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Correia de Sousa M, Delangre E, Berthou F, El Harane S, Maeder C, Fournier M, Krause KH, Gjorgjieva M, Foti M. Hepatic miR-149-5p upregulation fosters steatosis, inflammation and fibrosis development in mice and in human liver organoids. JHEP Rep 2024; 6:101126. [PMID: 39263327 PMCID: PMC11388170 DOI: 10.1016/j.jhepr.2024.101126] [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] [Received: 03/06/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 09/13/2024] Open
Abstract
Background & Aims The incidence of metabolic dysfunction-associated steatotic liver disease (MASLD) is increasing worldwide. Alterations of hepatic microRNA (miRNA) expression/activity significantly contribute to the development and progression of MASLD. Genetic polymorphisms of miR-149 are associated with an increased susceptibility to MASLD development in humans. Aberrant expression of miR-149 was also associated with metabolic alterations in several organs, but the impact of hepatic miR-149-5p deregulation in MASLD remains poorly characterized. Methods MiR-149-5p was downregulated in the livers of mice by in vivo transduction with hepatotropic adeno-associated virus 8 harboring short-hairpin RNAs (shRNAs) specific for miR-149-5p (shmiR149) or scrambled shRNAs (shCTL). MASLD was then induced with a methionine/choline-deficient (MCD, n = 7 per group) diet or a fructose/palmitate/cholesterol-enriched (FPC, n = 8-12 per group, per protocol) diet. The impact of miR-149-5p modulation on MASLD development was assessed in vivo and in vitro using multi-lineage 3D human liver organoids (HLOs) and Huh7 cells. Results MiR-149-5p expression was strongly upregulated in mouse livers from different models of MASLD (2-4-fold increase in ob/ob, db/db mice, high-fat and FPC-fed mice). In vivo downregulation of miR-149-5p led to an amelioration of diet-induced hepatic steatosis, inflammation/fibrosis, and to increased whole-body fatty acid consumption. In HLOs, miR-149-5p overexpression promoted lipid accumulation, inflammation and fibrosis. In vitro analyses of human Huh7 cells overexpressing miR-149-5p indicated that glycolysis and intracellular lipid accumulation was promoted, while mitochondrial respiration was impaired. Translatomic analyses highlighted deregulation of multiple potential miR-149-5p targets in hepatocytes involved in MASLD development. Conclusions MiR-149-5p upregulation contributes to MASLD development by affecting multiple metabolic/inflammatory/fibrotic pathways in hepatocytes. Our results further demonstrate that HLOs are a relevant 3D in vitro model to investigate hepatic steatosis and inflammation/fibrosis development. Impact and implications Our research shows compelling evidence that miR-149-5p plays a pivotal role in the development and progression of MASLD. By employing in vivo and innovative in vitro models using multi-lineage human liver organoids, we demonstrate that miR-149-5p upregulation significantly impacts hepatocyte energy metabolism, exacerbating hepatic steatosis and inflammation/fibrosis by modulating a wide network of target genes. These findings not only shed light on the intricate miR-149-5p-dependent molecular mechanisms underlying MASLD, but also underscore the importance of human liver organoids as valuable 3D in vitro models for studying the disease's pathogenesis.
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Affiliation(s)
- Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Etienne Delangre
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Flavien Berthou
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sanae El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Babaeenezhad E, Abdolvahabi Z, Asgharzadeh S, Abdollahi M, Shakeri S, Moradi Sarabi M, Yarahmadi S. Potential function of microRNA miRNA-206 in breast cancer pathogenesis: Mechanistic aspects and clinical implications. Pathol Res Pract 2024; 260:155454. [PMID: 39002434 DOI: 10.1016/j.prp.2024.155454] [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] [Received: 04/19/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
Breast cancer (BC) is a major public health problem that affects women worldwide. Growing evidence has highlighted the role of miRNA-206 in BC pathogenesis. Changes in its expression have diagnostic and prognostic potential as they are associated with clinicopathological parameters, including lymph node metastasis, overall survival, tumor size, metastatic stage, resistance to chemotherapy, and recurrence. In the present study, we summarized, assessed, and discussed the most recent understanding of the functions of miRNA-206 in BC. Unexpectedly, miRNA-206 was found to control both oncogenic and tumor-suppressive pathways. We also considered corresponding downstream effects and upstream regulators. Finally, we addressed the diagnostic and prognostic value of miRNA-206 and its potential for the development of new therapeutic strategies.
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Affiliation(s)
- Esmaeel Babaeenezhad
- Nutritional Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Zohreh Abdolvahabi
- Cellular and Molecular Research Centre, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sahar Asgharzadeh
- Cellular and Molecular Research Centre, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Masume Abdollahi
- Cellular and Molecular Research Centre, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sara Shakeri
- Cellular and Molecular Research Centre, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mostafa Moradi Sarabi
- Hepatities Research Center, Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Sahar Yarahmadi
- Nutritional Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.
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3
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Karabay AZ, Ozkan T, Karadag Gurel A, Koc A, Hekmatshoar Y, Sunguroglu A, Aktan F, Buyukbingöl Z. Identification of exosomal microRNAs and related hub genes associated with imatinib resistance in chronic myeloid leukemia. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03198-1. [PMID: 38916832 DOI: 10.1007/s00210-024-03198-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/29/2024] [Indexed: 06/26/2024]
Abstract
Chemotherapy resistance is a major obstacle in cancer therapy, and identifying novel druggable targets to reverse this phenomenon is essential. The exosome-mediated transmittance of drug resistance has been shown in various cancer models including ovarian and prostate cancer models. In this study, we aimed to investigate the role of exosomal miRNA transfer in chronic myeloid leukemia drug resistance. For this purpose, firstly exosomes were isolated from imatinib sensitive (K562S) and resistant (K562R) chronic myeloid leukemia (CML) cells and named as Sexo and Rexo, respectively. Then, miRNA microarray was used to compare miRNA profiles of K562S, K562R, Sexo, Rexo, and Rexo-treated K562S cells. According to our results, miR-125b-5p and miR-99a-5p exhibited increased expression in resistant cells, their exosomes, and Rexo-treated sensitive cells compared to their sensitive counterparts. On the other hand, miR-210-3p and miR-193b-3p were determined to be the two miRNAs which exhibited decreased expression profile in resistant cells and their exosomes compared to their sensitive counterparts. Gene targets, signaling pathways, and enrichment analysis were performed for these miRNAs by TargetScan, KEGG, and DAVID. Potential interactions between gene candidates at the protein level were analyzed via STRING and Cytoscape software. Our findings revealed CCR5, GRK2, EDN1, ARRB1, P2RY2, LAMC2, PAK3, PAK4, and GIT2 as novel gene targets that may play roles in exosomal imatinib resistance transfer as well as mTOR, STAT3, MCL1, LAMC1, and KRAS which are already linked to imatinib resistance. MDR1 mRNA exhibited higher expression in Rexo compared to Sexo as well as in K562S cells treated with Rexo compared to K562S cells which may suggest exosomal transfer of MDR1 mRNA.
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Affiliation(s)
- Arzu Zeynep Karabay
- Department of Biochemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey.
| | - Tulin Ozkan
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey.
| | - Aynur Karadag Gurel
- Department of Medical Biology, Faculty of Medicine, Usak University, Usak, Turkey.
| | - Asli Koc
- Department of Biochemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | - Yalda Hekmatshoar
- Department of Medical Biology, Faculty of Medicine, Altinbas University, Istanbul, Turkey
| | - Asuman Sunguroglu
- Department of Medical Biology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Fugen Aktan
- Department of Biochemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | - Zeliha Buyukbingöl
- Department of Biochemistry, Faculty of Pharmacy, Ankara University, Ankara, Turkey
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Zhou Q, Song W, Li X, Lin J, Zhu C, Cao L, Li W, Lin S. N6-Methyladenosine reader HNRNPC-mediated downregulation of circITCH prevents miR-224-3p sequestering and contributes to tumorigenesis in nasopharyngeal carcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:2893-2907. [PMID: 38299319 DOI: 10.1002/tox.24139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND N6-Methyladenosine (m6A) RNA methylation modulators are implicated in nasopharyngeal carcinoma (NPC). Circular RNAs (circRNAs) stimulate/inhibit the development of NPC by sponging microRNAs (miRNAs). Herein, m6A modifications affecting the circRNA/miRNA axis in NPC were explored. METHODS Twenty prognostic m6A RNA methylation regulators were identified from 504 head/neck squamous cell carcinoma and 44 normal samples from The Cancer Genome Atlas (TCGA). Differentially expressed miRNAs were screened from the TCGA and Gene Expression Omnibus (GEO) databases. RNA-binding protein (RBP)-circRNA and circRNA-miRNA interactive pairs were verified using RBPmap and RNAhybrid, respectively. The RBP/circRNA/miRNA network was constructed using Cytoscape. Furthermore, CircITCH (hsa_circ_00059948), HNRNPC, and miR-224-3p expressions were detected by western blotting and quantitative polymerase chain reaction. The role of circITCH in NPC was examined using apoptosis, scratch wound healing, transwell invasion, and cell counting kit-8 assays. Finally, CircITCH-miR-224-3p and circITCH-HNRNPC interactions were assessed by dual-luciferase reporter and RNA-immunoprecipitation (RIP) assays, respectively. RESULTS Bioinformatics analysis revealed that high pathological grade, late-stage tumors, and low survival were associated with increased HNRNPC expression. MiR-224-3p was upregulated in NPC and sequestered by circITCH. Construction of the RBP/circRNA/miRNA network highlighted the HNRNPC/circITCH/miR-224-3p axis. In vitro experiments demonstrated decreased circITCH expression and increased HNRNPC and miR-224-3p expressions in NPC. In NPC cells overexpressing circITCH, HNRNPC and miR-224-3p expressions were significantly decreased. Dual-luciferase assays demonstrated a targeting relationship between circITCH and miR-224-3p, and RIP assays demonstrated interaction of HNRNPC targets with circITCH. CONCLUSION CircITCH overexpression inhibited NPC progression by sequestering miR-224-3p, and HNRNPC reduced circITCH expression through direct interaction.
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Affiliation(s)
- Qiang Zhou
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Wei Song
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Xianhui Li
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Jinyan Lin
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Chuansai Zhu
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Longhe Cao
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Wanqing Li
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Sen Lin
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
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Jonas K, Prinz F, Ferracin M, Krajina K, Deutsch A, Madl T, Rinner B, Slaby O, Klec C, Pichler M. MiR-4646-5p Acts as a Tumor-Suppressive Factor in Triple Negative Breast Cancer and Targets the Cholesterol Transport Protein GRAMD1B. Noncoding RNA 2023; 10:2. [PMID: 38250802 PMCID: PMC10801495 DOI: 10.3390/ncrna10010002] [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: 07/20/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
MicroRNAs (miRNAs) are crucial post-transcriptional regulators of gene expression, and their deregulation contributes to many aspects of cancer development and progression. Thus, miRNAs provide insight into oncogenic mechanisms and represent promising targets for new therapeutic approaches. A type of cancer that is still in urgent need of improved treatment options is triple negative breast cancer (TNBC). Therefore, we aimed to characterize a novel miRNA with a potential role in TNBC. Based on a previous study, we selected miR-4646-5p, a miRNA with a still unknown function in breast cancer. We discovered that higher expression of miR-4646-5p in TNBC patients is associated with better survival. In vitro assays showed that miR-4646-5p overexpression reduces growth, proliferation, and migration of TNBC cell lines, whereas inhibition had the opposite effect. Furthermore, we found that miR-4646-5p inhibits the tube formation ability of endothelial cells, which may indicate anti-angiogenic properties. By whole transcriptome analysis, we not only observed that miR-4646-5p downregulates many oncogenic factors, like tumor-promoting cytokines and migration- and invasion-related genes, but were also able to identify a direct target, the GRAM domain-containing protein 1B (GRAMD1B). GRAMD1B is involved in cellular cholesterol transport and its knockdown phenocopied the growth-reducing effects of miR-4646-5p. We thus conclude that GRAMD1B may partly contribute to the diverse tumor-suppressive effects of miR-4646-5p in TNBC.
