification of disease-associated miRNAs (disease miRNAs) are critical for understanding etiology and pathogenesis. Most previous methods focus on integrating similarities and associating information contained in heterogeneous miRNA-disease networks. However, these methods establish only shallow prediction models that fail to capture complex relationships among miRNA similarities, disease similarities, and miRNA-disease associations. We propose a prediction method on the basis of network representation learning and convolutional neural networks to predict disease miRNAs, called CNNMDA. CNNMDA deeply integrates the similarity information of miRNAs and diseases, miRNA-disease associations, and representations of miRNAs and diseases in low-dimensional feature space. The new framework based on deep learning was built to learn the original and global representation of a miRNA-disease pair. First, diverse biological premises about miRNAs and diseases were combined to construct the embedding layer in the left part of the framework, from a biological perspective. Second, the various connection edges in the miRNA-disease network, such as similarity and association connections, were dependent on each other. Therefore, it was necessary to learn the low-dimensional representations of the miRNA and disease nodes based on the entire network. The right part of the framework learnt the low-dimensional representation of each miRNA and disease node based on non-negative matrix factorization, and these representations were used to establish the corresponding embedding layer. Finally, the left and right embedding layers went through convolutional modules to deeply learn the complex and non-linear relationships among the similarities and associations between miRNAs and diseases. Experimental results based on cross validation indicated that CNNMDA yields superior performance compared to several state-of-the-art methods. Furthermore, case studies on lung, breast, and pancreatic neoplasms demonstrated the powerful ability of CNNMDA to discover potential disease miRNAs.
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28
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Barber JL, Zellars KN, Barringhaus KG, Bouchard C, Spinale FG, Sarzynski MA. The Effects of Regular Exercise on Circulating Cardiovascular-related MicroRNAs. Sci Rep 2019; 9:7527. [PMID: 31101833 PMCID: PMC6525243 DOI: 10.1038/s41598-019-43978-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022] Open
Abstract
The purpose of the present study was to examine the effects of regular exercise on the abundance of targeted circulating microRNAs (miRNAs). The present analysis examined 20 previously sedentary adults from the HERITAGE Family Study who completed 20 weeks of endurance exercise training. The expression of 53 miRNAs related to cardiovascular disease were measured in serum collected at baseline and post-training by performing RT-qPCR on the Human Cardiovascular Disease miRNA array (Qiagen, Germany). The effect of regular exercise on circulating miRNAs was assessed using paired t-tests of baseline and post-training expression levels. A false discovery rate threshold of 5% was used to determine significance. Regular exercise resulted in significantly decreased mean serum expression of nine miRNAs (miR-486-5p, let-7b-5p, miR-29c-3p, let-7e-5p, miR-93-5p, miR-7-5p, miR-25-3p, miR-92a-3p, and miR-29b-3p; fold change range: 0.64–83, p = 0.0002–0.01) and increased mean expression of five miRNAs (miR-142-3p, miR-221-3p, miR-126-3p, miR-146a-5p, and miR-27b-3p; fold change range: 1.41–3.60, p = 0.001–0.006). Enrichment analysis found that these 14 miRNAs target genes related to over 345 different biological pathways. These results provide further evidence of the effects of regular exercise on the circulating miRNA profile.
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Affiliation(s)
- Jacob L Barber
- Department of Exercise Science, University of South Carolina, Columbia, SC, USA
| | - Kia N Zellars
- Cardiovascular Translational Research Center, University of South Carolina School of Medicine and WJB Dorn Veteran Affairs Medical Center, Columbia, SC, USA
| | - Kurt G Barringhaus
- Cardiovascular Translational Research Center, University of South Carolina School of Medicine and WJB Dorn Veteran Affairs Medical Center, Columbia, SC, USA
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Francis G Spinale
- Cardiovascular Translational Research Center, University of South Carolina School of Medicine and WJB Dorn Veteran Affairs Medical Center, Columbia, SC, USA
| | - Mark A Sarzynski
- Department of Exercise Science, University of South Carolina, Columbia, SC, USA.
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29
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Almiñana C, Bauersachs S. Extracellular Vesicles in the Oviduct: Progress, Challenges and Implications for the Reproductive Success. Bioengineering (Basel) 2019; 6:bioengineering6020032. [PMID: 31013857 PMCID: PMC6632016 DOI: 10.3390/bioengineering6020032] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/04/2019] [Accepted: 04/10/2019] [Indexed: 12/11/2022] Open
Abstract
The oviduct is the anatomical part of the female reproductive tract where the early reproductive events take place, from gamete transport, fertilization and early embryo development to the delivery of a competent embryo to the uterus, which can implant and develop to term. The success of all these events rely upon a two-way dialogue between the oviduct (lining epithelium and secretions) and the gametes/embryo(s). Recently, extracellular vesicles (EVs) have been identified as major components of oviductal secretions and pointed to as mediators of the gamete/embryo-maternal interactions. EVs, comprising exosomes and microvesicles, have emerged as important agents of cell-to-cell communication by the transfer of biomolecules (i.e., mRNAs, miRNAs, proteins) that can modulate the activities of recipient cells. Here, we provide the current knowledge of EVs in the oviductal environment, from isolation to characterization, and a description of the EVs molecular content and associated functional aspects in different species. The potential role of oviductal EVs (oEVs) as modulators of gamete/embryo-oviduct interactions and their implications in the success of early reproductive events is addressed. Lastly, we discuss current challenges and future directions towards the potential application of oEVs as therapeutic vectors to improve pregnancy disorders, infertility problems and increase the success of assisted reproductive technologies.
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Affiliation(s)
- Carmen Almiñana
- Genetics and Functional Genomics Group, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland.
- UMR85 PRC, INRA, CNRS 7247, Université de Tours, IFCE, 37380 Nouzilly, France.
| | - Stefan Bauersachs
- Genetics and Functional Genomics Group, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland.
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