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Affiliation(s)
- Katharina Jonas
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria; (K.J.)
- Research Unit for Non-Coding RNA and Genome Editing, Medical University of Graz, 8010 Graz, Austria
| | - Felix Prinz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria; (K.J.)
- Research Unit for Non-Coding RNA and Genome Editing, Medical University of Graz, 8010 Graz, Austria
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Katarina Krajina
- Translational Oncology, II. Med Clinics Hematology and Oncology, 86156 Augsburg, Germany
| | - Alexander Deutsch
- Division of Hematology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Tobias Madl
- Division of Molecular Biology & Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Beate Rinner
- Department for Biomedical Research, Medical University of Graz, 8036 Graz, Austria
| | - Ondrej Slaby
- Department of Biology, Faculty of Medicine and Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Christiane Klec
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria; (K.J.)
- Research Unit for Non-Coding RNA and Genome Editing, Medical University of Graz, 8010 Graz, Austria
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, 8036 Graz, Austria; (K.J.)
- Research Unit for Non-Coding RNA and Genome Editing, Medical University of Graz, 8010 Graz, Austria
- Translational Oncology, II. Med Clinics Hematology and Oncology, 86156 Augsburg, Germany
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6
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Grecco A, Macchiaroli N, Pérez MG, Casulli A, Cucher MA, Rosenzvit MC. microRNA silencing in a whole worm cestode model provides insight into miR-71 function. Int J Parasitol 2023; 53:699-710. [PMID: 37699506 DOI: 10.1016/j.ijpara.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/13/2023] [Accepted: 08/05/2023] [Indexed: 09/14/2023]
Abstract
Parasites belonging to the class Cestoda include zoonotic species such as Echinococcus spp. and Taenia spp. that cause morbidity and mortality in endemic areas, mainly affecting pastoral and rural communities in low income countries but also upper middle income countries. Cestodes show remarkable developmental plasticity, implying tight regulation of gene expression throughout their complex life cycles. Despite the recent availability of genomic data for cestodes, little progress was made on postgenomic functional studies. MicroRNAs (miRNAs) are key components of gene regulatory systems that guide diverse developmental processes in multicellular organisms. miR-71 is a highly expressed miRNA in cestodes, which is absent in vertebrates and targets essential parasite genes, representing a potential key player in understanding the role of miRNAs in cestodes biology. Here we used transfection with antisense oligonucleotides to perform whole worm miRNA knockdown in tetrathyridia of Mesocestoides vogae (syn. Mesocestoides corti), a laboratory model of cestodes. We believe this is the first report of miRNA knockdown at the organism level in these parasites. Our results showed that M. vogae miR-71 is involved in the control of strobilation in vitro and in the establishment of murine infection. In addition, we identified miR-71 targets in M. vogae, several of them being de-repressed upon miR-71 knockdown. This study provides new knowledge on gene expression regulation in cestodes and suggests that miRNAs could be evaluated as new selective therapeutic targets for treating Neglected Tropical Diseases prioritised by the World Health Organization.
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Affiliation(s)
- Andrés Grecco
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Natalia Macchiaroli
- Laboratorio de Genómica y Bioinformática de Patógenos, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Matías Gastón Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adriano Casulli
- WHO Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis. Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; European Reference Laboratory for Parasites. Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marcela Alejandra Cucher
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mara Cecilia Rosenzvit
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina.
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7
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Lin H, Chu J, Yuan D, Wang K, Chen F, Liu X. MiR-206 may regulate mitochondrial ROS contribute to the progression of Myocardial infarction via TREM1. BMC Cardiovasc Disord 2023; 23:470. [PMID: 37730550 PMCID: PMC10512505 DOI: 10.1186/s12872-023-03481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
Myocardial infarction (MI) is a leading cause of mortality. To better understand its molecular and cellular mechanisms, we used bioinformatic tools and molecular experiments to explore the pathogenesis and prognostic markers. Differential gene expression analysis was conducted using GSE60993 and GSE66360 datasets. Hub genes were identified through pathway enrichment analysis and PPI network construction, and four hub genes (AQP9, MMP9, FPR1, and TREM1) were evaluated for their predictive performance using AUC and qRT-PCR. miR-206 was identified as a potential regulator of TREM1. Finally, miR-206 was found to induce EC senescence and ER stress through upregulating mitochondrial ROS levels via TREM1. These findings may contribute to understanding the pathogenesis of MI and identifying potential prognostic markers.
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Affiliation(s)
- Hao Lin
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, No.389, Xincun Road, Shanghai, 200092, Putuo District, China
| | - Jiapeng Chu
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, No.389, Xincun Road, Shanghai, 200092, Putuo District, China
| | - Deqiang Yuan
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, No.389, Xincun Road, Shanghai, 200092, Putuo District, China
| | - Kangwei Wang
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, No.389, Xincun Road, Shanghai, 200092, Putuo District, China
| | - Fei Chen
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, No.389, Xincun Road, Shanghai, 200092, Putuo District, China.
| | - Xuebo Liu
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, No.389, Xincun Road, Shanghai, 200092, Putuo District, China.
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8
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Golebiewski C, Gastaldi C, Vieu DL, Mari B, Rezzonico R, Bernerd F, Marionnet C. Identification and functional validation of SRC and RAPGEF1 as new direct targets of miR-203, involved in regulation of epidermal homeostasis. Sci Rep 2023; 13:14006. [PMID: 37635193 PMCID: PMC10460794 DOI: 10.1038/s41598-023-40441-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
The epidermis is mostly composed of keratinocytes and forms a protecting barrier against external aggressions and dehydration. Epidermal homeostasis is maintained by a fine-tuned balance between keratinocyte proliferation and differentiation. In the regulation of this process, the keratinocyte-specific miR-203 microRNA is of the outmost importance as it promotes differentiation, notably by directly targeting and down-regulating mRNA expression of genes involved in keratinocyte proliferation, such as ΔNp63, Skp2 and Msi2. We aimed at identifying new miR-203 targets involved in the regulation of keratinocyte proliferation/differentiation balance. To this end, a transcriptome analysis of human primary keratinocytes overexpressing miR-203 was performed and revealed that miR-203 overexpression inhibited functions like proliferation, mitosis and cell cycling, and activated differentiation, apoptosis and cell death. Among the down-regulated genes, 24 putative target mRNAs were identified and 8 of them were related to proliferation. We demonstrated that SRC and RAPGEF1 were direct targets of miR-203. Moreover, both were down-regulated during epidermal morphogenesis in a 3D reconstructed skin model, while miR-203 was up-regulated. Finally silencing experiments showed that SRC or RAPGEF1 contributed to keratinocyte proliferation and regulated their differentiation. Preliminary results suggest their involvement in skin carcinoma hyperproliferation. Altogether this data indicates that RAPGEF1 and SRC could be new mediators of miR-203 in epidermal homeostasis regulation.
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Affiliation(s)
| | - Cécile Gastaldi
- Medical Biology Department, Centre Scientifique de Monaco, Monaco, Principality of Monaco
- LIA BAHN, CSM-UVSQ, Monaco, Principality of Monaco
| | | | - Bernard Mari
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
| | - Roger Rezzonico
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
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9
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Tastsoglou S, Alexiou A, Karagkouni D, Skoufos G, Zacharopoulou E, Hatzigeorgiou AG. DIANA-microT 2023: including predicted targets of virally encoded miRNAs. Nucleic Acids Res 2023:7137452. [PMID: 37094027 DOI: 10.1093/nar/gkad283] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
DIANA-microT-CDS is a state-of-the-art miRNA target prediction algorithm catering the scientific community since 2009. It is one of the first algorithms to predict miRNA binding sites in both the 3' Untranslated Region (3'-UTR) and the coding sequence (CDS) of transcripts, with increased performance. Its current version, DIANA-microT 2023 (www.microrna.gr/microt_webserver/), brings forward a significantly updated set of interactions. DIANA-microT-CDS has been executed utilizing annotation information from Ensembl v102, miRBase 22.1 and, for the first time, MirGeneDB 2.1, yielding more than 83 million interactions in human, mouse, rat, chicken, fly and worm species. Additionally, this version delivers predicted interactions of miRNAs encoded from 20 viruses against host transcripts from human, mouse and chicken species. Numerous resources have been interconnected into DIANA-microT, including DIANA-TarBase, plasmiR, HMDD, UCSC, dbSNP, ClinVar, as well as miRNA/gene abundance values for 369 distinct cell-lines/tissues. The server interface has been redesigned allowing users to use smart filtering options, identify abundance patterns of interest, pinpoint known SNPs residing on binding sites and obtain miRNA-disease information. The contents of DIANA-microT webserver are freely accessible and can also be locally downloaded without any login requirements.
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Affiliation(s)
- Spyros Tastsoglou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, Lamia 35131, Greece
- Hellenic Pasteur Institute, Athens 11521, Greece
| | - Athanasios Alexiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, Lamia 35131, Greece
- Hellenic Pasteur Institute, Athens 11521, Greece
| | - Dimitra Karagkouni
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Giorgos Skoufos
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, Lamia 35131, Greece
- Hellenic Pasteur Institute, Athens 11521, Greece
| | - Elissavet Zacharopoulou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, Lamia 35131, Greece
- Hellenic Pasteur Institute, Athens 11521, Greece
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly, Lamia 35131, Greece
- Hellenic Pasteur Institute, Athens 11521, Greece
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10
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Yuen JG, Hwang GR, Ju J. Analysis of MicroRNAs in Ferroptosis. Methods Mol Biol 2023; 2712:223-232. [PMID: 37578710 DOI: 10.1007/978-1-0716-3433-2_20] [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: 08/15/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that are involved in a wide range of biological processes, including development, differentiation, and disease. They function by binding to the 3' untranslated region (UTR) of target mRNAs, leading to mRNA degradation or translational repression. miRNAs are involved in the regulation of many cellular processes, including cell proliferation, apoptosis, and metabolism. MiRNAs have been shown to modulate ferroptosis in several ways. Some miRNAs have been shown to promote ferroptosis by increasing the expression of genes involved in lipid peroxidation. Other miRNAs have been shown to inhibit ferroptosis by decreasing the expression of genes involved in iron uptake. The role of miRNAs in ferroptosis is still being studied, but they play a significant role in this cell death pathway. miRNAs may be potential targets for therapeutic intervention in diseases associated with ferroptosis, such as cancer and neurodegenerative diseases. This chapter outlines several methods used to study the connection between miRNAs and ferroptosis through target discovery and validation.
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Affiliation(s)
- John G Yuen
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Ga-Ram Hwang
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Jingfang Ju
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
- The Northport Veteran's Administration Medical Center, Northport, NY, USA.
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11
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Gjorgjieva M, Ay AS, Correia de Sousa M, Delangre E, Dolicka D, Sobolewski C, Maeder C, Fournier M, Sempoux C, Foti M. MiR-22 Deficiency Fosters Hepatocellular Carcinoma Development in Fatty Liver. Cells 2022; 11:cells11182860. [PMID: 36139435 PMCID: PMC9496902 DOI: 10.3390/cells11182860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
MiR-22 is mostly considered as a hepatic tumor-suppressor microRNA based on in vitro analyses. Yet, whether miR-22 exerts a tumor-suppressive function in the liver has not been investigated in vivo. Herein, in silico analyses of miR-22 expression were performed in hepatocellular carcinomas from human patient cohorts and different mouse models. Diethylnitrosamine-induced hepatocellular carcinomas were then investigated in lean and diet-induced obese miR-22-deficient mice. The proteome of liver tissues from miR-22-deficient mice prior to hepatocellular carcinoma development was further analyzed to uncover miR-22 regulated factors that impact hepatocarcinogenesis with miR-22 deficiency. MiR-22 downregulation was consistently observed in hepatocellular carcinomas from all human cohorts and mouse models investigated. The time of appearance of the first tumors was decreased and the number of tumoral foci induced by diethylnitrosamine was significantly increased by miR-22-deficiency in vivo, two features which were further drastically exacerbated with diet-induced obesity. At the molecular level, we provide evidence that the loss of miR-22 significantly affects the energetic metabolism and mitochondrial functions of hepatocytes, and the expression of tumor-promoting factors such as thrombospondin-1. Our study demonstrates that miR-22 acts as a hepatic tumor suppressor in vivo by restraining pro-carcinogenic metabolic deregulations through pleiotropic mechanisms and the overexpression of relevant oncogenes.
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Affiliation(s)
- Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Anne-Sophie Ay
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Etienne Delangre
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Christine Sempoux
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital, University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Translational Research Centre in Onco-Haematology, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Correspondence:
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12
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Liu Z, Zhang L, Toma MA, Li D, Bian X, Pastar I, Tomic-Canic M, Sommar P, Xu Landén N. Integrative small and long RNA omics analysis of human healing and nonhealing wounds discovers cooperating microRNAs as therapeutic targets. eLife 2022; 11:80322. [PMID: 35942686 PMCID: PMC9374442 DOI: 10.7554/elife.80322] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/19/2022] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miR), as important epigenetic control factors, reportedly regulate wound repair. However, our insufficient knowledge of clinically relevant miRs hinders their potential therapeutic use. For this, we performed paired small and long RNA-sequencing and integrative omics analysis in human tissue samples, including matched skin and acute wounds collected at each healing stage and chronic nonhealing venous ulcers (VUs). On the basis of the findings, we developed a compendium (https://www.xulandenlab.com/humanwounds-mirna-mrna), which will be an open, comprehensive resource to broadly aid wound healing research. With this first clinical, wound-centric resource of miRs and mRNAs, we identified 17 pathologically relevant miRs that exhibited abnormal VU expression and displayed their targets enriched explicitly in the VU gene signature. Intermeshing regulatory networks controlled by these miRs revealed their high cooperativity in contributing to chronic wound pathology characterized by persistent inflammation and proliferative phase initiation failure. Furthermore, we demonstrated that miR-34a, miR-424, and miR-516, upregulated in VU, cooperatively suppressed keratinocyte migration and growth while promoting inflammatory response. By combining miR expression patterns with their specific target gene expression context, we identified miRs highly relevant to VU pathology. Our study opens the possibility of developing innovative wound treatment that targets pathologically relevant cooperating miRs to attain higher therapeutic efficacy and specificity.
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Affiliation(s)
- Zhuang Liu
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Letian Zhang
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria A Toma
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Dongqing Li
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Xiaowei Bian
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, United States
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, United States
| | - Pehr Sommar
- Department of Plastic and Reconstructive Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Ning Xu Landén
- Dermatology and Venereology Division, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institute, Stockholm, Sweden
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13
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Szuszkiewicz J, Myszczynski K, Reliszko ZP, Heifetz Y, Kaczmarek MM. Early steps of embryo implantation are regulated by exchange of extracellular vesicles between the embryo and the endometrium. FASEB J 2022; 36:e22450. [PMID: 35848638 DOI: 10.1096/fj.202200677r] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/12/2022] [Accepted: 06/30/2022] [Indexed: 11/11/2022]
Abstract
In early pregnancy, as the embryo arrives in the uterus, intensive communication between the embryo and uterus begins. Hundreds of molecules are known to be involved, but despite numerous findings, full understanding of the complexity of the embryo-maternal dialog remains elusive. Recently, extracellular vesicles, nanoparticles able to transfer functionally active cargo between cells, have emerged as important players in cell-cell communication, and as such, they have gained great attention over the past decade also in reproductive biology. Here, we use a domestic animal model (Sus scrofa) with an epitheliochorial, superficial type of placentation because of its advantage in studding uterine luminal fluid extracellular vesicles. We show that during early pregnancy, the uterine lumen is abundant with extracellular vesicles that carry a plethora of miRNAs able to target genes involved in embryonic and organismal development. These extracellular vesicles, upon the delivery to primary trophoblast cells, affect genes governing development as well as cell-to-cell signaling and interactions, consequently having an impact on trophoblast cell proliferation, migration, and invasion. We conclude that the exchange of a unique population of extracellular vesicles and their molecular cargo at the maternal-embryo interface is the key to the success of embryo implantation and pregnancy.
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Affiliation(s)
- Joanna Szuszkiewicz
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczynski
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Zaneta P Reliszko
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Yael Heifetz
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Monika M Kaczmarek
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland.,Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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14
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Czaja AJ. Epigenetic Aspects and Prospects in Autoimmune Hepatitis. Front Immunol 2022; 13:921765. [PMID: 35844554 PMCID: PMC9281562 DOI: 10.3389/fimmu.2022.921765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
The observed risk of autoimmune hepatitis exceeds its genetic risk, and epigenetic factors that alter gene expression without changing nucleotide sequence may help explain the disparity. Key objectives of this review are to describe the epigenetic modifications that affect gene expression, discuss how they can affect autoimmune hepatitis, and indicate prospects for improved management. Multiple hypo-methylated genes have been described in the CD4+ and CD19+ T lymphocytes of patients with autoimmune hepatitis, and the circulating micro-ribonucleic acids, miR-21 and miR-122, have correlated with laboratory and histological features of liver inflammation. Both epigenetic agents have also correlated inversely with the stage of liver fibrosis. The reduced hepatic concentration of miR-122 in cirrhosis suggests that its deficiency may de-repress the pro-fibrotic prolyl-4-hydroxylase subunit alpha-1 gene. Conversely, miR-155 is over-expressed in the liver tissue of patients with autoimmune hepatitis, and it may signify active immune-mediated liver injury. Different epigenetic findings have been described in diverse autoimmune and non-autoimmune liver diseases, and these changes may have disease-specificity. They may also be responses to environmental cues or heritable adaptations that distinguish the diseases. Advances in epigenetic editing and methods for blocking micro-ribonucleic acids have improved opportunities to prove causality and develop site-specific, therapeutic interventions. In conclusion, the role of epigenetics in affecting the risk, clinical phenotype, and outcome of autoimmune hepatitis is under-evaluated. Full definition of the epigenome of autoimmune hepatitis promises to enhance understanding of pathogenic mechanisms and satisfy the unmet clinical need to improve therapy for refractory disease.
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Affiliation(s)
- Albert J. Czaja
- *Correspondence: Albert J. Czaja, ; orcid.org/0000-0002-5024-3065
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15
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Czaja AJ. Examining micro-ribonucleic acids as diagnostic and therapeutic prospects in autoimmune hepatitis. Expert Rev Clin Immunol 2022; 18:591-607. [PMID: 35510750 DOI: 10.1080/1744666x.2022.2074839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Micro-ribonucleic acids modulate the immune response by affecting the post-transcriptional expression of genes that influence the proliferation and function of activated immune cells, including regulatory T cells. Individual expressions or patterns in peripheral blood and liver tissue may have diagnostic value, reflect treatment response, or become therapeutic targets. The goals of this review are to present the properties and actions of micro-ribonucleic acids, indicate the key individual expressions in autoimmune hepatitis, and describe prospective clinical applications in diagnosis and management. AREAS COVERED Abstracts were identified in PubMed using the search words "microRNAs", "microRNAs in liver disease", and "microRNAs in autoimmune hepatitis". The number of abstracts reviewed exceeded 2000, and the number of full-length articles reviewed was 108. EXPERT OPINION Individual micro-ribonucleic acids, miR-21, miR-122, and miR-155, have been associated with biochemical severity, histological grade of inflammation, and pivotal pathogenic mechanisms in autoimmune hepatitis. Antisense oligonucleotides that down-regulate deleterious individual gene expressions, engineered molecules that impair targeting of gene products, and drugs that non-selectively up-regulate the biogenesis of potentially deficient gene regulators are feasible treatment options. Micro-ribonucleic acids constitute an under-evaluated area in autoimmune hepatitis that promises to improve diagnosis, pathogenic concepts, and therapy.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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16
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Dori M, Caroli J, Forcato M. Circr, a Computational Tool to Identify miRNA:circRNA Associations. FRONTIERS IN BIOINFORMATICS 2022; 2:852834. [PMID: 36304313 PMCID: PMC9580875 DOI: 10.3389/fbinf.2022.852834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/21/2022] [Indexed: 08/21/2023] Open
Abstract
Circular RNAs (circRNAs) are known to act as important regulators of the microRNA (miRNA) activity. Yet, computational resources to identify miRNA:circRNA interactions are mostly limited to already annotated circRNAs or affected by high rates of false positive predictions. To overcome these limitations, we developed Circr, a computational tool for the prediction of associations between circRNAs and miRNAs. Circr combines three publicly available algorithms for de novo prediction of miRNA binding sites on target sequences (miRanda, RNAhybrid, and TargetScan) and annotates each identified miRNA:target pairs with experimentally validated miRNA:RNA interactions and binding sites for Argonaute proteins derived from either ChIPseq or CLIPseq data. The combination of multiple tools for the identification of a single miRNA recognition site with experimental data allows to efficiently prioritize candidate miRNA:circRNA interactions for functional studies in different organisms. Circr can use its internal annotation database or custom annotation tables to enhance the identification of novel and not previously annotated miRNA:circRNA sites in virtually any species. Circr is written in Python 3.6 and is released under the GNU GPL3.0 License at https://github.com/bicciatolab/Circr.
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Affiliation(s)
- Martina Dori
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena,Italy
| | - Jimmy Caroli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena,Italy
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena,Italy
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17
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Zhou Y, Ng DY, Richards AM, Wang P. Loss of full-length pumilio 1 abrogates miRNA-221-induced gene p27 silencing-mediated cell proliferation in the heart. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:456-470. [PMID: 35036057 PMCID: PMC8728526 DOI: 10.1016/j.omtn.2021.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022]
Abstract
Upregulated expression of microRNA (miR)-221 is associated with downregulation of p27 and subsequent increased cell proliferation in a variety of human cancers. It is unknown whether miR-221 mimics could trigger neoplastic cellular proliferation. In vitro, we demonstrated miR-221 significantly downregulates the expression of P27 and increases proliferation of H9c2 and cardiac fibroblasts. The knockdown of PUM1 but not PUM2 abolished such effects by miR-221, as verified by RT-qPCR and western blot, direct binding of p27 3′ UTR by luciferase reporter assay and cell proliferation by Ki67. In vivo expression of P27 in the rat liver, heart, kidney, spleen, and muscle were not affected by miR-221 at 1 and 4 mg/kg and concurrently full-length (FL) PUM1 (140 kDa) was not detected. Instead, isoforms of 105 and 90 kDa were observed and generated through alternative RNA slicing verified by cDNA cloning and sequencing and cathepsin K cleavage confirmed by studies with the inhibitor odanacatib. This is the first study to address the possible pro-proliferative effects of miR-221 mimic therapeutics in cardiovascular applications. Loss of FL PUM1 expression is a key factor abrogating miR-221-mediated p27 regulation, although other concurrent mechanisms cannot be excluded. Our findings provide essential insights into the context-dependent nature of miRNA functionality.
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18
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Mahlab-Aviv S, Linial N, Linial M. miRNA Combinatorics and its Role in Cell State Control-A Probabilistic Approach. Front Mol Biosci 2022; 8:772852. [PMID: 34993232 PMCID: PMC8724548 DOI: 10.3389/fmolb.2021.772852] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/29/2021] [Indexed: 12/16/2022] Open
Abstract
A hallmark of cancer evolution is that the tumor may change its cell identity and improve its survival and fitness. Drastic change in microRNA (miRNA) composition and quantities accompany such dynamic processes. Cancer samples are composed of cells’ mixtures of varying stages of cancerous progress. Therefore, cell-specific molecular profiling represents cellular averaging. In this study, we consider the degree to which altering miRNAs composition shifts cell behavior. We used COMICS, an iterative framework that simulates the stochastic events of miRNA-mRNA pairing, using a probabilistic approach. COMICS simulates the likelihood that cells change their transcriptome following many iterations (100 k). Results of COMICS from the human cell line (HeLa) confirmed that most genes are resistant to miRNA regulation. However, COMICS results suggest that the composition of the abundant miRNAs dictates the nature of the cells (across three cell lines) regardless of its actual mRNA steady-state. In silico perturbations of cell lines (i.e., by overexpressing miRNAs) allowed to classify genes according to their sensitivity and resilience to any combination of miRNA perturbations. Our results expose an overlooked quantitative dimension for a set of genes and miRNA regulation in living cells. The immediate implication is that even relatively modest overexpression of specific miRNAs may shift cell identity and impact cancer evolution.
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Affiliation(s)
- Shelly Mahlab-Aviv
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nathan Linial
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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19
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Zhang J, Liu L, Xu T, Zhang W, Zhao C, Li S, Li J, Rao N, Le TD. Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data. BMC Bioinformatics 2021; 22:578. [PMID: 34856921 PMCID: PMC8641245 DOI: 10.1186/s12859-021-04498-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Background Existing computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells, rather than the miRNA regulation unique to individual cells. Recent advance in single-cell miRNA-mRNA co-sequencing technology has opened a way for investigating miRNA regulation at single-cell level. However, as currently single-cell miRNA-mRNA co-sequencing data is just emerging and only available at small-scale, there is a strong need of novel methods to exploit existing single-cell data for the study of cell-specific miRNA regulation. Results In this work, we propose a new method, CSmiR (Cell-Specific miRNA regulation) to combine single-cell miRNA-mRNA co-sequencing data and putative miRNA-mRNA binding information to identify miRNA regulatory networks at the resolution of individual cells. We apply CSmiR to the miRNA-mRNA co-sequencing data in 19 K562 single-cells to identify cell-specific miRNA-mRNA regulatory networks for understanding miRNA regulation in each K562 single-cell. By analyzing the obtained cell-specific miRNA-mRNA regulatory networks, we observe that the miRNA regulation in each K562 single-cell is unique. Moreover, we conduct detailed analysis on the cell-specific miRNA regulation associated with the miR-17/92 family as a case study. The comparison results indicate that CSmiR is effective in predicting cell-specific miRNA targets. Finally, through exploring cell–cell similarity matrix characterized by cell-specific miRNA regulation, CSmiR provides a novel strategy for clustering single-cells and helps to understand cell–cell crosstalk. Conclusions To the best of our knowledge, CSmiR is the first method to explore miRNA regulation at a single-cell resolution level, and we believe that it can be a useful method to enhance the understanding of cell-specific miRNA regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04498-6.
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Affiliation(s)
- Junpeng Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China. .,School of Engineering, Dali University, Dali, 671003, Yunnan, China.
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Taosheng Xu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Wu Zhang
- School of Agriculture and Biological Sciences, Dali University, Dali, 671003, Yunnan, China
| | - Chunwen Zhao
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Sijing Li
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Nini Rao
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.
| | - Thuc Duy Le
- UniSA STEM, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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20
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Yadav P, Sharma P, Sundaram S, Venkatraman G, Bera AK, Karunagaran D. SLC7A11/ xCT is a target of miR-5096 and its restoration partially rescues miR-5096-mediated ferroptosis and anti-tumor effects in human breast cancer cells. Cancer Lett 2021; 522:211-224. [PMID: 34571083 DOI: 10.1016/j.canlet.2021.09.033] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/08/2021] [Accepted: 09/21/2021] [Indexed: 01/15/2023]
Abstract
Breast cancer cells evade cell death by overexpressing SLC7A11, which functions by transporting cystine into cells in exchange for intracellular glutamate facilitating glutathione synthesis and reducing reactive oxygen species (ROS)-mediated stress. Using an in silico approach, we predicted an miRNA (miR-5096) that can target and downregulate SLC7A11. We demonstrated SLC7A11 as a target of miR-5096 by 3'UTR luciferase assay and further validated it by identifying reduced mRNA and protein levels of SLC7A11 upon miR-5096 overexpression. miR-5096-induced ferroptotic cell death in human breast cancer cells was confirmed by concurrently increased ROS, OH-, lipid ROS, and iron accumulation levels and decreased GSH and mitochondrial membrane potential (MitoTracker™ Orange) with mitochondrial shrinkage and partial cristae loss (observed by TEM). miR-5096 inhibited colony formation, transwell migration, and breast cancer cell invasion, whereas antimiR-5096 promoted these tumorigenic properties. Ectopic expression of SLC7A11 partly reversed miR-5096-mediated effects on cell survival, ROS, lipid peroxides, iron accumulation, GSH, hydroxyl radicals, mitochondrial membrane potential, and colony formation. miR-5096 modulated the expression of epithelial-mesenchymal transition markers in vitro and inhibited the metastatic potential of MDA-MB-231 cells in a tumor xenograft model of zebrafish larvae. Our results demonstrate that miR-5096 is a tumor-suppressive miRNA in breast cancer cells, and this paper discusses its therapeutic implications.
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Affiliation(s)
- Poonam Yadav
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Priyanshu Sharma
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Sandhya Sundaram
- Department of Pathology, Sri Ramachandra Medical College and Research Institute, Sri Ramachandra University, Porur, Chennai, 600116, India
| | - Ganesh Venkatraman
- Department of Human Genetics, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Chennai, 600116, India
| | - Amal Kanti Bera
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Devarajan Karunagaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India.
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21
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Quillet A, Anouar Y, Lecroq T, Dubessy C. Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists. Comput Struct Biotechnol J 2021; 19:5811-5825. [PMID: 34765096 PMCID: PMC8567327 DOI: 10.1016/j.csbj.2021.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level. Because of their wide network of interactions, miRNAs have become the focus of many studies over the past decade, particularly in animal species. To streamline the number of potential wet lab experiments, the use of miRNA target prediction tools is currently the first step undertaken. However, the predictions made may vary considerably depending on the tool used, which is mostly due to the complex and still not fully understood mechanism of action of miRNAs. The discrepancies complicate the choice of the tool for miRNA target prediction. To provide a comprehensive view of this issue, we highlight in this review the main characteristics of miRNA-target interactions in bilaterian animals, describe the prediction models currently used, and provide some insights for the evaluation of predictor performance.
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Affiliation(s)
- Aurélien Quillet
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France
| | - Youssef Anouar
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France
| | - Thierry Lecroq
- Normandie Université, UNIROUEN, UNIHAVRE, INSA Rouen, Laboratoire d'Informatique du Traitement de l'Information et des Systèmes, 76000 Rouen, France
| | - Christophe Dubessy
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France.,Normandie Université, UNIROUEN, INSERM, PRIMACEN, 76000 Rouen, France
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22
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Walgrave H, Zhou L, De Strooper B, Salta E. The promise of microRNA-based therapies in Alzheimer's disease: challenges and perspectives. Mol Neurodegener 2021; 16:76. [PMID: 34742333 PMCID: PMC8572071 DOI: 10.1186/s13024-021-00496-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/17/2021] [Indexed: 02/06/2023] Open
Abstract
Multi-pathway approaches for the treatment of complex polygenic disorders are emerging as alternatives to classical monotarget therapies and microRNAs are of particular interest in that regard. MicroRNA research has come a long way from their initial discovery to the cumulative appreciation of their regulatory potential in healthy and diseased brain. However, systematic interrogation of putative therapeutic or toxic effects of microRNAs in (models of) Alzheimer's disease is currently missing and fundamental research findings are yet to be translated into clinical applications. Here, we review the literature to summarize the knowledge on microRNA regulation in Alzheimer's pathophysiology and to critically discuss whether and to what extent these increasing insights can be exploited for the development of microRNA-based therapeutics in the clinic.
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Affiliation(s)
- Hannah Walgrave
- VIB Center for Brain & Disease Research, Leuven, KU, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Lujia Zhou
- Division of Janssen Pharmaceutica NV, Discovery Neuroscience, Janssen Research and Development, Beerse, Belgium
| | - Bart De Strooper
- VIB Center for Brain & Disease Research, Leuven, KU, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
- UK Dementia Research Institute at University College London, London, UK
| | - Evgenia Salta
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
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23
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Florijn BW, Bijkerk R, Kruyt ND, van Zonneveld AJ, Wermer MJH. Sex-Specific MicroRNAs in Neurovascular Units in Ischemic Stroke. Int J Mol Sci 2021; 22:11888. [PMID: 34769320 PMCID: PMC8585074 DOI: 10.3390/ijms222111888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence pinpoints sex differences in stroke incidence, etiology and outcome. Therefore, more understanding of the sex-specific mechanisms that lead to ischemic stroke and aggravation of secondary damage after stroke is needed. Our current mechanistic understanding of cerebral ischemia states that endothelial quiescence in neurovascular units (NVUs) is a major physiological parameter affecting the cellular response to neuron, astrocyte and vascular smooth muscle cell (VSMC) injury. Although a hallmark of the response to injury in these cells is transcriptional activation, noncoding RNAs such as microRNAs exhibit cell-type and context dependent regulation of gene expression at the post-transcriptional level. This review assesses whether sex-specific microRNA expression (either derived from X-chromosome loci following incomplete X-chromosome inactivation or regulated by estrogen in their biogenesis) in these cells controls NVU quiescence, and as such, could differentiate stroke pathophysiology in women compared to men. Their adverse expression was found to decrease tight junction affinity in endothelial cells and activate VSMC proliferation, while their regulation of paracrine astrocyte signaling was shown to neutralize sex-specific apoptotic pathways in neurons. As such, these microRNAs have cell type-specific functions in astrocytes and vascular cells which act on one another, thereby affecting the cell viability of neurons. Furthermore, these microRNAs display actual and potential clinical implications as diagnostic and prognostic biomarkers in ischemic stroke and in predicting therapeutic response to antiplatelet therapy. In conclusion, this review improves the current mechanistic understanding of the molecular mechanisms leading to ischemic stroke in women and highlights the clinical promise of sex-specific microRNAs as novel diagnostic biomarkers for (silent) ischemic stroke.
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Affiliation(s)
- Barend W. Florijn
- Department of Neurology, Leiden University Medical Center, 2333 ZR Leiden, The Netherlands; (N.D.K.); (M.J.H.W.)
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.B.); (A.J.v.Z.)
| | - Roel Bijkerk
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.B.); (A.J.v.Z.)
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Nyika D. Kruyt
- Department of Neurology, Leiden University Medical Center, 2333 ZR Leiden, The Netherlands; (N.D.K.); (M.J.H.W.)
| | - Anton Jan van Zonneveld
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.B.); (A.J.v.Z.)
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marieke J. H. Wermer
- Department of Neurology, Leiden University Medical Center, 2333 ZR Leiden, The Netherlands; (N.D.K.); (M.J.H.W.)
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24
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Raab N, Zeh N, Schlossbauer P, Mathias S, Lindner B, Stadermann A, Gamer M, Fischer S, Holzmann K, Handrick R, Otte K. A blueprint from nature: miRNome comparison of plasma cells and CHO cells to optimize therapeutic antibody production. N Biotechnol 2021; 66:79-88. [PMID: 34710621 DOI: 10.1016/j.nbt.2021.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 12/13/2022]
Abstract
Chinese Hamster Ovary (CHO) cells are the most frequently used biopharmaceutical production hosts, although industry is presently suffering from their variable recombinant product quality, insufficient long-term stability and low productivity. Here, we present an effort to address overall cell line engineering by a novel bottom-up microRNA (miRNA) screening approach. miRNAs are small non-coding RNAs known to regulate global gene expression at the post-transcriptional level and have proved to serve as promising tools for cell line engineering for over a decade. Here the miRNome of plasma cells (PCs) has been analyzed as the natural blueprint for optimized production and secretion of antibodies. Performing comparative miRNome cross-species expression analysis of four murine/human PC-derived (PCD) and two CHO cell lines showed 147 conserved miRNAs to be differentially expressed between PCDs and CHOs. Conducting a targeted miRNA screen of this PC-specific miRNA subset revealed 14 miRNAs to improve bioprocess relevant parameters in CHO cells, among them the PC-characteristic miR-183 cluster. Finally, miRNA target prediction tools and transcriptome analysis were combined to elucidate differentially regulated lysine degradation and fatty acid metabolism pathways in monoclonal antibody (mAb) expressing CHO-DG44 and CHO-K1 cells, respectively. Thus, substantial new insights into molecular and cellular mechanisms of biopharmaceutical production cell lines can be gained by targeted bottom-up miRNA screenings.
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Affiliation(s)
- Nadja Raab
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Nikolas Zeh
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Patrick Schlossbauer
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Sven Mathias
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany; Early Stage Bioprocess Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Benjamin Lindner
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Anna Stadermann
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Martin Gamer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | - Simon Fischer
- Cell Line Development, Bioprocess Development Biologicals, Boehringer Ingelheim GmbH & Co KG, Biberach, Germany
| | | | - René Handrick
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, Biberach University of Applied Sciences, Biberach, Germany.
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25
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Hu M, Yu B, Zhang B, Wang B, Qian D, Li H, Ma J, Liu DX. Human Cytomegalovirus Infection Activates Glioma Activating Transcription Factor 5 via microRNA in a Stress-Induced Manner. ACS Chem Neurosci 2021; 12:3947-3956. [PMID: 34617722 DOI: 10.1021/acschemneuro.1c00576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human cytomegalovirus (HCMV) harnesses a cell-specific manner to infect human nervous system cancer cells, establishes a life-long persistent infection without cell death, and modulates signaling pathways associated with cancer. We previously identified that the HCMV immediate-early 2 (IE2-86) protein binds and activates activating transcription factor 5 (ATF5), a survival factor in many tumor cells. In this study, we investigated a new mechanism of stress-induced miRNA regulation at the ATF5 3' UTR under the HCMV infection and other cellular stress conditions. We employed RNA-Seq and in silico analysis to screen stress response gene sets and identify miRNA candidates as potential regulators of ATF5 following HCMV infection. We found that ATF5 and cellular stress response genes were significantly upregulated under HCMV infection and diverse stress conditions. Three downregulated miRNAs were filtrated based on our threshold, and their binding sites for 3' UTR of ATF5 were predicted. Then, luciferase reporter assays were carried out to verify the binding sites for all three miRNA candidates targeting ATF5. However, in vitro validation has shown that miR-134-5p is the only candidate that can reverse the ATF5 protein upregulation under infection and other cell stresses. Additionally, miR-134-5p levels were significantly reduced and inversely related to ATF5 mRNA under HCMV infection. These results provide new evidence that quiescent HCMV infection can trigger a stress response in glioma cells and modulate ATF5 levels by downregulating specific miRNA.
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Affiliation(s)
- Ming Hu
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao, Shandong 266071, P. R.China
| | - Bo Yu
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao, Shandong 266071, P. R.China
| | - Bingxu Zhang
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao, Shandong 266071, P. R.China
| | - Bin Wang
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao, Shandong 266071, P. R.China
| | - Dongmeng Qian
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao, Shandong 266071, P. R.China
| | - Huanting Li
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong 266000, P. R.China
| | - Junwei Ma
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong 266000, P. R.China
| | - David X. Liu
- Department of Natural Sciences, College of Science and Health Professions, Northeastern State University, Broken Arrow, Oklahoma 74014, United States
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26
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Wang P, Zhou Y, Richards AM. Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. Theranostics 2021; 11:8771-8796. [PMID: 34522211 PMCID: PMC8419061 DOI: 10.7150/thno.62642] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
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Affiliation(s)
- Peipei Wang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Yue Zhou
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Arthur M. Richards
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
- Christchurch Heart Institute, Department of Medicine, University of Otago Christchurch, New Zealand
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27
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Miliotis C, Slack FJ. miR-105-5p regulates PD-L1 expression and tumor immunogenicity in gastric cancer. Cancer Lett 2021; 518:115-126. [PMID: 34098061 DOI: 10.1016/j.canlet.2021.05.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/18/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022]
Abstract
Cancer immunotherapies targeting the interaction between Programmed death 1 (PD-1) and Programmed death ligand 1 (PD-L1) have recently been approved for the treatment of multiple cancer types, including gastric cancer. However, not all patients respond to these therapies, while some eventually acquire resistance. A partial predictive biomarker for positive response to PD-1/PD-L1 therapy is PD-L1 expression, which has been shown to be under strict post-transcriptional control in cancer. By fractionating the PD-L1 3' untranslated region (3'UTR) into multiple overlapping fragments, we identified a small 100-nucleotide-long cis-acting region as being necessary and sufficient for post-transcriptional repression of PD-L1 expression in gastric cancer. In parallel, we performed a correlation analysis between PD-L1 expression and all host miRNAs in stomach cancer patient samples. A single miRNA, miR-105-5p, was predicted to bind to the identified cis-acting 3'UTR region and to negatively correlate with PD-L1 expression. Overexpression of miR-105-5p in gastric cancer cell lines resulted in decreased expression of PD-L1, both at the total protein and surface expression levels, and induced CD8+ T cell activation in co-culture assays. Finally, we show that expression of miR-105-5p in gastric cancer is partly controlled by DNA methylation of a cancer- and germline-specific promoter of its host gene, GABRA3. Dysregulation of miR-105-5p is observed in many cancer types and this study shows the importance of this miRNA in controlling the immunogenicity of cancer cells, thus highlighting it as a potential biomarker for PD-1/PD-L1 therapy and target for combinatorial immunotherapy.
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Affiliation(s)
- Christos Miliotis
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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28
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Xu Y, Guo B, Liu X, Tao K. miR-34a inhibits melanoma growth by targeting ZEB1. Aging (Albany NY) 2021; 13:15538-15547. [PMID: 34102608 PMCID: PMC8221330 DOI: 10.18632/aging.203114] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Melanoma is a highly lethal cutaneous cancer with the tendency for early invasion and metastasis. Integrated miRNA transcriptome sequence analysis of human melanoma tumors and adjacent control tissues identified 17 miRNAs differentially expressed in melanoma tissues: let-7a-5p, let-7b-5p, let-7c, miR-374a-3p, miR-100-5p, miR-7, miR-195, miR-1908, miR-214, miR-221, miR-199a-5p, miR-21, miR-18, miR-34a, miR-199a-3p, miR-92a and miR-106b. Among these, miR-34a was most significantly down-regulated in melanoma tissues, and its expression correlated with TNM melanoma stage. miR-34a overexpression inhibited expression and activity of the transcription factor ZEB1, resulting in decreased proliferation and migration of melanoma cells. Moreover, miR-34a overexpression inhibited ZEB1 expression and melanoma tumor growth in vivo, in a melanoma nude mouse model. Together, these findings demonstrate that miR-34a inhibits melanoma growth by targeting the proto-oncogene ZEB1 and suggest the miR-34a -ZEB1 axis may serve as a novel target for melanoma treatment.
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Affiliation(s)
- Yazhen Xu
- Reconstructive and Plastic Surgery, General Hospital of Northern Theater Command, Shenyang, P.R. China
| | - Bingyu Guo
- Reconstructive and Plastic Surgery, General Hospital of Northern Theater Command, Shenyang, P.R. China
| | - Xiaoyan Liu
- Reconstructive and Plastic Surgery, General Hospital of Northern Theater Command, Shenyang, P.R. China
| | - Kai Tao
- Reconstructive and Plastic Surgery, General Hospital of Northern Theater Command, Shenyang, P.R. China
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29
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Abstract
Hundreds of microRNAs (miRNAs) are expressed in distinct spatial and temporal patterns during embryonic and postnatal mouse development. The loss of all miRNAs through the deletion of critical miRNA biogenesis factors results in early lethality. The function of each miRNA stems from their cumulative negative regulation of multiple mRNA targets expressed in a particular cell type. During development, miRNAs often coordinate the timing and direction of cell fate transitions. In adults, miRNAs frequently contribute to organismal fitness through homeostatic roles in physiology. Here, we review how the recent dissection of miRNA-knockout phenotypes in mice as well as advances related to their targets, dosage, and interactions have collectively informed our understanding of the roles of miRNAs in mammalian development and adaptive responses.
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30
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Villanueva-Paz M, Morán L, López-Alcántara N, Freixo C, Andrade RJ, Lucena MI, Cubero FJ. Oxidative Stress in Drug-Induced Liver Injury (DILI): From Mechanisms to Biomarkers for Use in Clinical Practice. Antioxidants (Basel) 2021; 10:390. [PMID: 33807700 PMCID: PMC8000729 DOI: 10.3390/antiox10030390] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Idiosyncratic drug-induced liver injury (DILI) is a type of hepatic injury caused by an uncommon drug adverse reaction that can develop to conditions spanning from asymptomatic liver laboratory abnormalities to acute liver failure (ALF) and death. The cellular and molecular mechanisms involved in DILI are poorly understood. Hepatocyte damage can be caused by the metabolic activation of chemically active intermediate metabolites that covalently bind to macromolecules (e.g., proteins, DNA), forming protein adducts-neoantigens-that lead to the generation of oxidative stress, mitochondrial dysfunction, and endoplasmic reticulum (ER) stress, which can eventually lead to cell death. In parallel, damage-associated molecular patterns (DAMPs) stimulate the immune response, whereby inflammasomes play a pivotal role, and neoantigen presentation on specific human leukocyte antigen (HLA) molecules trigger the adaptive immune response. A wide array of antioxidant mechanisms exists to counterbalance the effect of oxidants, including glutathione (GSH), superoxide dismutase (SOD), catalase, and glutathione peroxidase (GPX), which are pivotal in detoxification. These get compromised during DILI, triggering an imbalance between oxidants and antioxidants defense systems, generating oxidative stress. As a result of exacerbated oxidative stress, several danger signals, including mitochondrial damage, cell death, and inflammatory markers, and microRNAs (miRNAs) related to extracellular vesicles (EVs) have already been reported as mechanistic biomarkers. Here, the status quo and the future directions in DILI are thoroughly discussed, with a special focus on the role of oxidative stress and the development of new biomarkers.
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Affiliation(s)
- Marina Villanueva-Paz
- Unidad de Gestión Clínica de Gastroenterología, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, 29071 Málaga, Spain; (M.V.-P.); (M.I.L.)
| | - Laura Morán
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, 28040 Madrid, Spain; (L.M.); (N.L.-A.)
- Health Research Institute Gregorio Marañón (IiSGM), 28009 Madrid, Spain
| | - Nuria López-Alcántara
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, 28040 Madrid, Spain; (L.M.); (N.L.-A.)
| | - Cristiana Freixo
- CINTESIS, Center for Health Technology and Services Research, do Porto University School of Medicine, 4200-319 Porto, Portugal;
| | - Raúl J. Andrade
- Unidad de Gestión Clínica de Gastroenterología, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, 29071 Málaga, Spain; (M.V.-P.); (M.I.L.)
| | - M Isabel Lucena
- Unidad de Gestión Clínica de Gastroenterología, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, CIBERehd, 29071 Málaga, Spain; (M.V.-P.); (M.I.L.)
| | - Francisco Javier Cubero
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, 28040 Madrid, Spain; (L.M.); (N.L.-A.)
- 12 de Octubre Health Research Institute (imas12), 28041 Madrid, Spain
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31
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Nong W, Wei ZQ, Mo XN, Wu L, Tang N. miR-137 overexpression protects neurons from Aβ-induced neurotoxicity via ERK1/2. ALL LIFE 2021. [DOI: 10.1080/26895293.2021.1932612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Wei Nong
- Scientific Experimental Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, People’s Republic of China
| | - Zhi-quan Wei
- Scientific Experimental Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, People’s Republic of China
| | - Xue-Ni Mo
- Guangxi Key Laboratory of Basic Research in Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, People’s Republic of China
| | - Lin Wu
- Guangxi Key Laboratory of Basic Research in Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, People’s Republic of China
| | - Nong Tang
- Guangxi Key Laboratory of Basic Research in Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, People’s Republic of China
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32
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Delivery of muscle-derived exosomal miRNAs induced by HIIT improves insulin sensitivity through down-regulation of hepatic FoxO1 in mice. Proc Natl Acad Sci U S A 2020; 117:30335-30343. [PMID: 33199621 DOI: 10.1073/pnas.2016112117] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Implementation of regular physical activity helps in the maintenance of a healthy metabolic profile both in humans and mice through molecular mechanisms not yet completely defined. Here, we show that high-intensity interval training (HIIT) modifies the microRNA (miRNA) profile of circulating exosomes in mice, including significant increases in miR-133a and miR-133b Importantly, treatment of sedentary mice with exosomes isolated from the plasma of trained mice improves glucose tolerance, insulin sensitivity, and decreases plasma levels of triglycerides. Moreover, exosomes isolated from the muscle of trained mice display similar changes in miRNA content, and their administration to sedentary mice reproduces the improvement of glucose tolerance. Exosomal miRNAs up-regulated by HIIT target insulin-regulated transcription factor forkhead box O1 (FoxO1) and, accordingly, expression of FoxO1 is decreased in the liver of trained and exosome-treated mice. Treatment with exosomes transfected with a miR-133b mimic or with a specific siRNA targeting FoxO1 recapitulates the metabolic effects observed in trained mice. Overall, our data suggest that circulating exosomes released by the muscle carry a specific miRNA signature that is modified by exercise and induce expression changes in the liver that impact whole-body metabolic profile.
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33
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Gjorgjieva M, Sobolewski C, Ay AS, Abegg D, Correia de Sousa M, Portius D, Berthou F, Fournier M, Maeder C, Rantakari P, Zhang FP, Poutanen M, Picard D, Montet X, Nef S, Adibekian A, Foti M. Genetic Ablation of MiR-22 Fosters Diet-Induced Obesity and NAFLD Development. J Pers Med 2020; 10:jpm10040170. [PMID: 33066497 PMCID: PMC7711493 DOI: 10.3390/jpm10040170] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
miR-22 is one of the most abundant miRNAs in the liver and alterations of its hepatic expression have been associated with the development of hepatic steatosis and insulin resistance, as well as cancer. However, the pathophysiological roles of miR-22-3p in the deregulated hepatic metabolism with obesity and cancer remains poorly characterized. Herein, we observed that alterations of hepatic miR-22-3p expression with non-alcoholic fatty liver disease (NAFLD) in the context of obesity are not consistent in various human cohorts and animal models in contrast to the well-characterized miR-22-3p downregulation observed in hepatic cancers. To unravel the role of miR-22 in obesity-associated NAFLD, we generated constitutive Mir22 knockout (miR-22KO) mice, which were subsequently rendered obese by feeding with fat-enriched diet. Functional NAFLD- and obesity-associated metabolic parameters were then analyzed. Insights about the role of miR-22 in NAFLD associated with obesity were further obtained through an unbiased proteomic analysis of miR-22KO livers from obese mice. Metabolic processes governed by miR-22 were finally investigated in hepatic transformed cancer cells. Deletion of Mir22 was asymptomatic when mice were bred under standard conditions, except for an onset of glucose intolerance. However, when challenged with a high fat-containing diet, Mir22 deficiency dramatically exacerbated fat mass gain, hepatomegaly, and liver steatosis in mice. Analyses of explanted white adipose tissue revealed increased lipid synthesis, whereas mass spectrometry analysis of the liver proteome indicated that Mir22 deletion promotes hepatic upregulation of key enzymes in glycolysis and lipid uptake. Surprisingly, expression of miR-22-3p in Huh7 hepatic cancer cells triggers, in contrast to our in vivo observations, a clear induction of a Warburg effect with an increased glycolysis and an inhibited mitochondrial respiration. Together, our study indicates that miR-22-3p is a master regulator of the lipid and glucose metabolism with differential effects in specific organs and in transformed hepatic cancer cells, as compared to non-tumoral tissue.
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Affiliation(s)
- Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Anne-Sophie Ay
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Dorothea Portius
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Flavien Berthou
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Pia Rantakari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Fu-Ping Zhang
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Didier Picard
- Department of Cell Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland;
| | - Xavier Montet
- Department of Radiology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
- Diabetes Center, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Correspondence: ; Tel.: +41-22-37-95-204; Fax: +41-22-37-95-260
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Boscher E, Hernandez-Rapp J, Petry S, Keraudren R, Rainone S, Loiselle A, Goupil C, Turgeon A, St-Amour I, Planel E, Hébert SS. Advances and Challenges in Understanding MicroRNA Function in Tauopathies: A Case Study of miR-132/212. Front Neurol 2020; 11:578720. [PMID: 33117266 PMCID: PMC7553085 DOI: 10.3389/fneur.2020.578720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/01/2020] [Indexed: 01/08/2023] Open
Abstract
In the past decade, several groups have reported that microRNAs (miRNAs) can participate in the regulation of tau protein at different levels, including its expression, alternative splicing, phosphorylation, and aggregation. These observations are significant, since the abnormal regulation and deposition of tau is associated with nearly 30 neurodegenerative disorders. Interestingly, miRNA profiles go awry in tauopathies such as Alzheimer's disease, progressive supranuclear palsy, and frontotemporal dementia. Understanding the role and impact of miRNAs on tau biology could therefore provide important insights into disease risk, diagnostics, and perhaps therapeutics. In this Perspective article, we discuss recent advances in miRNA research related to tau. While proof-of-principle studies hold promise, physiological validation remains limited. To help fill this gap, we describe herein a pure tauopathy mouse model deficient for the miR-132/212 cluster. This miRNA family is strongly downregulated in human tauopathies and shown to regulate tau in vitro and in vivo. No significant differences in survival, motor deficits or body weight were observed in PS19 mice lacking miR-132/212. Age-specific effects were seen on tau expression and phosphorylation but not aggregation. Moreover, various miR-132/212 targets previously implicated in tau modulation were unaffected (GSK-3β, Foxo3a, Mapk1, p300) or, unexpectedly, reduced (Mapk3, Foxo1, p300, Calpain 2) in miR-132/212-deficient PS19 mice. These observations highlight the challenges of miRNA research in living models, and current limitations of transgenic tau mouse models lacking functional miRNA binding sites. Based on these findings, we finally recommend different strategies to better understand the role of miRNAs in tau physiology and pathology.
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Affiliation(s)
- Emmanuelle Boscher
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Julia Hernandez-Rapp
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Serena Petry
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Remi Keraudren
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Sara Rainone
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Andréanne Loiselle
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Claudia Goupil
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Andréanne Turgeon
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Isabelle St-Amour
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Emmanuel Planel
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Sébastien S Hébert
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
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35
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Xue Y, Zhu X, Meehan B, Venneti S, Martinez D, Morin G, Maïga RI, Chen H, Papadakis AI, Johnson RM, O'Sullivan MJ, Erdreich-Epstein A, Gotlieb WH, Park M, Judkins AR, Pelletier J, Foulkes WD, Rak J, Huang S. SMARCB1 loss induces druggable cyclin D1 deficiency via upregulation of MIR17HG in atypical teratoid rhabdoid tumors. J Pathol 2020; 252:77-87. [PMID: 32558936 DOI: 10.1002/path.5493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 06/10/2020] [Indexed: 01/04/2023]
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is a fatal pediatric malignancy of the central neural system lacking effective treatment options. It belongs to the rhabdoid tumor family and is usually caused by biallelic inactivation of SMARCB1, encoding a key subunit of SWI/SNF chromatin remodeling complexes. Previous studies proposed that SMARCB1 loss drives rhabdoid tumor by promoting cell cycle through activating transcription of cyclin D1 while suppressing p16. However, low cyclin D1 protein expression is observed in most ATRT patient tumors. The underlying mechanism and therapeutic implication of this molecular trait remain unknown. Here, we show that SMARCB1 loss in ATRT leads to the reduction of cyclin D1 expression by upregulating MIR17HG, a microRNA (miRNA) cluster known to generate multiple miRNAs targeting CCND1. Furthermore, we find that this cyclin D1 deficiency in ATRT results in marked in vitro and in vivo sensitivity to the CDK4/6 inhibitor palbociclib as a single agent. Our study identifies a novel genetic interaction between SMARCB1 and MIR17HG in regulating cyclin D1 in ATRT and suggests a rationale to treat ATRT patients with FDA-approved CDK4/6 inhibitors. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Yibo Xue
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Brian Meehan
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sriram Venneti
- Pathology and Neuropathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel Martinez
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Rayelle I Maïga
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Hongbo Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, PR China
| | - Andreas I Papadakis
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Radia M Johnson
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Maureen J O'Sullivan
- School of Medicine, University of Dublin, Trinity College, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Anat Erdreich-Epstein
- Departments of Pediatrics and Pathology, The Saban Research Institute at Children's Hospital Los Angeles and the Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Walter H Gotlieb
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Canada.,Department of Medical Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada.,Department of Medical Genetics and Cancer Research Program, McGill University Health Centre, Montreal, Canada
| | - Janusz Rak
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
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36
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Borja-Gonzalez M, Casas-Martinez JC, McDonagh B, Goljanek-Whysall K. Aging Science Talks: The role of miR-181a in age-related loss of muscle mass and function. TRANSLATIONAL MEDICINE OF AGING 2020; 4:81-85. [PMID: 32835152 PMCID: PMC7341035 DOI: 10.1016/j.tma.2020.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Affiliation(s)
- Maria Borja-Gonzalez
- School of Medicine, Physiology, National University of Ireland Galway, Galway, H91 W5P7, Ireland
| | - Jose C Casas-Martinez
- School of Medicine, Physiology, National University of Ireland Galway, Galway, H91 W5P7, Ireland
| | - Brian McDonagh
- School of Medicine, Physiology, National University of Ireland Galway, Galway, H91 W5P7, Ireland
| | - Katarzyna Goljanek-Whysall
- School of Medicine, Physiology, National University of Ireland Galway, Galway, H91 W5P7, Ireland
- Institute of Aging and Chronic Disease & The Medical Research Council Versus Arthritis Centre for Integrated Research Into Musculoskeletal Aging, CIMA, University of Liverpool, Liverpool, L7 8TJ, UK
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37
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Wang P, Li Q, Sun N, Gao Y, Liu JS, Deng K, He J. MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model. Brief Bioinform 2020; 22:5868068. [PMID: 34020537 DOI: 10.1093/bib/bbaa117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 12/13/2022] Open
Abstract
Deciphering microRNA (miRNA) targets is important for understanding the function of miRNAs as well as miRNA-based diagnostics and therapeutics. Given the highly cell-specific nature of miRNA regulation, recent computational approaches typically exploit expression data to identify the most physiologically relevant target messenger RNAs (mRNAs). Although effective, those methods usually require a large sample size to infer miRNA-mRNA interactions, thus limiting their applications in personalized medicine. In this study, we developed a novel miRNA target prediction algorithm called miRACLe (miRNA Analysis by a Contact modeL). It integrates sequence characteristics and RNA expression profiles into a random contact model, and determines the target preferences by relative probability of effective contacts in an individual-specific manner. Evaluation by a variety of measures shows that fitting TargetScan, a frequently used prediction tool, into the framework of miRACLe can improve its predictive power with a significant margin and consistently outperform other state-of-the-art methods in prediction accuracy, regulatory potential and biological relevance. Notably, the superiority of miRACLe is robust to various biological contexts, types of expression data and validation datasets, and the computation process is fast and efficient. Additionally, we show that the model can be readily applied to other sequence-based algorithms to improve their predictive power, such as DIANA-microT-CDS, miRanda-mirSVR and MirTarget4. MiRACLe is publicly available at https://github.com/PANWANG2014/miRACLe.
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Affiliation(s)
- Pan Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Li
- Center for Statistical Science & Department of Industry Engineering, Tsinghua University, Beijing, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Ke Deng
- Center for Statistical Science & Department of Industry Engineering, Tsinghua University, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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38
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Expression of activating transcription factor 5 (ATF5) is mediated by microRNA-520b-3p under diverse cellular stress in cancer cells. PLoS One 2020; 15:e0225044. [PMID: 32603335 PMCID: PMC7326155 DOI: 10.1371/journal.pone.0225044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Cellular stress response mechanisms normally function to enhance survival and allow for cells to return to homeostasis following an adverse event. Cancer cells often co-opt these same mechanisms as a means to evade apoptosis and mitigate a state of constant cellular stress. Activating transcription factor 5 (ATF5) is upregulated under diverse stress conditions and is overexpressed in a variety of cancers. It was demonstrated ATF5 is a survival factor in transformed, but not normal cells. However, the regulation of ATF5 is not fully understood. The purpose of the present study was to investigate miRNA regulation at the 3’ untranslated region (UTR) of ATF5, with the goal of demonstrating a reversal of the upregulation of ATF5 induced under diverse cellular stress in cancer cells. A multifactorial approach using in silico analysis was employed to identify miRNAs 433-3p, 520b-3p, and 129-5p as potential regulators of ATF5, based on their predicted binding sites over the span of the ATF5 3’ UTR. Luciferase reporter assay data validated all three miRNA candidates by demonstrating direct binding to the target ATF5 3’. However, functional studies revealed miR-520b-3p as the sole candidate able to reverse the upregulation of ATF5 protein under diverse cellular stress. Additionally, miR-520b-3p levels were inversely related to ATF5 mRNA under endoplasmic reticulum stress and amino acid deprivation. This is the first evidence that regulation at the 3’ UTR is involved in modulating ATF5 levels under cellular stress and suggests an important role for miRNA-520b-3p in the regulation of ATF5.
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39
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Ji D, An M, Fang Q. Whether miR-4293 rs12220909 variant affects cancer susceptibility: evidence from 11255 subjects. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2020; 48:933-938. [PMID: 32496828 DOI: 10.1080/21691401.2020.1773483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: miR-4293 rs12220909 polymorphism was reported associated with tumorigenesis, but the results are controversial. Thus, we planned to verify and obtain precise results.Methods: Databases were searched and reviewed up to November, 2019. Case-control studies which concern about the association between cancer risks and miR-4293 polymorphisms were all enrolled. The odds ratios (ORs) and 95% confidence intervals (CIs) calculated by the Z test were used to assess the underlying links. We also prospected how the miR-4293 impacts biological process through its target genes.Result: Finally, there are seven independent studies meet the enrolled criteria, along with 5147 cases and 6108 healthy controls. We revealed that there is a significant decrease effect of miR-4293 rs12220909 to cancer risks in heterozygote genetic model (BA vs. AA: OR = 0.857, p = .032), the similar results were also uncovered in PB control group, lung cancer and the studies conform to HWE. Results from GO items and KEGG pathway analysis illustrated that myeloid cell development, transcription factor complex, RNA polymerase II regulatory region DNA binding were regulated by miR-4293.Conclusion: In summary, our meta-analysis chase down heterozygote rs12220909 polymorphism of miR-4293 is a protective factor to cancer initiation, especially for lung cancer.
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Affiliation(s)
- Dan Ji
- Department of foundation courses, Anhui Medical College, Hefei, China
| | - Mei An
- Department of foundation courses, Anhui Medical College, Hefei, China
| | - Qiong Fang
- Department of foundation courses, Anhui Medical College, Hefei, China
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40
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Rosano S, Corà D, Parab S, Zaffuto S, Isella C, Porporato R, Hoza RM, Calogero RA, Riganti C, Bussolino F, Noghero A. A regulatory microRNA network controls endothelial cell phenotypic switch during sprouting angiogenesis. eLife 2020; 9:48095. [PMID: 31976858 PMCID: PMC7299339 DOI: 10.7554/elife.48095] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
Angiogenesis requires the temporal coordination of the proliferation and the migration of endothelial cells. Here, we investigated the regulatory role of microRNAs (miRNAs) in harmonizing angiogenesis processes in a three-dimensional in vitro model. We described a microRNA network which contributes to the observed down- and upregulation of proliferative and migratory genes, respectively. Global analysis of miRNA-target gene interactions identified two sub-network modules, the first organized in upregulated miRNAs connected with downregulated target genes and the second with opposite features. miR-424-5p and miR-29a-3p were selected for the network validation. Gain- and loss-of-function approaches targeting these microRNAs impaired angiogenesis, suggesting that these modules are instrumental to the temporal coordination of endothelial migration and proliferation. Interestingly, miR-29a-3p and its targets belong to a selective biomarker that is able to identify colorectal cancer patients who are responding to anti-angiogenic treatments. Our results provide a view of higher-order interactions in angiogenesis that has potential to provide diagnostic and therapeutic insights.
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Affiliation(s)
- Stefania Rosano
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases - CAAD, Novara, Italy
| | - Sushant Parab
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Serena Zaffuto
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Claudio Isella
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | | | - Roxana Maria Hoza
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Raffaele A Calogero
- Molecular Biotechnology Center, Department of Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, Candiolo, Italy
| | - Federico Bussolino
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
| | - Alessio Noghero
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute FPO-IRCCS, Candiolo, Italy
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41
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Smolinska A, Swoboda J, Fendler W, Lerch MM, Sendler M, Moskwa P. MiR-502 is the first reported miRNA simultaneously targeting two components of the classical non-homologous end joining (C-NHEJ) in pancreatic cell lines. Heliyon 2020; 6:e03187. [PMID: 32042960 PMCID: PMC7002776 DOI: 10.1016/j.heliyon.2020.e03187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 11/22/2019] [Accepted: 01/06/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers. Acquired inherited and/or somatic mutations drive its development. In order to prevent the formation of these mutations, precise and immediate repair of any DNA damage is indispensable. Non-homologous end-joining (NHEJ) is the key mechanism of DNA double-strand break repair. Here, we report that miR-502 targets two components in pancreatic cell lines, Ku70 and XLF of the C-NHEJ. Interestingly, we also observed an attenuated cell cycle response to gamma ionizing radiation (γ-IR) via diminished phosphorylation of checkpoint kinase 1 (Chk1) on serine 345 in these cell lines. Altogether, pancreatic cells showed increased susceptibility to γ-IR via direct inhibition of DNA double-strand break repair and attenuation of the cell cycle response.
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Affiliation(s)
- Agnieszka Smolinska
- University Medicine Greifswald, Department of Internal Medicine A, Greifswald, Germany
| | - Julia Swoboda
- University Medicine Greifswald, Department of Internal Medicine A, Greifswald, Germany
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Markus M Lerch
- University Medicine Greifswald, Department of Internal Medicine A, Greifswald, Germany
| | - Matthias Sendler
- University Medicine Greifswald, Department of Internal Medicine A, Greifswald, Germany
| | - Patryk Moskwa
- University Medicine Greifswald, Department of Internal Medicine A, Greifswald, Germany
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42
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Mahlab-Aviv S, Linial N, Linial M. A cell-based probabilistic approach unveils the concerted action of miRNAs. PLoS Comput Biol 2019; 15:e1007204. [PMID: 31790387 PMCID: PMC6922470 DOI: 10.1371/journal.pcbi.1007204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/19/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022] Open
Abstract
Mature microRNAs (miRNAs) regulate most human genes through direct base-pairing with mRNAs. We investigate the underlying principles of miRNA regulation in living cells. To this end, we overexpressed miRNAs in different cell types and measured the mRNA decay rate under a paradigm of a transcriptional arrest. Based on an exhaustive matrix of mRNA-miRNA binding probabilities, and parameters extracted from our experiments, we developed a computational framework that captures the cooperative action of miRNAs in living cells. The framework, called COMICS, simulates the stochastic binding events between miRNAs and mRNAs in cells. The input of COMICS is cell-specific profiles of mRNAs and miRNAs, and the outcome is the retention level of each mRNA at the end of 100,000 iterations. The results of COMICS from thousands of miRNA manipulations reveal gene sets that exhibit coordinated behavior with respect to all miRNAs (total of 248 families). We identified a small set of genes that are highly responsive to changes in the expression of almost any of the miRNAs. In contrast, about 20% of the tested genes remain insensitive to a broad range of miRNA manipulations. The set of insensitive genes is strongly enriched with genes that belong to the translation machinery. These trends are shared by different cell types. We conclude that the stochastic nature of miRNAs reveals unexpected robustness of gene expression in living cells. By applying a systematic probabilistic approach some key design principles of cell states are revealed, emphasizing in particular, the immunity of the translational machinery vis-a-vis miRNA manipulations across cell types. We propose COMICS as a valuable platform for assessing the outcome of miRNA regulation of cells in health and disease. Alteration in miRNA expression occurs throughout cell differentiation, inflammation, viral infection, tumorigenesis, and other pathologies. Notwithstanding a rich body of experimental data intended to assess the outcome of miRNA alterations in cells, the underlying design principles remain obscure and fragmented. In this study, we develop a quantitative stochastic model that simulates the mRNA steady-state in view of alteration in miRNAs’ abundance. We systematically analyzed the behavior of miRNA-mRNA regulation and confirm that the stochastic nature of miRNA regulation reveals unexpected robustness of cell behavior across cell types. Specifically, we expose the immunity of the translational machinery towards miRNA regulation. The developed platform, called COMICS compares the results of miRNA regulation across various cell types. Based on stochastic and probabilistic considerations, we provide a dynamic and flexible framework that quantifies the competition of miRNAs within cells in health and disease.
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Affiliation(s)
- Shelly Mahlab-Aviv
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nathan Linial
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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Besnier M, Shantikumar S, Anwar M, Dixit P, Chamorro-Jorganes A, Sweaad W, Sala-Newby G, Madeddu P, Thomas AC, Howard L, Mushtaq S, Petretto E, Caporali A, Emanueli C. miR-15a/-16 Inhibit Angiogenesis by Targeting the Tie2 Coding Sequence: Therapeutic Potential of a miR-15a/16 Decoy System in Limb Ischemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:49-62. [PMID: 31220779 PMCID: PMC6586592 DOI: 10.1016/j.omtn.2019.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/09/2019] [Accepted: 05/05/2019] [Indexed: 12/13/2022]
Abstract
MicroRNA-15a (miR-15a) and miR-16, which are transcribed from the miR-15a/miR-16-1 cluster, inhibit post-ischemic angiogenesis. MicroRNA (miRNA) binding to mRNA coding sequences (CDSs) is a newly emerging mechanism of gene expression regulation. We aimed to (1) identify new mediators of the anti-angiogenic action of miR-15a and -16, (2) develop an adenovirus (Ad)-based miR-15a/16 decoy system carrying a luciferase reporter (Luc) to both sense and inhibit miR-15a/16 activity, and (3) investigate Ad.Luc-Decoy-15a/16 therapeutic potential in a mouse limb ischemia (LI) model. LI increased miR-15a and -16 expression in mouse muscular endothelial cells (ECs). The miRNAs also increased in cultured human umbilical vein ECs (HUVECs) exposed to serum starvation, but not hypoxia. Using bioinformatic tools and luciferase activity assays, we characterized miR-15a and -16 binding to Tie2 CDS. In HUVECs, miR-15a or -16 overexpression reduced Tie2 at the protein, but not the mRNA, level. Conversely, miR-15a or -16 inhibition improved angiogenesis in a Tie2-dependent manner. Local Ad.Luc-Decoy-15a/16 delivery increased Tie2 levels in ischemic skeletal muscle and improved post-LI angiogenesis and perfusion recovery, with reduced toe necrosis. Bioluminescent imaging (in vivo imaging system [IVIS]) provided evidence that the Ad.Luc-Decoy-15a/16 system responds to miR-15a/16 increases. In conclusion, we have provided novel mechanistic evidence of the therapeutic potential of local miR-15a/16 inhibition in LI.
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Affiliation(s)
- Marie Besnier
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | | | - Maryam Anwar
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Parul Dixit
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Walid Sweaad
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Paolo Madeddu
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Anita C Thomas
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Lynsey Howard
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Sobia Mushtaq
- Bristol Heart Institute, University of Bristol, Bristol, UK
| | - Enrico Petretto
- Institute of Clinical Sciences, Imperial College London, London, UK; Cardiovascular & Metabolic Disorders Programme, Centre for Computational Biology, Duke NUS Medical School, Singapore, Singapore
| | - Andrea Caporali
- Bristol Heart Institute, University of Bristol, Bristol, UK; BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Costanza Emanueli
- Bristol Heart Institute, University of Bristol, Bristol, UK; National Heart and Lung Institute, Imperial College London, London, UK.
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Morenikeji OB, Hawkes ME, Hudson AO, Thomas BN. Computational Network Analysis Identifies Evolutionarily Conserved miRNA Gene Interactions Potentially Regulating Immune Response in Bovine Trypanosomosis. Front Microbiol 2019; 10:2010. [PMID: 31555241 PMCID: PMC6722470 DOI: 10.3389/fmicb.2019.02010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022] Open
Abstract
Bovine trypanosomosis is a devastating disease that causes huge economic loss to the global cattle industry on a yearly basis. Selection of accurate biomarkers are important in early disease diagnosis and treatment. Of late, micro-RNAs (miRNAs) are becoming the most useful biomarkers for both infectious and non-infectious diseases in humans, but this is not the case in animals. miRNAs are non-coding RNAs that regulate gene expression through binding to the 3'-, 5'-untranslated regions (UTR) or coding sequence (CDS) region of one or more target genes. The molecular identification of miRNAs that regulates the expression of immune genes responding to bovine trypanosomosis is poorly defined, as is the possibility that these miRNAs could serve as potential biomarkers for disease diagnosis and treatment currently unknown. To this end, we utilized in silico tools to elucidate conserved miRNAs regulating immune response genes during infection, in addition to cataloging significant genes. Based on the p value of 1.77E-32, we selected 25 significantly expressed immune genes. Using prediction analysis, we identified a total of 4,251 bovine miRNAs targeting these selected genes across the 3'UTR, 5'UTR and CDS regions. Thereafter, we identified candidate miRNAs based on the number of gene targets and their abundance at the three regions. In all, we found the top 13 miRNAs that are significantly conserved targeting 7 innate immune response genes, including bta-mir-2460, bta-mir-193a, bta-mir-2316, and bta-mir-2456. Our gene ontology analysis suggests that these miRNAs are involved in gene silencing, cellular protein modification process, RNA-induced silencing complex, regulation of humoral immune response mediated by circulating immunoglobulin and negative regulation of chronic inflammatory response, among others. In conclusion, this study identifies specific miRNAs that may be involved in the regulation of gene expression during bovine trypanosomosis. These miRNAs have the potential to be used as biomarkers in the animal and veterinary research community to facilitate the development of tools for early disease diagnosis/detection, drug targeting, and the rational design of drugs to facilitate disease treatment.
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Affiliation(s)
- Olanrewaju B. Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Megan E. Hawkes
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
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Does miR-618 rs2682818 variant affect cancer susceptibility? Evidence from 10 case-control studies. Biosci Rep 2019; 39:BSR20190741. [PMID: 31383788 PMCID: PMC6706600 DOI: 10.1042/bsr20190741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/11/2019] [Accepted: 08/02/2019] [Indexed: 12/17/2022] Open
Abstract
Piles of evidence have supported the relationship between miR-618 rs2682818 polymorphism and tumorigenesis, but the conclusion remains inconsistent. In the present study, we conducted a meta-analysis to sniff out the potential risk between miR-618 rs2682818 and overall cancers. Crude odds ratios (ORs) and 95% confidence intervals (CIs) analyzed by Z-test were employed to estimate the potential interrelation in five genetic models. We also prospected how the rs2682818 affects the second structure of miR-618. Finally, 10 independent studies meet the enrolled criteria, along with 4099 cancer cases and 5057 healthy controls. Overall, no exceeding interrelation was sniffed out in the pooled data among five inherited models, as well as stratified analyses. Whereas, the enhanced cancer risk of miR-618 rs2682818 variant stratified by breast cancer was revealed, in heterozygote genetic model (AC vs. CC: OR = 1.291, 95%CI = 1.012-1.648, P = 0.040) and dominant contrast model (AA + AC vs. CC: OR = 1.280, 95%CI = 1.009-1.623, P = 0.042). The second structure prediction result shown that the mutant A allele might change the first stem-loop of miR-618, and the free energy of it would turn from -39.1 to -35.1 kcal/mol. All in all, our meta-analysis had successfully chased down that miR-618 rs2682818 polymorphism is not linked with overall cancer risk, but in the dominant genotype of breast cancer.
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Sethuraman S, Thomas M, Gay LA, Renne R. Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. Nucleic Acids Res 2019; 46:8574-8589. [PMID: 29846699 PMCID: PMC6144796 DOI: 10.1093/nar/gky459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi’s Sarcoma-associated herpes virus (KSHV) and Epstein–Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA–miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA–lncRNA interactions broadly contribute to the regulation of gene expression.
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Affiliation(s)
- Sunantha Sethuraman
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Merin Thomas
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.,UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.,UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Differential Inhibition of Target Gene Expression by Human microRNAs. Cells 2019; 8:cells8080791. [PMID: 31366019 PMCID: PMC6721455 DOI: 10.3390/cells8080791] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 12/12/2022] Open
Abstract
microRNAs (miRNAs) exert their functions by repressing the expression of their target genes, but most miRNA target genes are unknown, and the degree to which a miRNA differentially inhibits the expression of its targets is underappreciated. We selected human miR-1, miR-122, and miR-124 as representatives to investigate the reliability of miRNA target predictions and examine how miRNAs suppress their targets. We constructed miRNA target gene reporter libraries based on prediction programs TargetScan, miRanda, and PicTar, and performed large-scale reporter assays to directly evaluate whether and how strongly a predicted target gene is repressed by its miRNA. We then performed statistical analyses to examine parameters that contributed to the miRNA inhibition of target genes. We found that the three programs have approximately 72–85% success rates in predicting genuine targets and that the miRNA inhibition of different targets varies in extent. We also identified parameters that could predict the degrees of miRNA repression, and further showed that differential miR-124 repression might contribute to differential gene expression in vivo. Our studies systematically investigated hundreds of miRNA target genes, shed light on factors influencing miRNA functions, and suggested a new mechanism by which differential target repression by miRNAs regulates endogenous gene expression.
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Li X, Tian Y, Tu MJ, Ho PY, Batra N, Yu AM. Bioengineered miR-27b-3p and miR-328-3p modulate drug metabolism and disposition via the regulation of target ADME gene expression. Acta Pharm Sin B 2019; 9:639-647. [PMID: 31193825 PMCID: PMC6543075 DOI: 10.1016/j.apsb.2018.12.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/07/2018] [Accepted: 11/15/2018] [Indexed: 12/31/2022] Open
Abstract
Drug-metabolizing enzymes, transporters, and nuclear receptors are essential for the absorption, distribution, metabolism, and excretion (ADME) of drugs and xenobiotics. MicroRNAs participate in the regulation of ADME gene expression via imperfect complementary Watson-Crick base pairings with target transcripts. We have previously reported that Cytochrome P450 3A4 (CYP3A4) and ATP-binding cassette sub-family G member 2 (ABCG2) are regulated by miR-27b-3p and miR-328-3p, respectively. Here we employed our newly established RNA bioengineering technology to produce bioengineered RNA agents (BERA), namely BERA/miR-27b-3p and BERA/miR-328-3p, via fermentation. When introduced into human cells, BERA/miR-27b-3p and BERA/miR-328-3p were selectively processed to target miRNAs and thus knock down CYP3A4 and ABCG2 mRNA and their protein levels, respectively, as compared to cells treated with vehicle or control RNA. Consequently, BERA/miR-27b-3p led to a lower midazolam 1'-hydroxylase activity, indicating the reduction of CYP3A4 activity. Likewise, BERA/miR-328-3p treatment elevated the intracellular accumulation of anticancer drug mitoxantrone, a classic substrate of ABCG2, hence sensitized the cells to chemotherapy. The results indicate that biologic miRNA agents made by RNA biotechnology may be applied to research on miRNA functions in the regulation of drug metabolism and disposition that could provide insights into the development of more effective therapies.
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Key Words
- 3′-UTR, 3′-untranslated region;, VDR, vitamin D receptor
- ABCG2
- ABCG2, ATP-binding cassette sub-family G member 2;, ADME, absorption, distribution, metabolism, and excretion
- BERA, bioengineered RNA agent;, CYP, cytochrome P450
- Bioengineered RNA
- CYP3A4
- Drug disposition
- E. coli, Escherichia coli;, FPLC, fast protein liquid chromatography
- LC--MS/MS, liquid chromatographytandem mass spectroscopy;, microRNA, miR or miRNA
- RNAi, RNA interference;, RT-qPCR, reverse transcription quantitative real-time polymerase chain reaction
- RXRα, retinoid X receptor α;, tRNA, transfer RNA
- miR-27b
- miR-328
- ncRNA, noncoding RNA;, PAGE, polyacrylamide gel electrophoresis
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Affiliation(s)
- Xin Li
- Key Laboratory of Molecular Target & Clinical Pharmacology, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Ye Tian
- Lab for Bone Metabolism, Key Lab for Space Biosciences and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi׳an 710072, China
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Pui Yan Ho
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Neelu Batra
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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Tiong KL, Yeang CH. MGSEA - a multivariate Gene set enrichment analysis. BMC Bioinformatics 2019; 20:145. [PMID: 30885118 PMCID: PMC6421703 DOI: 10.1186/s12859-019-2716-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 03/06/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene Set Enrichment Analysis (GSEA) is a powerful tool to identify enriched functional categories of informative biomarkers. Canonical GSEA takes one-dimensional feature scores derived from the data of one platform as inputs. Numerous extensions of GSEA handling multimodal OMIC data are proposed, yet none of them explicitly captures combinatorial relations of feature scores from multiple platforms. RESULTS We propose multivariate GSEA (MGSEA) to capture combinatorial relations of gene set enrichment among multiple platform features. MGSEA successfully captures designed feature relations from simulated data. By applying it to the scores of delineating breast cancer and glioblastoma multiforme (GBM) subtypes from The Cancer Genome Atlas (TCGA) datasets of CNV, DNA methylation and mRNA expressions, we find that breast cancer and GBM data yield both similar and distinct outcomes. Among the enriched functional categories, subtype-specific biomarkers are dominated by mRNA expression in many functional categories in both cancer types and also by CNV in many functional categories in breast cancer. The enriched functional categories belonging to distinct combinatorial patterns are involved different oncogenic processes: cell proliferation (such as cell cycle control, estrogen responses, MYC and E2F targets) for mRNA expression in breast cancer, invasion and metastasis (such as cell adhesion and epithelial-mesenchymal transition (EMT)) for CNV in breast cancer, and diverse processes (such as immune and inflammatory responses, cell adhesion, angiogenesis, and EMT) for mRNA expression in GBM. These observations persist in two external datasets (Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) for breast cancer and Repository for Molecular Brain Neoplasia Data (REMBRANDT) for GBM) and are consistent with knowledge of cancer subtypes. We further compare the characteristics of MGSEA with several extensions of GSEA and point out the pros and cons of each method. CONCLUSIONS We demonstrated the utility of MGSEA by inferring the combinatorial relations of multiple platforms for cancer subtype delineation in three multi-OMIC datasets: TCGA, METABRIC and REMBRANDT. The inferred combinatorial patterns are consistent with the current knowledge and also reveal novel insights about cancer subtypes. MGSEA can be further applied to any genotype-phenotype association problems with multimodal OMIC data.
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Affiliation(s)
- Khong-Loon Tiong
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
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Abstract
MicroRNAs (miRNA) are small non-coding RNAs (∼22 nt in length) that are known as potent master regulators of eukaryotic gene expression. miRNAs have been shown to play a critical role in cancer pathogenesis, and the misregulation of miRNAs is a well-known feature of cancer. In recent years, miR-29 has emerged as a critical miRNA in various cancers, and it has been shown to regulate multiple oncogenic processes, including epigenetics, proteostasis, metabolism, proliferation, apoptosis, metastasis, fibrosis, angiogenesis, and immunomodulation. Although miR-29 has been thoroughly documented as a tumor suppressor in the majority of studies, some controversy remains with conflicting reports of miR-29 as an oncogene. In this review, we provide a systematic overview of miR-29's functional role in various mechanisms of cancer and introspection on the contradictory roles of miR-29.
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